[1] "ofn"        "-oTBLCA-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/BLCA-TP/19775034/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/19780563/transformed.cor.cli.txt"

nPatients in clinical file=412, in cluster file=408, common to both=408
[1]  69 408
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          101                           307 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          101                           307 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          202                           206 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          202                           206 
[1] "AMP PEAK  3(1Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          216                           192 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          216                           192 
[1] "AMP PEAK  4(2P25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          150                           258 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          150                           258 
[1] "AMP PEAK  5(3P25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          190                           218 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          190                           218 
[1] "AMP PEAK  6(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           218                            190 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           218                            190 
[1] "AMP PEAK  7(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           73                           335 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           73                           335 
[1] "AMP PEAK  8(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           62                           346 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           62                           346 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           205                            203 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           205                            203 
[1] "AMP PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          170                           238 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          170                           238 
[1] "AMP PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         35                         373 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         35                         373 
[1] "AMP PEAK 12(6Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           46                           362 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           46                           362 
[1] "AMP PEAK 13(7P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          201                           207 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          201                           207 
[1] "AMP PEAK 14(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          190                           218 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          190                           218 
[1] "AMP PEAK 15(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           123                            285 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           123                            285 
[1] "AMP PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           140                            268 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           140                            268 
[1] "AMP PEAK 17(8Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          264                           144 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          264                           144 
[1] "AMP PEAK 18(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           88                           320 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           88                           320 
[1] "AMP PEAK 19(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                         182                          226 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                         182                          226 
[1] "AMP PEAK 20(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          51                          357 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          51                          357 
[1] "AMP PEAK 21(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                           135                            273 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                           135                            273 
[1] "AMP PEAK 22(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            71                            337 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            71                            337 
[1] "AMP PEAK 23(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                           131                            277 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                           131                            277 
[1] "AMP PEAK 24(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                         118                          290 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                         118                          290 
[1] "AMP PEAK 25(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                           128                            280 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                           128                            280 
[1] "AMP PEAK 26(16P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            87                            321 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            87                            321 
[1] "AMP PEAK 27(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                           108                            300 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                           108                            300 
[1] "AMP PEAK 28(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         166                          242 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         166                          242 
[1] "AMP PEAK 29(17Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                           194                            214 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                           194                            214 
[1] "AMP PEAK 30(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                         164                          244 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                         164                          244 
[1] "AMP PEAK 31(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                            154                             254 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                            154                             254 
[1] "AMP PEAK 32(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                            262                             146 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                            262                             146 
[1] "AMP PEAK 33(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            87                            321 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            87                            321 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            91                            317 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            91                            317 
[1] "DEL PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           71                           337 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           71                           337 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          134                           274 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          134                           274 
[1] "DEL PEAK  4(2Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        174                         234 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        174                         234 
[1] "DEL PEAK  5(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          208                           200 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          208                           200 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          117                           291 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          117                           291 
[1] "DEL PEAK  7(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          162                           246 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          162                           246 
[1] "DEL PEAK  8(4Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          177                           231 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          177                           231 
[1] "DEL PEAK  9(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          202                           206 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          202                           206 
[1] "DEL PEAK 10(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                          106                           302 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                          106                           302 
[1] "DEL PEAK 11(6Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        190                         218 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        190                         218 
[1] "DEL PEAK 12(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        190                         218 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        190                         218 
[1] "DEL PEAK 13(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           60                           348 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           60                           348 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          242                           166 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          242                           166 
[1] "DEL PEAK 15(8P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          252                           156 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          252                           156 
[1] "DEL PEAK 16(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        178                         230 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        178                         230 
[1] "DEL PEAK 17(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          239                           169 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          239                           169 
[1] "DEL PEAK 18(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                           178                            230 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                           178                            230 
[1] "DEL PEAK 19(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             74                             334 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             74                             334 
[1] "DEL PEAK 20(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            166                             242 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            166                             242 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           211                            197 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           211                            197 
[1] "DEL PEAK 22(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           155                            253 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           155                            253 
[1] "DEL PEAK 23(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         143                          265 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         143                          265 
[1] "DEL PEAK 24(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            68                            340 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            68                            340 
[1] "DEL PEAK 25(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             88                             320 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             88                             320 
[1] "DEL PEAK 26(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           156                            252 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           156                            252 
[1] "DEL PEAK 27(14Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                           137                            271 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                           137                            271 
[1] "DEL PEAK 28(15Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                           160                            248 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                           160                            248 
[1] "DEL PEAK 29(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           174                            234 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           174                            234 
[1] "DEL PEAK 30(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           119                            289 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           119                            289 
[1] "DEL PEAK 31(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         209                          199 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         209                          199 
[1] "DEL PEAK 32(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         180                          228 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         180                          228 
[1] "DEL PEAK 33(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           146                            262 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           146                            262 
[1] "DEL PEAK 34(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            187                             221 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            187                             221 
[1] "DEL PEAK 35(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           92                           316 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           92                           316 
[1] "DEL PEAK 36(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            84                            324 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            84                            324 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 408 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=158,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=269,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DAYS_TO_LAST_KNOWN_ALIVE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=71,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 408 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"              "PATHOLOGIC_STAGE"           
 [3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
 [5] "PATHOLOGY_M_STAGE"           "GENDER"                     
 [7] "RADIATION_THERAPY"           "KARNOFSKY_PERFORMANCE_SCORE"
 [9] "NUMBER_PACK_YEARS_SMOKED"    "NUMBER_OF_LYMPH_NODES"      
[11] "RACE"                        "ETHNICITY"                  
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, 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   3 119 195  58 
[1] "table(vv)"
vv
T0+T1+T2       T3       T4 
     123      195       58 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1   3 119 195  58 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T0+T1+T2       T3       T4 
     123      195       58 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
235  47  75   9 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
235  47  75   9 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
235  47  75   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
235  47  75   9 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=71, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=21, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P34.2) MUTATED    50  51
  AMP PEAK  1(1P34.2) WILD-TYPE 179 126
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          101                           305 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           51                           126 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       11.97        16.77        27.62        51.16        10.22        47.80 
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       19.04         5.06        17.16        20.48        12.82         9.96 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A3QU 
       36.43         8.98         1.94        12.56        12.92         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL 
       21.86        18.41        16.70        17.95       142.78        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-AA6L 
        8.15         8.22        23.21        17.98        64.18        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A541 
       15.02       166.03        11.18        15.35        38.83        25.58 
TCGA-E7-A5KE TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.56         8.09         8.94         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BU 
       23.41        19.79        12.85         7.56        15.58        19.33 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
       18.08        58.92         6.15         3.06         9.67        31.07 
TCGA-FJ-A3ZF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RD 
       17.23        26.93        20.12        21.40        15.81        14.07 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
       24.92         0.49         7.73        20.98         7.36        10.92 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE 
        4.73        32.98        21.34        19.07        22.72        38.60 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-MV-A51V TCGA-UY-A78M TCGA-UY-A78N 
       21.24        11.70        15.42        13.48        22.68        86.83 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HD TCGA-XF-A9SK 
       69.34         3.02        17.82         6.21        97.45        15.98 
TCGA-XF-A9SU TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 
        5.98         7.63        98.99        44.32        86.30        18.15 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RN TCGA-ZF-AA4T 
       13.64        30.28        94.29         3.48        20.22        19.69 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       63.02        56.35        35.41        19.40        19.17 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       41.75        66.54        15.12        29.65         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       13.15        26.14        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       14.96         5.06         8.35         8.25        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       17.56        28.70        28.41        23.01        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
        4.90        15.12        18.48        29.79         1.84        13.58 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        2.14        66.41        19.00       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK 
       17.62        15.62        46.68         7.79        87.32         4.80 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       17.72        50.27        21.30         9.67        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
      163.30        66.05        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T 
       50.70        36.66        52.01        13.58       165.73        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       19.00        13.64        15.35        13.64        56.15        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       20.32        43.59        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
       16.70         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.66         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 
       15.32        14.37        32.02        16.77        33.04        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       22.52        27.98        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       46.78        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       53.88        11.01         5.36         5.69         8.25        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
        2.70         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 
       12.69        12.36         2.27         4.31        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B 
       15.95        59.31        33.01         7.23        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        70.32        29.36        20.71        19.13        15.91 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 
       17.75         8.94        13.91         2.10         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         7.00        14.27        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ 
        8.48        36.49        27.35         8.58         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       64.01         9.01        12.16        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        9.14        27.68         9.07        17.72         1.81        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R 
       11.80        52.73        50.56        35.97        46.98        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K 
       14.24         1.84        16.54        12.43        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       37.05        76.01        78.25       112.83         3.91        29.56 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF 
        3.85        51.32        45.04         6.58       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        66.41        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
        2.24        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82       110.60        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        2.96         8.32         6.77        56.48        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       11.97        22.36        25.41        21.11        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       21.86        28.41        13.41        64.08        58.72        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84         2.89        34.06         8.61        59.38        60.16 
TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90         8.52        54.21         5.52        12.23 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                         0.49                          0.10 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                       166.03                        165.73 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                        18.08                         16.67 
[1] "0.5 - 166.0 (18.1)" "0.1 - 165.7 (16.7)"
[1] "hr=" "1.2"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1P34.2) MUTATED         0       29        29       42
  AMP PEAK  1(1P34.2) WILD-TYPE       2      100       111       93
D1V3, multiclass
           clus
vv          AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           29                           100
  STAGE III                          29                           111
  STAGE IV                           42                            93
[1] 4 2
[1] 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(1P34.2) MUTATED         33  48  14
  AMP PEAK  1(1P34.2) WILD-TYPE       90 147  44
D1V4, multiclass
          clus
vv         AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T0+T1+T2                          33                            90
  T3                                48                           147
  T4                                14                            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                             N0  N1  N2  N3
  AMP PEAK  1(1P34.2) MUTATED    45  18  23   3
  AMP PEAK  1(1P34.2) WILD-TYPE 190  29  52   6
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  N0                          45                           190
  N1                          18                            29
  N2                          23                            52
  N3                           3                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    43   2
  AMP PEAK  1(1P34.2) WILD-TYPE 149   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     43    2
  AMP PEAK  1(1P34.2) WILD-TYPE  149    9
   clus
vv  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  0                          43                           149
  1                           2                             9
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    28  73
  AMP PEAK  1(1P34.2) WILD-TYPE  79 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     28   73
  AMP PEAK  1(1P34.2) WILD-TYPE   79  228
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                          28                            79
  MALE                            73                           228
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED    88   4
  AMP PEAK  1(1P34.2) WILD-TYPE 276  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     88    4
  AMP PEAK  1(1P34.2) WILD-TYPE  276   15
     clus
vv    AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  NO                           88                           276
  YES                           4                            15
[1] 2 2
[1] FALSE
D1V9, continuous
D1V10, continuous
D1V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.2) MUTATED       4                         6    86
  AMP PEAK  1(1P34.2) WILD-TYPE    39                        16   241
D1V12, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              86
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                39
  BLACK OR AFRICAN AMERICAN                            16
  WHITE                                               241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.2) MUTATED     3  90
  AMP PEAK  1(1P34.2) WILD-TYPE   6 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      3   90
  AMP PEAK  1(1P34.2) WILD-TYPE    6  279
                        clus
vv                       AMP PEAK  1(1P34.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          90
                        clus
vv                       AMP PEAK  1(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           279
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED   111  91
  AMP PEAK  2(1Q21.3) WILD-TYPE 118  86
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          202                           204 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           91                            86 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W 
       24.13         8.35        16.27        16.83        16.77        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J 
        0.62        41.75        15.12        10.22        47.80         2.66 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
        6.74        19.04        26.14         5.06        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        17.16        16.18        20.48        28.70         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A47V TCGA-CF-A8HX TCGA-CF-A8HY 
        1.94        12.56        12.16        12.46        11.34        11.34 
TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
       18.58        18.48         5.19         1.84        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       18.41       130.88       112.44        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT 
      142.78         4.80        13.58         8.15         8.22        21.30 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L 
       23.21        66.05        17.98        67.36        15.68        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       15.02        13.58       165.73       166.03        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        13.64        11.18        20.32        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A5KF 
       38.83        29.72         0.10        22.16         0.56         0.66 
TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B7 
       24.03         1.22        13.68        12.95         8.09         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SR 
       60.66        24.30        23.41        17.98         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BU 
       12.85         7.56        27.35        15.58        11.01        19.33 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF 
       27.45        18.08         6.28         6.15        12.36         2.27 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
        4.31         9.67        31.07        10.65        17.23         3.25 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F 
       11.08        33.01        20.12        17.62        66.02        29.36 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       21.40        15.81        19.13        17.75        24.92         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P 
       13.91         7.73         2.10        20.98         7.36        10.92 
TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       20.05        10.65        32.98        14.27        21.34        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.82        20.28        36.49         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AC 
        1.51        38.60        64.01         9.01        25.02         9.14 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41P TCGA-KQ-A41Q 
       11.70        17.72        15.42        11.80        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        13.48        12.23 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       16.54        38.99        17.62        37.05        22.68        86.83 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HI 
       29.56        17.82         6.58        97.45        15.35        17.88 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SU 
       48.62        79.66         3.22        15.98         4.21         5.98 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAML 
       11.90        66.64         2.10        13.74       110.60         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 
       71.57         2.96         6.77        98.99        56.48        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       86.30        18.15         0.66        11.97        13.64        22.36 
TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       30.28        21.86        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       20.22        34.06        19.69        59.38        63.02        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        54.21        19.17 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7R 
       11.97        94.88       104.65       108.95        44.94        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-5N-A9KI 
       34.98        50.04        51.16        66.54        29.65         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42        40.08         7.33        12.39         6.58        13.15 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PH 
       12.16        17.88        19.50        14.96         8.25         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
       12.82         9.96        17.56        36.43        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       12.79        13.97        12.59        12.13        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       12.10        11.87        13.08        12.92         4.90        15.12 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       29.79        13.58        66.41        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IV 
       17.62        15.62        87.32        17.72        50.27         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       163.30        64.18        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 
       50.70        36.66        52.01        15.35        56.15        12.03 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
        2.24        16.70        25.58        26.96        26.24         4.24 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       24.66         0.92        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94        33.04        12.62        22.52        27.98 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       29.16        25.74        46.78        14.96        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
       26.73        53.88         5.36         5.69         8.25        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        2.70         7.10        13.35        62.86        18.81        12.69 
TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ 
        3.06        10.85        12.66         8.94        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D 
       15.95        26.93        59.31         7.23         6.94        70.32 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 
       20.71        15.91        14.07         8.94         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        32.78         5.62         4.73 
TCGA-GU-AATQ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WU 
        7.00         8.48        27.35        19.40        12.16         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P 
       21.24         2.76        27.68         9.07         1.81        16.27 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        21.07        16.67        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       12.43        76.01        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HE 
        3.91         6.21         3.85        51.32        45.04       125.49 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12         1.87        64.80        66.41        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       12.76        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        16.27        92.98        10.82        11.31        54.90 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       91.73         8.32        44.32        30.94        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        3.88        18.84         9.63        25.41        21.11        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
       35.84        28.41        58.72        88.87        47.84         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.61        60.16        19.40         8.52         5.52        12.23 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.10                          0.92 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       166.03                        163.30 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        17.67                         16.70 
[1] "0.1 - 166.0 (17.7)" "0.9 - 163.3 (16.7)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED         0       65        59       77
  AMP PEAK  2(1Q21.3) WILD-TYPE       2       64        81       58
D2V3, multiclass
           clus
vv          AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           65                            64
  STAGE III                          59                            81
  STAGE IV                           77                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  AMP PEAK  2(1Q21.3) MUTATED         60 98 27
  AMP PEAK  2(1Q21.3) WILD-TYPE       63 97 31
D2V4, multiclass
          clus
vv         AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T0+T1+T2                          60                            63
  T3                                98                            97
  T4                                27                            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                             N0  N1  N2  N3
  AMP PEAK  2(1Q21.3) MUTATED   101  29  41   7
  AMP PEAK  2(1Q21.3) WILD-TYPE 134  18  34   2
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                         101                           134
  N1                          29                            18
  N2                          41                            34
  N3                           7                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    91   8
  AMP PEAK  2(1Q21.3) WILD-TYPE 101   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     91    8
  AMP PEAK  2(1Q21.3) WILD-TYPE  101    3
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                          91                           101
  1                           8                             3
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    52 150
  AMP PEAK  2(1Q21.3) WILD-TYPE  55 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     52  150
  AMP PEAK  2(1Q21.3) WILD-TYPE   55  151
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          52                            55
  MALE                           150                           151
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   173  10
  AMP PEAK  2(1Q21.3) WILD-TYPE 191   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    173   10
  AMP PEAK  2(1Q21.3) WILD-TYPE  191    9
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                          173                           191
  YES                          10                             9
[1] 2 2
[1] FALSE
D2V9, continuous
D2V10, continuous
D2V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED      16                        10   166
  AMP PEAK  2(1Q21.3) WILD-TYPE    27                        12   161
D2V12, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                              16
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             166
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                27
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     4 180
  AMP PEAK  2(1Q21.3) WILD-TYPE   5 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      4  180
  AMP PEAK  2(1Q21.3) WILD-TYPE    5  189
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         180
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           189
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q23.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q23.3) MUTATED   122  93
  AMP PEAK  3(1Q23.3) WILD-TYPE 107  84
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          215                           191 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                           93                            84 
$`AMP PEAK  3(1Q23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7O 
       24.13        11.97       108.95         8.35        16.27        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.77        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       15.12        10.22        47.80        40.08         2.66         6.74 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA 
       19.04        26.14        14.89         5.06         8.35        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       16.18        20.48         4.67        12.82         9.96        28.70 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A47V TCGA-CF-A8HX 
        8.98         1.94        12.56        12.16        12.46        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 
       11.34        11.87        18.58        15.12        18.48         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 
       21.86         2.14        18.41       130.88       112.44        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       142.78        87.32         4.80        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        50.27        21.30        23.21        66.05        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       67.36        15.68        38.24        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 
      166.03        18.81        19.00        13.64        11.18        20.32 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 
       43.59        38.83        29.72         0.10        22.16        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
        0.56         0.66        24.03         1.22        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        8.09        16.77         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       17.98         5.52        25.74        19.79        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BZ 
       27.35         3.62        15.58        11.01        19.33        27.45 
TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.28         6.15        12.36         3.06         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A3VY 
       31.07        10.65        17.23         3.25        61.94        17.62 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A3YS 
       66.02        29.36        21.40        15.81        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A76B 
        0.49        13.91         7.73         2.10        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV 
       10.92        20.05         4.73        10.65        32.98        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40G 
       21.34        19.10        19.82        20.28        36.49        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60        64.01         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       25.02         3.45         9.14         9.07        11.70        17.72 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       15.42        11.80        35.97        46.98        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 
       15.32        15.58        13.48        12.23        16.54        38.99 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE 
       37.05        22.68        86.83         3.02        17.82         6.21 
TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SG 
       51.32         6.58        97.45        15.35        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW 
       79.66         3.22        15.98         4.21         5.98        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAML 
       28.24        66.64         2.10        13.74       110.60         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       71.57         2.96         6.77        98.99        44.32        56.48 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
       86.30        27.06        18.15         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       22.36        30.28        21.86        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       64.08        20.22        34.06        59.38        63.02        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       35.41        57.90        54.21        19.17        12.23 

$`AMP PEAK  3(1Q23.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       94.88       104.65        44.94        34.98        50.04        66.54 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0S7 
       29.65         2.50        17.42         7.33        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       13.15        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR 
        8.25        17.56        36.43        28.41        23.01        12.79 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       13.97        12.59        12.13        13.08        10.95        12.66 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
       13.08        12.92         4.90         5.19        29.79        13.58 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        19.00        16.70        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       46.68        17.72         9.67        20.81        10.55       163.30 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M 
       64.18        53.29        76.60        50.70        36.66        52.01 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E7-A4XJ 
       13.64        15.35        56.15        12.03        15.35         2.24 
TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU 
       16.70        26.96        26.24         4.24        24.66         0.92 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.07        15.32        14.37        32.02         8.94        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43S 
       12.62        22.52        27.98        29.16        46.78        14.96 
TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       20.91        26.73        53.88         5.36         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         2.70         7.10        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
       18.81        12.69         2.27        10.85        12.66         8.94 
TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
       11.08        48.00        15.95        26.93        59.31        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RB 
        7.23        20.12         6.94        70.32        20.71        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.91        14.07         8.94         3.12         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3QH 
       18.97         7.63        32.78         5.62         7.00         8.48 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       27.35         8.58        12.16        21.24         2.76        27.68 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41O TCGA-LT-A8JT TCGA-PQ-A6FN 
        1.81        16.27        52.73        50.56        21.07        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A78P 
       14.24         1.84        12.43        17.62        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB 
       69.34       112.83         3.91        29.56         3.85        45.04 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM 
      125.49        97.12         1.87        64.80        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       14.93        12.76        23.64        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        16.27        92.98        10.82        11.31        54.90 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN8 
       91.73         8.32        30.94        61.45        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       18.84         9.63        25.41        21.11        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4T 
       28.41        58.72        88.87        47.84         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
        8.61        60.16        19.40         8.52         5.52 

  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                         0.10                          0.92 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                       166.03                        163.30 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                        17.23                         16.70 
[1] "0.1 - 166.0 (17.2)" "0.9 - 163.3 (16.7)"
[1] "hr=" "1"  
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(1Q23.3) MUTATED         1       68        63       83
  AMP PEAK  3(1Q23.3) WILD-TYPE       1       61        77       52
D3V3, multiclass
           clus
vv          AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           68                            61
  STAGE III                          63                            77
  STAGE IV                           83                            52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK  3(1Q23.3) MUTATED         70 101  29
  AMP PEAK  3(1Q23.3) WILD-TYPE       53  94  29
D3V4, multiclass
          clus
vv         AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  T0+T1+T2                          70                            53
  T3                               101                            94
  T4                                29                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  3(1Q23.3) MUTATED   110  30  43   9
  AMP PEAK  3(1Q23.3) WILD-TYPE 125  17  32   0
D3V5, multiclass
    clus
vv   AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  N0                         110                           125
  N1                          30                            17
  N2                          43                            32
  N3                           9                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q23.3) MUTATED   96  8
  AMP PEAK  3(1Q23.3) WILD-TYPE 96  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED     96    8
  AMP PEAK  3(1Q23.3) WILD-TYPE   96    3
   clus
vv  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  0                          96                            96
  1                           8                             3
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q23.3) MUTATED    53 163
  AMP PEAK  3(1Q23.3) WILD-TYPE  54 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED     53  163
  AMP PEAK  3(1Q23.3) WILD-TYPE   54  138
        clus
vv       AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  FEMALE                          53                            54
  MALE                           163                           138
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q23.3) MUTATED   191   9
  AMP PEAK  3(1Q23.3) WILD-TYPE 173  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED    191    9
  AMP PEAK  3(1Q23.3) WILD-TYPE  173   10
     clus
vv    AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE
  NO                          191                           173
  YES                           9                            10
[1] 2 2
[1] FALSE
D3V9, continuous
D3V10, continuous
D3V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q23.3) MUTATED      17                        14   175
  AMP PEAK  3(1Q23.3) WILD-TYPE    26                         8   152
D3V12, multiclass
                           clus
vv                          AMP PEAK  3(1Q23.3) MUTATED
  ASIAN                                              17
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             175
                           clus
vv                          AMP PEAK  3(1Q23.3) WILD-TYPE
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q23.3) MUTATED     4 192
  AMP PEAK  3(1Q23.3) WILD-TYPE   5 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED      4  192
  AMP PEAK  3(1Q23.3) WILD-TYPE    5  177
                        clus
vv                       AMP PEAK  3(1Q23.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         192
                        clus
vv                       AMP PEAK  3(1Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           177
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P25.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P25.1) MUTATED    79  70
  AMP PEAK  4(2P25.1) WILD-TYPE 150 107
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          149                           257 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                           70                           107 
$`AMP PEAK  4(2P25.1) MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       16.77        17.16         0.62        41.75        51.16        15.12 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.50        17.42        12.39        13.15        19.04        26.14 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06        14.89         5.06         8.35        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS 
       12.82        28.70        28.41         8.98        23.01        12.56 
TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FL 
       13.97        12.13        12.62        12.10        11.34        18.58 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
       15.12        21.86         2.14        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
      112.44        17.95         7.79        87.32         4.80         8.15 
TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 
        8.22        66.05        17.98        64.18        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       36.66        38.24        15.02       166.03        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A541 
       13.64        11.18        12.03        20.32        43.59        25.58 
TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SQ 
       24.03         8.09         8.94        60.66        24.30        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O 
       19.79        12.85        27.35        20.91        27.45         7.10 
TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28         6.15        12.36         2.27         3.06         4.31 
TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3B 
       10.85        17.23         3.25        11.08        17.62        66.02 
TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       29.36        19.13        14.07         8.94        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW 
        2.10        20.98        20.05        10.65        32.98        21.34 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ 
       20.28         8.48        36.49        27.35        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ 
       38.60        12.16        25.02        21.24        11.70         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R 
       15.42        16.27        11.80        50.56        35.97        44.38 
TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD 
       13.48        17.62        22.68        69.34       112.83        17.82 
TCGA-UY-A9PE TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SK 
        6.21        97.45        15.35         1.87        48.62        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T5 
       14.93         4.21        12.76        28.24        26.27        66.64 
TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN8 
      110.60         7.63         6.77        44.32        61.45         3.88 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RC TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
       22.36        31.20        94.29        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       19.69        59.38        56.35        19.40         8.52 

$`AMP PEAK  4(2P25.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.27        44.94        16.83        34.98        27.62        50.04 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        47.80        29.65        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        2.66         6.74         6.58        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
       14.96         8.25        17.16         4.67         9.96        17.56 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI 
       36.43         1.94        12.79        12.59        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       12.00        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1AA 
       18.48         5.19        29.79         1.84        13.58        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 
       16.70        16.14        17.62        15.62        46.68       142.78 
TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
       20.81        10.55       163.30        53.29        76.60        50.70 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       52.01        13.58       165.73        15.35        13.64        56.15 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       16.70         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.66         0.92         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.32        14.37        32.02        16.77        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       12.62        22.52        27.98        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
        5.52        25.74         7.56        14.96         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       26.73        53.88        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA 
        8.25        18.08        58.92         2.70        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       18.81        12.69         9.67        31.07        12.66        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM 
       33.01         7.23        20.12         6.94        70.32        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       20.71        15.81        15.91        17.75        24.92         0.49 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        3.12         2.20         7.36        10.92        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        32.78         5.62         4.73         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OF 
       19.10        19.82         8.58        19.07         1.51        64.01 
TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        9.01         3.45         2.76         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       17.72        52.73        46.98         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       21.07        12.23        16.67        14.24         1.84        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       12.43        38.99        37.05        86.83        76.01        78.25 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
        3.02         3.91        29.56         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
        6.58       125.49        97.12        17.88        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX 
        3.22        66.41        34.45         5.98        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        18.90         2.24        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       92.98        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 
        2.96         8.32        98.99        56.48        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39        18.15        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       11.97        13.64        25.41        21.11        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        28.41        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       88.87         2.89         8.61        60.16        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        54.21        19.17         5.52        12.23 

  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                         0.62                          0.10 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                       166.03                        165.73 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                        17.95                         16.67 
[1] "0.6 - 166.0 (17.9)" "0.1 - 165.7 (16.7)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(2P25.1) MUTATED         0       42        46       61
  AMP PEAK  4(2P25.1) WILD-TYPE       2       87        94       74
D4V3, multiclass
           clus
vv          AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           42                            87
  STAGE III                          46                            94
  STAGE IV                           61                            74
[1] 4 2
[1] 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(2P25.1) MUTATED         44  73  21
  AMP PEAK  4(2P25.1) WILD-TYPE       79 122  37
D4V4, multiclass
          clus
vv         AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  T0+T1+T2                          44                            79
  T3                                73                           122
  T4                                21                            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                             N0  N1  N2  N3
  AMP PEAK  4(2P25.1) MUTATED    75  22  33   6
  AMP PEAK  4(2P25.1) WILD-TYPE 160  25  42   3
D4V5, multiclass
    clus
vv   AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  N0                          75                           160
  N1                          22                            25
  N2                          33                            42
  N3                           6                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED    64   6
  AMP PEAK  4(2P25.1) WILD-TYPE 128   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED     64    6
  AMP PEAK  4(2P25.1) WILD-TYPE  128    5
   clus
vv  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  0                          64                           128
  1                           6                             5
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED    48 102
  AMP PEAK  4(2P25.1) WILD-TYPE  59 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED     48  102
  AMP PEAK  4(2P25.1) WILD-TYPE   59  199
        clus
vv       AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  FEMALE                          48                            59
  MALE                           102                           199
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED   131   7
  AMP PEAK  4(2P25.1) WILD-TYPE 233  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED    131    7
  AMP PEAK  4(2P25.1) WILD-TYPE  233   12
     clus
vv    AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  NO                          131                           233
  YES                           7                            12
[1] 2 2
[1] FALSE
D4V9, continuous
D4V10, continuous
D4V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P25.1) MUTATED      11                         9   123
  AMP PEAK  4(2P25.1) WILD-TYPE    32                        13   204
D4V12, multiclass
                           clus
vv                          AMP PEAK  4(2P25.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             123
                           clus
vv                          AMP PEAK  4(2P25.1) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED     4 131
  AMP PEAK  4(2P25.1) WILD-TYPE   5 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED      4  131
  AMP PEAK  4(2P25.1) WILD-TYPE    5  238
                        clus
vv                       AMP PEAK  4(2P25.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         131
                        clus
vv                       AMP PEAK  4(2P25.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           238
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(3P25.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(3P25.2) MUTATED   112  77
  AMP PEAK  5(3P25.2) WILD-TYPE 117 100
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          189                           217 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                           77                           100 
$`AMP PEAK  5(3P25.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        11.97       108.95         8.35        16.27        44.94 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA87 
       16.77        17.16        27.62         0.62        15.12        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
        2.50        17.42        40.08         7.33         2.66        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       26.14         8.35        17.16        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI 
        9.96        28.70        12.79        12.59        12.13        12.16 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
        4.90        15.12         5.19        29.79         1.84        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX 
        2.14        66.41        18.41       130.88       112.44        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       17.95       142.78        87.32         8.15         8.22        50.27 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       23.21        66.05        17.98        64.18        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 
       36.66        15.02       165.73       166.03        19.00        13.64 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       11.18        20.32        15.35        38.83         0.10        22.16 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW 
       25.58         0.56         4.24        24.03         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.95         8.09         8.94        33.04        24.30        23.41 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5C0 TCGA-FD-A62O 
        7.56        27.35        20.91         5.36        18.08         7.10 
TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        9.67        31.07        10.65        17.23         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        59.31        33.01        20.12        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW 
       70.32        29.36        15.81        19.13        14.07         0.49 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
       13.91         2.10        20.98         2.20         7.36        10.92 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
        4.73        10.65        32.98        14.27        21.34        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       20.28         8.48        36.49        27.35        19.07        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH 
        1.51        38.60        25.02         3.45        21.24         9.07 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R 
       15.42        11.80        52.73        50.56        35.97        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X 
        1.15        15.32        15.58        13.48        12.23        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O 
        1.84        12.43        17.62        37.05        86.83        76.01 
TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HC 
        3.02        29.56        17.82         6.21        51.32         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI 
       97.45        97.12        15.35         1.87        48.62        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T6 TCGA-XF-AAMF 
        3.22        15.98         5.98        12.76         2.10        10.82 
TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
      110.60         7.63        71.57         6.77        98.99        44.32 
TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RL 
       22.36        30.28        28.41        94.29        64.08        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84        19.69        59.38        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5P 
       57.90        19.40        12.23 

$`AMP PEAK  5(3P25.2) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 
       94.88       104.65        16.83        34.98        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A3JM TCGA-BT-A0S7 
       51.16        66.54        10.22        29.65         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        19.04        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A3PJ TCGA-BT-A42B 
       14.89        14.96         5.06         8.25        12.82        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS 
       36.43        28.41         8.98         1.94        23.01        12.56 
TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.97        13.08        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ 
       11.34        11.87        18.58        13.08        12.92        18.48 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       13.58        19.00        16.70        16.14        17.62        15.62 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV 
        7.79         4.80        13.58        17.72        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       20.81        10.55       163.30        53.29        76.60        67.36 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X 
       38.24        52.01        13.58        18.81        13.64        15.35 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A519 
       56.15        12.03        43.59        29.72         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN 
        0.66        26.96        26.24        24.66         0.92        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 
       15.32        14.37        32.02        16.77         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       22.52        27.98        60.66        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X 
       25.74        46.78        19.79        12.85        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA 
        8.25        27.45        58.92         2.70        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EJ 
       18.81         6.15        10.85        12.66         8.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
       15.95        26.93         7.23         6.94        21.40        20.71 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       15.91        17.75        24.92         8.94         7.73         3.12 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A40E TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
        7.00        19.10         8.58        19.40        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ 
       12.16         2.76         9.14        27.68        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41Q TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 
        1.81        16.27        46.98        21.07        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA 
       38.99        22.68        78.25        69.34       112.83         3.91 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL 
        3.85        45.04       125.49        17.88        64.80        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       34.45        14.93         4.21        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT 
       13.74        92.98        11.31        54.90        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
        8.32        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.15         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       11.97        13.64        25.41        21.11        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        13.41         3.48        58.72        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       34.06         8.61        60.16         8.52        54.21        19.17 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                         0.10                          0.66 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                       166.03                        163.30 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                        17.62                         16.70 
[1] "0.1 - 166.0 (17.6)" "0.7 - 163.3 (16.7)"
[1] "hr=" "1.2"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(3P25.2) MUTATED         1       56        59       73
  AMP PEAK  5(3P25.2) WILD-TYPE       1       73        81       62
D5V3, multiclass
           clus
vv          AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           56                            73
  STAGE III                          59                            81
  STAGE IV                           73                            62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK  5(3P25.2) MUTATED         55  84  35
  AMP PEAK  5(3P25.2) WILD-TYPE       68 111  23
D5V4, multiclass
          clus
vv         AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  T0+T1+T2                          55                            68
  T3                                84                           111
  T4                                35                            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                             N0  N1  N2  N3
  AMP PEAK  5(3P25.2) MUTATED    94  22  45   6
  AMP PEAK  5(3P25.2) WILD-TYPE 141  25  30   3
D5V5, multiclass
    clus
vv   AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  N0                          94                           141
  N1                          22                            25
  N2                          45                            30
  N3                           6                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED    87   6
  AMP PEAK  5(3P25.2) WILD-TYPE 105   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED     87    6
  AMP PEAK  5(3P25.2) WILD-TYPE  105    5
   clus
vv  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  0                          87                           105
  1                           6                             5
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED    37 153
  AMP PEAK  5(3P25.2) WILD-TYPE  70 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED     37  153
  AMP PEAK  5(3P25.2) WILD-TYPE   70  148
        clus
vv       AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  FEMALE                          37                            70
  MALE                           153                           148
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED   170   7
  AMP PEAK  5(3P25.2) WILD-TYPE 194  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED    170    7
  AMP PEAK  5(3P25.2) WILD-TYPE  194   12
     clus
vv    AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  NO                          170                           194
  YES                           7                            12
[1] 2 2
[1] FALSE
D5V9, continuous
D5V10, continuous
D5V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3P25.2) MUTATED      13                         7   165
  AMP PEAK  5(3P25.2) WILD-TYPE    30                        15   162
D5V12, multiclass
                           clus
vv                          AMP PEAK  5(3P25.2) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             165
                           clus
vv                          AMP PEAK  5(3P25.2) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P25.2) MUTATED     3 172
  AMP PEAK  5(3P25.2) WILD-TYPE   6 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED      3  172
  AMP PEAK  5(3P25.2) WILD-TYPE    6  197
                        clus
vv                       AMP PEAK  5(3P25.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         172
                        clus
vv                       AMP PEAK  5(3P25.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           197
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(3Q26.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(3Q26.33) MUTATED   117 100
  AMP PEAK  6(3Q26.33) WILD-TYPE 112  77
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           217                            189 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           100                             77 
$`AMP PEAK  6(3Q26.33) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S 
       24.13       104.65         8.35        16.27        16.77        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       27.62         0.62        15.12         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74        12.39        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       26.14         5.06         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
       16.18         4.67        12.82         9.96        28.70        36.43 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A5UA TCGA-CU-A0YN 
       12.79        12.56        12.59        12.13        12.00        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
        4.90        15.12        18.48        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX 
       66.41        18.41       130.88       112.44        16.14        46.68 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 
       17.95         4.80         8.15        50.27        23.21        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       17.98        64.18        15.68        50.70        36.66        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       15.02        13.58       165.73       166.03        19.00        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        56.15        12.03        20.32        43.59        15.35 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME 
        0.10        22.16        25.58         0.56         4.24        24.03 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
        1.22        13.68        12.95         8.09        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P 
       33.04        22.52        60.66        24.30        23.41        27.35 
TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 
       20.91        15.58        19.33         5.36         8.25        18.08 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
        7.10         6.28         6.15        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
        4.31         9.67        10.65        11.08        61.94        48.00 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       59.31        33.01         7.23        17.62        66.02        70.32 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       20.71        15.81        19.13        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OS TCGA-GD-A76B 
       24.92         0.49         8.94        13.91        20.98         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ 
       10.92        11.31         7.63         4.73        10.65         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       21.34        19.10        20.28         8.48        36.49        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        22.72        19.40        38.60         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB 
       25.02         3.45        21.24         9.07        11.70        15.42 
TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI 
       11.80        50.56        35.97        44.38         1.15        12.23 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        38.99        17.62        37.05 
TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PH 
       86.83        69.34         3.02        29.56        17.82        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        97.45        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SU 
       17.88        79.66         3.22        15.98         4.21         5.98 
TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMG 
       12.76        28.24        26.27        66.64        13.74       110.60 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
        7.63        71.57         2.96         6.77        98.99        44.32 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30        27.06        13.64        22.36        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       94.29        13.41         3.48        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22         2.89        34.06        19.69        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       63.02        56.35        35.41        57.90        19.40        19.17 
TCGA-ZF-AA5P 
       12.23 

$`AMP PEAK  6(3Q26.33) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       11.97        94.88       108.95        44.94        16.83        17.16 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04        41.75        51.16        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       29.65         6.58        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       14.96        20.48        17.56        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       23.01        13.97        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3QU 
       11.34        11.34        11.87        18.58        13.08         5.19 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG 
       13.58         2.14        19.00        16.70        17.62        15.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       142.78        87.32        13.58         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW 
       21.30         9.67        20.81        10.55       163.30        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6M TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA75 
       76.60        67.36        52.01        18.81        15.35        11.18 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       38.83        29.72         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24        24.66         0.92        14.07        15.32        14.37 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN 
        8.94         4.01        12.62        27.98        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85         7.56 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       14.96         3.62        26.73        53.88        11.01         5.69 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       27.45        58.92         2.70        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 
       12.69        10.85        31.07        12.66        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F 
        3.25        15.95        26.93        20.12         6.94        29.36 
TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R 
       21.40         7.73         2.10         3.12         2.20        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JZ 
       32.78        20.05         5.62        32.98        14.27        19.82 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        8.58         1.51        64.01         2.76         9.14        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-LC-A66R 
       17.72         1.81        16.27        52.73        46.98        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78M 
       15.58        21.07        13.48        16.67        16.54        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        78.25       112.83         3.91         6.21         3.85 
TCGA-XF-A8HE TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
      125.49        48.62        64.80        66.41        34.45        14.93 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       11.90        23.64        21.04        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR 
        2.10        92.98        10.82        11.31        54.90        91.73 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 
        8.32        56.48        30.94        61.45        75.39        18.15 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-AA4U 
       31.20        35.84        21.86        28.41        88.87         8.61 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
        8.52        54.21         5.52 

  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                          0.10                           0.66 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                         17.75                          16.70 
[1] "0.1 - 166.0 (17.8)" "0.7 - 163.3 (16.7)"
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(3Q26.33) MUTATED         1       63        76       77
  AMP PEAK  6(3Q26.33) WILD-TYPE       1       66        64       58
D6V3, multiclass
           clus
vv          AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            63                             66
  STAGE III                           76                             64
  STAGE IV                            77                             58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK  6(3Q26.33) MUTATED         57 110  33
  AMP PEAK  6(3Q26.33) WILD-TYPE       66  85  25
D6V4, multiclass
          clus
vv         AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  T0+T1+T2                           57                             66
  T3                                110                             85
  T4                                 33                             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                              N0  N1  N2  N3
  AMP PEAK  6(3Q26.33) MUTATED   114  25  47   6
  AMP PEAK  6(3Q26.33) WILD-TYPE 121  22  28   3
D6V5, multiclass
    clus
vv   AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  N0                          114                            121
  N1                           25                             22
  N2                           47                             28
  N3                            6                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                                cls
clus                              0  1
  AMP PEAK  6(3Q26.33) MUTATED   99  7
  AMP PEAK  6(3Q26.33) WILD-TYPE 93  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED     99    7
  AMP PEAK  6(3Q26.33) WILD-TYPE   93    4
   clus
vv  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  0                           99                             93
  1                            7                              4
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.33) MUTATED    60 158
  AMP PEAK  6(3Q26.33) WILD-TYPE  47 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED     60  158
  AMP PEAK  6(3Q26.33) WILD-TYPE   47  143
        clus
vv       AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  FEMALE                           60                             47
  MALE                            158                            143
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.33) MUTATED   198   8
  AMP PEAK  6(3Q26.33) WILD-TYPE 166  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED    198    8
  AMP PEAK  6(3Q26.33) WILD-TYPE  166   11
     clus
vv    AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE
  NO                           198                            166
  YES                            8                             11
[1] 2 2
[1] FALSE
D6V9, continuous
D6V10, continuous
D6V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(3Q26.33) MUTATED      14                        10   186
  AMP PEAK  6(3Q26.33) WILD-TYPE    29                        12   141
D6V12, multiclass
                           clus
vv                          AMP PEAK  6(3Q26.33) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              186
                           clus
vv                          AMP PEAK  6(3Q26.33) WILD-TYPE
  ASIAN                                                 29
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                                cls
clus                               0   1
  AMP PEAK  6(3Q26.33) MUTATED     5 197
  AMP PEAK  6(3Q26.33) WILD-TYPE   4 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED      5  197
  AMP PEAK  6(3Q26.33) WILD-TYPE    4  172
                        clus
vv                       AMP PEAK  6(3Q26.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          197
                        clus
vv                       AMP PEAK  6(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            172
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(4P16.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(4P16.3) MUTATED    49  24
  AMP PEAK  7(4P16.3) WILD-TYPE 180 153
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           73                           333 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           24                           153 
$`AMP PEAK  7(4P16.3) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA87 TCGA-BT-A20P 
       11.97       108.95        17.16        50.04        47.80        17.88 
TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF 
       14.89        12.82         1.94        23.01        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY 
       12.13        13.08        12.46        12.62        12.00        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 
       11.87        18.58        18.48         1.84         2.14        66.41 
TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A6AV 
      130.88         7.79        87.32         8.15        50.27        64.18 
TCGA-DK-A6B1 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE 
       67.36        11.18        12.03        38.83        25.58         0.56 
TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C1 
        0.92        60.66        23.41         5.36        27.45        58.92 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B 
        6.15        12.36        59.31        33.01        17.62        66.02 
TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GD-A76B TCGA-GU-A42R TCGA-GV-A6ZA TCGA-H4-A2HO 
       21.40        15.91         7.36        18.97        22.72         1.51 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41R 
        9.01        25.02         9.14         1.81        15.42        44.38 
TCGA-MV-A51V TCGA-UY-A78N TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMY TCGA-XF-AAMZ 
       13.48        86.83        28.24         2.24        98.99        44.32 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA51 
       11.97        13.64        21.11        58.72         8.61        56.35 
TCGA-ZF-AA5H 
       19.17 

$`AMP PEAK  7(4P16.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        94.88       104.65         8.35        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        16.77        34.98        27.62         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI 
       51.16        66.54        15.12        10.22        29.65         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       17.42        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        6.58        13.15        19.04        26.14        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       16.18        20.48         4.67         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MI 
       36.43        28.41         8.98        12.79        12.56        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       10.95        12.66        12.10        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU 
       11.34        13.08        12.92         4.90        15.12         5.19 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       29.79        13.58        21.86        18.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      142.78         4.80        13.58         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       17.98        53.29        76.60        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       38.24        52.01        15.02        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       18.81        19.00        13.64        15.35        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       20.32        43.59        15.35        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
        2.24        16.70         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       24.03        24.66         1.22        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
       33.04         4.01        12.62        22.52        27.98        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85         7.56        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX 
       15.58        26.73        53.88        11.01        19.33         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
        8.25        18.08         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       62.86        18.81        12.69         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        9.67        10.85        31.07        12.66        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        11.08        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       26.93         7.23        20.12         6.94        70.32        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       20.71        15.81        19.13        14.07        17.75        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20        10.92        11.31         7.63        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
       20.05         5.62         4.73        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
       36.49        27.35         8.58        19.07        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R 
       64.01        12.16         3.45        21.24         2.76        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
        9.07        11.70        17.72        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       50.56        35.97        46.98         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       21.07        12.23        16.67        14.24         1.84        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       12.43        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       78.25        69.34         3.02       112.83         3.91        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       17.82         6.21         3.85        51.32        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL 
       48.62        64.80        79.66         3.22        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       34.45        14.93         4.21         5.98        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       23.64        21.04        26.27        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
        6.77        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.15         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        25.41        31.20        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL 
       28.41        94.29        13.41         3.48        64.08        88.87 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       47.84        20.22         2.89        34.06        19.69        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        63.02        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21         5.52        12.23 

  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                         0.56                          0.10 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       130.88                        166.03 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                        17.16                         17.23 
[1] "0.6 - 130.9 (17.2)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.5"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(4P16.3) MUTATED         0       32        24       17
  AMP PEAK  7(4P16.3) WILD-TYPE       2       97       116      118
D7V3, multiclass
           clus
vv          AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           32                            97
  STAGE III                          24                           116
  STAGE IV                           17                           118
[1] 4 2
[1] 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(4P16.3) MUTATED         32  31   8
  AMP PEAK  7(4P16.3) WILD-TYPE       91 164  50
D7V4, multiclass
          clus
vv         AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  T0+T1+T2                          32                            91
  T3                                31                           164
  T4                                 8                            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                             N0  N1  N2  N3
  AMP PEAK  7(4P16.3) MUTATED    52   7   8   2
  AMP PEAK  7(4P16.3) WILD-TYPE 183  40  67   7
D7V5, multiclass
    clus
vv   AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  N0                          52                           183
  N1                           7                            40
  N2                           8                            67
  N3                           2                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED    45   1
  AMP PEAK  7(4P16.3) WILD-TYPE 147  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     45    1
  AMP PEAK  7(4P16.3) WILD-TYPE  147   10
   clus
vv  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  0                          45                           147
  1                           1                            10
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED    20  53
  AMP PEAK  7(4P16.3) WILD-TYPE  87 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     20   53
  AMP PEAK  7(4P16.3) WILD-TYPE   87  248
        clus
vv       AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  FEMALE                          20                            87
  MALE                            53                           248
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED    63   6
  AMP PEAK  7(4P16.3) WILD-TYPE 301  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     63    6
  AMP PEAK  7(4P16.3) WILD-TYPE  301   13
     clus
vv    AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  NO                           63                           301
  YES                           6                            13
[1] 2 2
[1] FALSE
D7V9, continuous
D7V10, continuous
D7V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(4P16.3) MUTATED      13                         2    52
  AMP PEAK  7(4P16.3) WILD-TYPE    30                        20   275
D7V12, multiclass
                           clus
vv                          AMP PEAK  7(4P16.3) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              52
                           clus
vv                          AMP PEAK  7(4P16.3) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED     2  63
  AMP PEAK  7(4P16.3) WILD-TYPE   7 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED      2   63
  AMP PEAK  7(4P16.3) WILD-TYPE    7  306
                        clus
vv                       AMP PEAK  7(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       AMP PEAK  7(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           306
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(4Q13.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(4Q13.3) MUTATED    40  22
  AMP PEAK  8(4Q13.3) WILD-TYPE 189 155
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           62                           344 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           22                           155 
$`AMP PEAK  8(4Q13.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-BT-A20N TCGA-BT-A2LD 
       16.27        27.62         0.62        51.16        26.14        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A8HX 
        9.96        28.70        36.43        23.01        12.62        11.34 
TCGA-CF-A8HY TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A2I2 TCGA-DK-A2I6 
       11.34        18.48         2.14        18.41         7.79        87.32 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA6R TCGA-E5-A4U1 
       66.05        17.98        64.18        67.36       165.73        38.83 
TCGA-E7-A541 TCGA-E7-A6MD TCGA-FD-A3NA TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BV 
       25.58         4.24        60.66        19.79        15.58         5.36 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-A2EJ 
       27.45        18.08        13.35         6.15        12.36        48.00 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A76B 
       17.62        66.02        17.75         0.49         7.73         7.36 
TCGA-GU-A42P TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WV TCGA-KQ-A41Q 
       10.92        21.34        22.72         9.01        21.24        46.98 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       44.38        15.58        13.48        17.62        37.05        76.01 
TCGA-UY-A8OD TCGA-XF-A9T4 TCGA-XF-AAMZ TCGA-YF-AA3L TCGA-ZF-A9R2 TCGA-ZF-A9RN 
      112.83        16.27        44.32        11.97        21.11        20.22 
TCGA-ZF-AA4T TCGA-ZF-AA5H 
       19.69        19.17 

$`AMP PEAK  8(4Q13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        66.54        15.12        10.22        47.80        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
        8.25        17.16        16.18         4.67        12.82        17.56 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         8.98         1.94        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.19        29.79         1.84        13.58        21.86        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        46.68        17.95       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        20.81        10.55       163.30        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       15.68        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.64        56.15        11.18        12.03        20.32        43.59 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24        24.03        24.66 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.62        22.52        27.98        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS 
       17.98        29.16         5.52        25.74        46.78        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
        7.56        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
       53.88        11.01        19.33         5.69         8.25        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        2.70         7.10         6.28        62.86        18.81        12.69 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
        2.27         3.06         4.31         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
       12.66        10.65        17.23         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        15.95        26.93        59.31        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       20.12         6.94        70.32        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81        19.13        15.91        14.07        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
       10.65        32.98         7.00        14.27        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       20.28         8.48        36.49        27.35         8.58        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS 
        1.51        19.40        38.60        64.01        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI 
       50.56        35.97         1.15        15.32        21.07        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84        16.54        12.43        38.99 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       22.68        86.83        78.25        69.34         3.02         3.91 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
       29.56        17.82         6.21         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
      110.60        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 
        2.96         8.32         6.77        98.99        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       61.45        86.30        27.06        75.39        18.15         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        13.64        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
        2.89        34.06         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       56.35        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                         0.49                          0.10 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                       165.73                        166.03 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                       19.430                        16.605 
[1] "0.5 - 165.7 (19.4)" "0.1 - 166.0 (16.6)"
[1] "hr=" "1.4"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(4Q13.3) MUTATED         0       26        15       21
  AMP PEAK  8(4Q13.3) WILD-TYPE       2      103       125      114
D8V3, multiclass
           clus
vv          AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           26                           103
  STAGE III                          15                           125
  STAGE IV                           21                           114
[1] 4 2
[1] 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(4Q13.3) MUTATED         25  25   6
  AMP PEAK  8(4Q13.3) WILD-TYPE       98 170  52
D8V4, multiclass
          clus
vv         AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  T0+T1+T2                          25                            98
  T3                                25                           170
  T4                                 6                            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                             N0  N1  N2  N3
  AMP PEAK  8(4Q13.3) MUTATED    37  10  10   1
  AMP PEAK  8(4Q13.3) WILD-TYPE 198  37  65   8
D8V5, multiclass
    clus
vv   AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  N0                          37                           198
  N1                          10                            37
  N2                          10                            65
  N3                           1                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED    32   0
  AMP PEAK  8(4Q13.3) WILD-TYPE 160  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED     32    0
  AMP PEAK  8(4Q13.3) WILD-TYPE  160   11
   clus
vv  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  0                          32                           160
  1                           0                            11
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED    24  38
  AMP PEAK  8(4Q13.3) WILD-TYPE  83 263
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED     24   38
  AMP PEAK  8(4Q13.3) WILD-TYPE   83  263
        clus
vv       AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  FEMALE                          24                            83
  MALE                            38                           263
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED    54   2
  AMP PEAK  8(4Q13.3) WILD-TYPE 310  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED     54    2
  AMP PEAK  8(4Q13.3) WILD-TYPE  310   17
     clus
vv    AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  NO                           54                           310
  YES                           2                            17
[1] 2 2
[1] FALSE
D8V9, continuous
D8V10, continuous
D8V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(4Q13.3) MUTATED       5                         3    49
  AMP PEAK  8(4Q13.3) WILD-TYPE    38                        19   278
D8V12, multiclass
                           clus
vv                          AMP PEAK  8(4Q13.3) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              49
                           clus
vv                          AMP PEAK  8(4Q13.3) WILD-TYPE
  ASIAN                                                38
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED     2  53
  AMP PEAK  8(4Q13.3) WILD-TYPE   7 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED      2   53
  AMP PEAK  8(4Q13.3) WILD-TYPE    7  316
                        clus
vv                       AMP PEAK  8(4Q13.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       AMP PEAK  8(4Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           316
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(5P15.33) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(5P15.33) MUTATED   118  87
  AMP PEAK  9(5P15.33) WILD-TYPE 111  90
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           205                            201 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            87                             90 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
      108.95         8.35        16.27        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20P 
       41.75        10.22         2.50         6.74        12.39        17.88 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.89         5.06         8.35        17.16        12.82         9.96 
TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MF 
       28.70        36.43         8.98        23.01        12.56        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A0YR 
       12.13        13.08        10.95        12.00        12.92        15.12 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A2I6 
        5.19         1.84        21.86       112.44       142.78        87.32 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A6AV 
        8.15         8.22        23.21         9.67        10.55        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       67.36        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       165.73       166.03        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        56.15        12.03        15.35        38.83        29.72 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A85H 
       22.16        25.58         4.24        24.03         1.22        12.95 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.09        32.02        16.77         8.94        22.52        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43Y 
       24.30        29.16         5.52        25.74        19.79        15.58 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N 
       26.73        19.33         5.36         8.25        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3ZF TCGA-FT-A3EE 
       12.36         3.06         4.31        10.85        17.23         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       11.08        61.94        59.31         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02        70.32        29.36        20.71        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP 
       15.91        14.07        24.92         0.49        13.91         2.10 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 
       20.98         7.36        10.92         7.63         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65         7.00        14.27        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.48        36.49         8.58        19.07        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
       64.01         9.01        12.16         2.76         9.14         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q 
       11.70         1.81        15.42        52.73        50.56        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       44.38         1.15        15.32        13.48        16.67        14.24 
TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A8OB 
        1.84        38.99        17.62        37.05        86.83        69.34 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A9SG 
      112.83        29.56         6.21         6.58        97.12        48.62 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SX 
       79.66         3.22        15.98        34.45        14.93        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME 
       28.24        26.27         2.24        66.64         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX 
       10.82       110.60        54.90         7.63         2.96         6.77 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       86.30        18.15        13.64        21.11        31.20        30.28 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       21.86        94.29        58.72        88.87        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
        2.89        34.06        19.69        59.38        63.02        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        57.90        19.40         8.52        54.21        19.17 
TCGA-ZF-AA5P 
       12.23 

$`AMP PEAK  9(5P15.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        11.97        94.88       104.65        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       16.77        17.16        34.98        51.16        66.54        15.12 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80        29.65        17.42        40.08         7.33         2.66 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q 
        6.58        13.15        19.04        26.14        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.96         8.25        16.18        20.48         4.67 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MI 
       17.56        28.41         1.94        12.79        13.97        12.16 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.90        18.48        29.79        13.58         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00        16.70       130.88        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        46.68        17.95         7.79         4.80        13.58 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       17.72        50.27        21.30        20.81       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA6T TCGA-DK-AA75 
       17.98        53.29        76.60        15.68        18.81        11.18 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       20.32        43.59         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
        0.66        26.96        26.24        24.66         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.07        15.32        14.37        33.04         4.01        12.62 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       27.98        23.41        17.98        46.78        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91         3.62        53.88        11.01 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TF TCGA-FD-A6TI 
        5.69        27.45        18.08        62.86         2.27         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK 
       31.07        12.66        10.65         8.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A6I1 
       26.93        33.01         6.94        21.40        17.75         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
        7.73         3.12         2.20        11.31        18.97        32.78 
TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO 
       20.05        32.98        21.34        27.35        22.72         1.51 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P 
       25.02         3.45        21.24        27.68        17.72        16.27 
TCGA-K4-AAQO TCGA-KQ-A41P TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 
       11.80        35.97        15.58        21.07        12.23        16.54 
TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       12.43        22.68        76.01        78.25         3.02         3.91 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
       17.82         3.85        51.32        45.04        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9ST 
       15.35         1.87        17.88        64.80        66.41         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T4 
        5.98        12.76        11.90        21.04        18.90        16.27 
TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY 
       13.74        11.31        71.57        91.73         8.32        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
       44.32        56.48        30.94        61.45        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       25.41        35.84        28.41        13.41         3.48        64.08 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA5N 
        8.61        60.16         5.52 

  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                         17.16                          17.42 
[1] "0.5 - 166.0 (17.2)" "0.1 - 163.3 (17.4)"
[1] "hr=" "1.1"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(5P15.33) MUTATED         0       65        74       65
  AMP PEAK  9(5P15.33) WILD-TYPE       2       64        66       70
D9V3, multiclass
           clus
vv          AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            65                             64
  STAGE III                           74                             66
  STAGE IV                            65                             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"
                                vv
clus                             T0+T1+T2 T3 T4
  AMP PEAK  9(5P15.33) MUTATED         57 98 29
  AMP PEAK  9(5P15.33) WILD-TYPE       66 97 29
D9V4, multiclass
          clus
vv         AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T0+T1+T2                           57                             66
  T3                                 98                             97
  T4                                 29                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  9(5P15.33) MUTATED   113  26  36   4
  AMP PEAK  9(5P15.33) WILD-TYPE 122  21  39   5
D9V5, multiclass
    clus
vv   AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  N0                          113                            122
  N1                           26                             21
  N2                           36                             39
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    90   2
  AMP PEAK  9(5P15.33) WILD-TYPE 102   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     90    2
  AMP PEAK  9(5P15.33) WILD-TYPE  102    9
   clus
vv  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  0                           90                            102
  1                            2                              9
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    54 151
  AMP PEAK  9(5P15.33) WILD-TYPE  53 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     54  151
  AMP PEAK  9(5P15.33) WILD-TYPE   53  150
        clus
vv       AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  FEMALE                           54                             53
  MALE                            151                            150
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED   184   8
  AMP PEAK  9(5P15.33) WILD-TYPE 180  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED    184    8
  AMP PEAK  9(5P15.33) WILD-TYPE  180   11
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  NO                           184                            180
  YES                            8                             11
[1] 2 2
[1] FALSE
D9V9, continuous
D9V10, continuous
D9V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(5P15.33) MUTATED      15                        13   167
  AMP PEAK  9(5P15.33) WILD-TYPE    28                         9   160
D9V12, multiclass
                           clus
vv                          AMP PEAK  9(5P15.33) MUTATED
  ASIAN                                               15
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              167
                           clus
vv                          AMP PEAK  9(5P15.33) WILD-TYPE
  ASIAN                                                 28
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED     5 185
  AMP PEAK  9(5P15.33) WILD-TYPE   4 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      5  185
  AMP PEAK  9(5P15.33) WILD-TYPE    4  184
                        clus
vv                       AMP PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          185
                        clus
vv                       AMP PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            184
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(6P22.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(6P22.3) MUTATED   111  59
  AMP PEAK 10(6P22.3) WILD-TYPE 118 118
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          170                           236 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           59                           118 
$`AMP PEAK 10(6P22.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.27        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BT-A0S7 TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA 
       15.12        47.80         6.58         5.06         8.35        17.16 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47V 
       20.48        12.82        28.70         8.98        12.56        12.46 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1A6 
       12.62        12.00        12.92         5.19         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       18.41       130.88       112.44        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A6AV 
       87.32        13.58         8.15        50.27        10.55        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       67.36        15.68       165.73       166.03        19.00        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        56.15        11.18        12.03        43.59        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW 
       22.16        25.58         0.56        24.03         1.22        13.68 
TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       12.95        32.02        33.04         4.01        22.52        24.30 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A5BU TCGA-FD-A5C1 
       25.74        19.79         7.56        27.35        19.33        58.92 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FJ-A3Z7 
       62.86         6.15        12.36         2.27         3.06        31.07 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3VY 
       10.65        17.23         3.25        11.08        61.94        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       66.02        70.32        29.36        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 
       19.13        15.91        14.07        24.92         0.49        13.91 
TCGA-GD-A2C5 TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 
        7.73        10.92        18.97         7.63        20.05         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A40E 
       10.65        32.98        21.34        19.82         8.48         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AC 
       19.07        22.72        38.60        12.16        21.24         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       27.68         9.07        15.42        16.27        11.80        52.73 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       46.98        44.38         1.15        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        12.43        38.99        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD 
       86.83        76.01        69.34         3.02        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF 
        6.21         3.85        51.32         6.58        97.45        97.12 
TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9T0 
       48.62         3.22        34.45        14.93         4.21        26.27 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY 
        2.24        10.82       110.60         7.63        71.57        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       44.32        18.15        11.97        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4R 
       94.29        13.41        64.08        58.72        47.84        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       19.69        59.38        63.02        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        12.23 

$`AMP PEAK 10(6P22.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       44.94        16.83        16.77        34.98        50.04        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        29.65         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        2.66         6.74        12.39        13.15        19.04        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
        8.25        16.18         4.67         9.96        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       28.41         1.94        23.01        12.79        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       12.13        13.08        12.16        10.95        12.66        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.10        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
       18.58        13.08         4.90        15.12        18.48        29.79 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
        1.84        13.58        21.86        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ 
       17.62        15.62        46.68         4.80         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21         9.67        20.81       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       17.98        53.29        76.60        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA77 
       52.01        15.02        13.58        18.81        15.35        20.32 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       38.83        29.72         0.10         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN 
       26.96        26.24         4.24        24.66         0.92        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       15.32        14.37         8.09        16.77         8.94        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        23.41        17.98        29.16         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       46.78        12.85        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       26.73        53.88        11.01         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       27.45        18.08         2.70         7.10         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
       18.81        12.69         4.31         9.67        10.85        12.66 
TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        8.94        48.00        15.95        26.93        59.31        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GD-A3OP 
        7.23        20.12         6.94        17.75         8.94         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 
        3.12        20.98         2.20         7.36        11.31        32.78 
TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI 
        5.62         7.00        14.27        19.10        20.28        36.49 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         1.51        19.40        64.01         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41O 
        3.45         2.76        11.70        17.72         1.81        50.56 
TCGA-KQ-A41P TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       35.97        21.07        13.48        14.24         1.84        16.54 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HG 
       78.25       112.83         3.91        45.04       125.49        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL 
        1.87        17.88        64.80        79.66        15.98        66.41 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        5.98        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       11.31        54.90        91.73         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         9.63         0.66        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RL 
       31.20        35.84        21.86        28.41         3.48        88.87 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22         2.89         8.61        60.16        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA5N 
       57.90         5.52 

  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                         0.49                          0.10 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                       166.03                        163.30 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                       18.280                        16.405 
[1] "0.5 - 166.0 (18.3)" "0.1 - 163.3 (16.4)"
[1] "hr=" "1.6"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(6P22.3) MUTATED         0       55        51       63
  AMP PEAK 10(6P22.3) WILD-TYPE       2       74        89       72
D10V3, multiclass
           clus
vv          AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           55                            74
  STAGE III                          51                            89
  STAGE IV                           63                            72
[1] 4 2
[1] 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(6P22.3) MUTATED         59  75  24
  AMP PEAK 10(6P22.3) WILD-TYPE       64 120  34
D10V4, multiclass
          clus
vv         AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  T0+T1+T2                          59                            64
  T3                                75                           120
  T4                                24                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 10(6P22.3) MUTATED    92  23  36   5
  AMP PEAK 10(6P22.3) WILD-TYPE 143  24  39   4
D10V5, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  N0                          92                           143
  N1                          23                            24
  N2                          36                            39
  N3                           5                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED    73   4
  AMP PEAK 10(6P22.3) WILD-TYPE 119   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     73    4
  AMP PEAK 10(6P22.3) WILD-TYPE  119    7
   clus
vv  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  0                          73                           119
  1                           4                             7
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED    38 132
  AMP PEAK 10(6P22.3) WILD-TYPE  69 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     38  132
  AMP PEAK 10(6P22.3) WILD-TYPE   69  169
        clus
vv       AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  FEMALE                          38                            69
  MALE                           132                           169
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED   151   8
  AMP PEAK 10(6P22.3) WILD-TYPE 213  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED    151    8
  AMP PEAK 10(6P22.3) WILD-TYPE  213   11
     clus
vv    AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  NO                          151                           213
  YES                           8                            11
[1] 2 2
[1] FALSE
D10V9, continuous
D10V10, continuous
D10V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(6P22.3) MUTATED      13                         9   142
  AMP PEAK 10(6P22.3) WILD-TYPE    30                        13   185
D10V12, multiclass
                           clus
vv                          AMP PEAK 10(6P22.3) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             142
                           clus
vv                          AMP PEAK 10(6P22.3) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED     6 149
  AMP PEAK 10(6P22.3) WILD-TYPE   3 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED      6  149
  AMP PEAK 10(6P22.3) WILD-TYPE    3  220
                        clus
vv                       AMP PEAK 10(6P22.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         149
                        clus
vv                       AMP PEAK 10(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           220
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(6Q21) MUTATION ANALYSIS
D11V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 11(6Q21) MUTATED    23  12
  AMP PEAK 11(6Q21) WILD-TYPE 206 165
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         35                         371 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         12                         165 
$`AMP PEAK 11(6Q21) MUTATED`
TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A2LA TCGA-CF-A47V 
       17.16        40.08         6.58        19.04        17.16        12.46 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A3WX TCGA-DK-A6B5 
       15.12        21.86        18.41       130.88        10.55        50.70 
TCGA-DK-AA75 TCGA-E7-A6ME TCGA-FD-A43P TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       11.18        24.03        27.35        31.07        10.65        17.23 
TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GU-AATO 
       21.40        15.81        24.92        13.91         7.73        10.65 
TCGA-K4-A5RH TCGA-UY-A78K TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9T5 TCGA-XF-AAMG 
        9.07        17.62        86.83        51.32        66.64       110.60 
TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA51 
       71.57        30.28        58.72        59.38        56.35 

$`AMP PEAK 11(6Q21) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I 
       10.22        47.80        29.65         2.50        17.42         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        2.66         6.74        12.39        13.15        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35         8.25        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        1.94        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       12.13        13.08        12.16        10.95        12.66        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.87        18.58        13.08        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
       18.48         5.19        29.79         1.84        13.58         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62        46.68        17.95         7.79       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        4.80        13.58         8.15         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21         9.67        20.81       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       36.66        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 
       56.15        12.03        20.32        43.59        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       29.72         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24         4.24        24.66 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        0.92         1.22        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.37         8.09        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85         7.56        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
        5.69         8.25        27.45        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        7.10         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.85        12.66         8.94         3.25        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       48.00        15.95        26.93        59.31        33.01         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        70.32        29.36 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW 
       20.71        19.13        15.91        14.07        17.75         0.49 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        8.94         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        18.97         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        5.62         4.73        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        36.49        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.58        19.07        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       64.01         9.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        2.76         9.14        27.68        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       15.42        16.27        11.80        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       46.98        44.38         1.15        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       12.43        38.99        37.05        22.68        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       69.34         3.02       112.83         3.91        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        6.21         3.85        45.04         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.12        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       79.66         3.22        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 
       28.24        26.27        18.90         2.24        16.27         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98        10.82        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       13.64        22.36        25.41        21.11        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       21.86        28.41        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       88.87        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
        8.61        60.16        63.02        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                       6.58                        0.10 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                     130.88                      166.03 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                       21.4                        16.7 
[1] "6.6 - 130.9 (21.4)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.6"
D11V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(6Q21) MUTATED         1       10        10       14
  AMP PEAK 11(6Q21) WILD-TYPE       1      119       130      121
D11V3, multiclass
           clus
vv          AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  STAGE I                           1                           1
  STAGE II                         10                         119
  STAGE III                        10                         130
  STAGE IV                         14                         121
[1] 4 2
[1] 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(6Q21) MUTATED         13  13   6
  AMP PEAK 11(6Q21) WILD-TYPE      110 182  52
D11V4, multiclass
          clus
vv         AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                        13                         110
  T3                              13                         182
  T4                               6                          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                           N0  N1  N2  N3
  AMP PEAK 11(6Q21) MUTATED    18   4   8   1
  AMP PEAK 11(6Q21) WILD-TYPE 217  43  67   8
D11V5, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  N0                        18                         217
  N1                         4                          43
  N2                         8                          67
  N3                         1                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    18   1
  AMP PEAK 11(6Q21) WILD-TYPE 174  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     18    1
  AMP PEAK 11(6Q21) WILD-TYPE  174   10
   clus
vv  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  0                        18                         174
  1                         1                          10
[1] 2 2
[1] FALSE
D11V7, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     8  27
  AMP PEAK 11(6Q21) WILD-TYPE  99 274
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      8   27
  AMP PEAK 11(6Q21) WILD-TYPE   99  274
        clus
vv       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  FEMALE                         8                          99
  MALE                          27                         274
[1] 2 2
[1] FALSE
D11V8, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED    30   2
  AMP PEAK 11(6Q21) WILD-TYPE 334  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     30    2
  AMP PEAK 11(6Q21) WILD-TYPE  334   17
     clus
vv    AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  NO                         30                         334
  YES                         2                          17
[1] 2 2
[1] FALSE
D11V9, continuous
D11V10, continuous
D11V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(6Q21) MUTATED       2                         3    30
  AMP PEAK 11(6Q21) WILD-TYPE    41                        19   297
D11V12, multiclass
                           clus
vv                          AMP PEAK 11(6Q21) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            30
                           clus
vv                          AMP PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              41
  BLACK OR AFRICAN AMERICAN                          19
  WHITE                                             297
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                             cls
clus                            0   1
  AMP PEAK 11(6Q21) MUTATED     1  32
  AMP PEAK 11(6Q21) WILD-TYPE   8 337
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED      1   32
  AMP PEAK 11(6Q21) WILD-TYPE    8  337
                        clus
vv                       AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             1                           8
  NOT HISPANIC OR LATINO                        32                         337
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(6Q23.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(6Q23.3) MUTATED    26  20
  AMP PEAK 12(6Q23.3) WILD-TYPE 203 157
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           46                           360 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           20                           157 
$`AMP PEAK 12(6Q23.3) MUTATED`
TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A20T TCGA-BT-A2LA TCGA-CF-A1HS TCGA-CF-A47V 
       34.98         6.58        14.89        17.16        12.56        12.46 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A3IM TCGA-DK-A3WX 
       15.12        18.48        18.41       130.88         8.15        10.55 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA75 TCGA-E7-A541 TCGA-E7-A97Q TCGA-FD-A3SS 
       36.66        15.02        11.18        25.58         8.09        12.85 
TCGA-FD-A6TD TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO 
       12.69        10.65        17.23        29.36        21.40        15.81 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A40G 
       19.13        24.92         0.49        10.65        14.27        19.07 
TCGA-HQ-A2OE TCGA-K4-A5RH TCGA-UY-A78N TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A9SV 
       38.60         9.07        86.83         6.21        51.32        12.76 
TCGA-XF-A9SZ TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAN8 TCGA-ZF-A9R4 
       28.24        66.64       110.60        71.57         3.88        30.28 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4V 
       64.08        58.72        20.22        59.38 

$`AMP PEAK 12(6Q23.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W 
       16.27        44.94        16.83        16.77        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       10.22        47.80        29.65         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66         6.74        12.39        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       26.14        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
        8.98         1.94        23.01        12.79        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       12.13        13.08        12.16        10.95        12.66        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.62        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.87        18.58        13.08        12.92         4.90 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62        46.68        17.95         7.79       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        4.80        13.58         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21         9.67        20.81       163.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       38.24        52.01        13.58       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 
       19.00        13.64        15.35        13.64        56.15        12.03 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       20.32        43.59        15.35        38.83        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.24         4.24        24.03        24.66         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       13.68        14.07        12.95        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       16.77         8.94        33.04         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       27.98        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        46.78        19.79         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       18.08        58.92         2.70         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       62.86        18.81         6.15        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A871 
        4.31         9.67        10.85        31.07        12.66         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        11.08        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       59.31        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        6.94        70.32        20.71        15.91        14.07        17.75 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        8.94        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       32.78        20.05         5.62         4.73        32.98         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
       27.35         8.58        22.72         1.51        19.40        64.01 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
        9.01        12.16        25.02         3.45        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        9.14        27.68        11.70        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       16.27        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       44.38         1.15        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       12.23        16.67        14.24         1.84        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       38.99        17.62        37.05        22.68        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       69.34         3.02       112.83         3.91        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.85        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       15.35         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        3.22        15.98        66.41        34.45        14.93         4.21 
TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        5.98        11.90        23.64        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        6.77        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39        18.15        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        0.66        11.97        13.64        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       31.20        35.84        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
        3.48        88.87        47.84         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        60.16        63.02        56.35        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21        19.17         5.52        12.23 

  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                         0.49                          0.10 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                       130.88                        166.03 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                       17.820                        16.995 
[1] "0.5 - 130.9 (17.8)" "0.1 - 166.0 (17.0)"
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(6Q23.3) MUTATED         0       11        19       15
  AMP PEAK 12(6Q23.3) WILD-TYPE       2      118       121      120
D12V3, multiclass
           clus
vv          AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           11                           118
  STAGE III                          19                           121
  STAGE IV                           15                           120
[1] 4 2
[1] 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(6Q23.3) MUTATED         13  22   7
  AMP PEAK 12(6Q23.3) WILD-TYPE      110 173  51
D12V4, multiclass
          clus
vv         AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  T0+T1+T2                          13                           110
  T3                                22                           173
  T4                                 7                            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 12(6Q23.3) MUTATED    26   6   7   3
  AMP PEAK 12(6Q23.3) WILD-TYPE 209  41  68   6
D12V5, multiclass
    clus
vv   AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  N0                          26                           209
  N1                           6                            41
  N2                           7                            68
  N3                           3                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED    23   2
  AMP PEAK 12(6Q23.3) WILD-TYPE 169   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED     23    2
  AMP PEAK 12(6Q23.3) WILD-TYPE  169    9
   clus
vv  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  0                          23                           169
  1                           2                             9
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED    10  36
  AMP PEAK 12(6Q23.3) WILD-TYPE  97 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED     10   36
  AMP PEAK 12(6Q23.3) WILD-TYPE   97  265
        clus
vv       AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  FEMALE                          10                            97
  MALE                            36                           265
[1] 2 2
[1] FALSE
D12V8, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED    42   2
  AMP PEAK 12(6Q23.3) WILD-TYPE 322  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED     42    2
  AMP PEAK 12(6Q23.3) WILD-TYPE  322   17
     clus
vv    AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  NO                           42                           322
  YES                           2                            17
[1] 2 2
[1] FALSE
D12V9, continuous
D12V10, continuous
D12V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(6Q23.3) MUTATED       2                         1    42
  AMP PEAK 12(6Q23.3) WILD-TYPE    41                        21   285
D12V12, multiclass
                           clus
vv                          AMP PEAK 12(6Q23.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              42
                           clus
vv                          AMP PEAK 12(6Q23.3) WILD-TYPE
  ASIAN                                                41
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                               cls
clus                              0   1
  AMP PEAK 12(6Q23.3) MUTATED     1  42
  AMP PEAK 12(6Q23.3) WILD-TYPE   8 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED      1   42
  AMP PEAK 12(6Q23.3) WILD-TYPE    8  327
                        clus
vv                       AMP PEAK 12(6Q23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       AMP PEAK 12(6Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           327
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(7P21.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(7P21.1) MUTATED   105  96
  AMP PEAK 13(7P21.1) WILD-TYPE 124  81
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          201                           205 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                           96                            81 
$`AMP PEAK 13(7P21.1) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       11.97       108.95         8.35        16.27        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       27.62         0.62        41.75        15.12        10.22        47.80 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O 
       40.08         2.66        12.39         6.58        26.14        12.16 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06         8.35         8.25        17.16        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
       12.82         9.96        28.70        36.43        28.41        23.01 
TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5U8 TCGA-CU-A0YN TCGA-CU-A0YO 
       12.79        12.13        12.16        13.12        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
       18.48         5.19        13.58        21.86         2.14        18.41 
TCGA-DK-A1AC TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      130.88        17.95         7.79       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58         8.15         8.22        50.27        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       66.05        17.98        64.18        67.36        15.68        36.66 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA75 
       38.24        15.02       165.73       166.03        19.00        11.18 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DU 
       43.59        15.35        22.16        25.58        24.03         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.22        13.68         8.09        32.02        16.77         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR 
       33.04         4.01        22.52        24.30        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       12.85         7.56        27.35        20.91         3.62        26.73 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       11.01         5.36        27.45        18.08        58.92         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
        6.28        13.35        12.69        12.36         2.27         3.06 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P 
        9.67        31.07        10.65        17.23         3.25        11.08 
TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       59.31        17.62        66.02        70.32        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I3 
       20.71        19.13        15.91        14.07        24.92        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A766 
        7.73        20.98         2.20        10.92        11.31         5.62 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QI 
        4.73        32.98         7.00        21.34        19.82        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE 
       27.35         8.58        22.72        19.40         9.01        12.16 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41P 
        9.07        11.70         1.81        15.42        16.27        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G0 
       46.98         1.15        15.32        13.48         1.84        12.43 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HD 
        3.02         3.91        29.56         6.21        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.12        15.35        48.62        79.66         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45        14.93         4.21         5.98        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT 
        2.24        66.64       110.60         7.63        71.57         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 
        6.77        98.99        44.32        56.48        61.45        75.39 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       18.15        13.64        22.36        31.20        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       58.72         2.89        34.06        19.69        59.38        63.02 
TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5P 
        8.52        19.17        12.23 

$`AMP PEAK 13(7P21.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       24.13        94.88       104.65        44.94        16.83        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       50.04        51.16        66.54        29.65         2.50        17.42 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.74        13.15        19.04        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0EZ 
        5.06        14.89        14.96         4.67        17.56         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
        1.94        12.56        13.97        12.59        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA 
       12.66        12.46        12.10        12.62        12.26        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        29.79         1.84        66.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A3IQ 
      112.44        16.14        17.62        15.62        46.68        17.72 
TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30        20.81        10.55       163.30        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X 
       50.70        52.01        13.58        18.81        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.64        56.15        12.03        20.32        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       26.24         4.24        24.66        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       14.37        12.62        27.98        60.66        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS 
       29.16         5.52        25.74        14.96        15.58        53.88 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB 
       19.33         5.69         8.25         2.70        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF 
        6.15         4.31        10.85        12.66         8.94        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        33.01         7.23        20.12 
TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP 
        6.94        15.81        17.75         0.49         8.94         2.10 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        3.12         7.36        18.97         7.63        32.78        20.05 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40G 
       10.65        14.27        19.10        20.28         8.48        19.07 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51        38.60        64.01        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41N 
        2.76         9.14        27.68        17.72        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       50.56        44.38        15.58        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       14.24        16.54        38.99        78.25       112.83        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.85        45.04         6.58       125.49         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        66.41        12.76        11.90        23.64        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN3 
       11.31        54.90        91.73         8.32        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       25.41        21.11        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U 
       94.29         3.48        88.87        47.84        20.22         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       60.16        56.35        35.41        57.90        19.40        54.21 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                         0.62                          0.10 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                       166.03                        163.30 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                        17.16                         17.56 
[1] "0.6 - 166.0 (17.2)" "0.1 - 163.3 (17.6)"
[1] "hr=" "1.2"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 13(7P21.1) MUTATED         1       50        68       82
  AMP PEAK 13(7P21.1) WILD-TYPE       1       79        72       53
D13V3, multiclass
           clus
vv          AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           50                            79
  STAGE III                          68                            72
  STAGE IV                           82                            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 13(7P21.1) MUTATED         52 103  32
  AMP PEAK 13(7P21.1) WILD-TYPE       71  92  26
D13V4, multiclass
          clus
vv         AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  T0+T1+T2                          52                            71
  T3                               103                            92
  T4                                32                            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 13(7P21.1) MUTATED   101  29  44   8
  AMP PEAK 13(7P21.1) WILD-TYPE 134  18  31   1
D13V5, multiclass
    clus
vv   AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  N0                         101                           134
  N1                          29                            18
  N2                          44                            31
  N3                           8                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED    84   5
  AMP PEAK 13(7P21.1) WILD-TYPE 108   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED     84    5
  AMP PEAK 13(7P21.1) WILD-TYPE  108    6
   clus
vv  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  0                          84                           108
  1                           5                             6
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED    50 151
  AMP PEAK 13(7P21.1) WILD-TYPE  57 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED     50  151
  AMP PEAK 13(7P21.1) WILD-TYPE   57  150
        clus
vv       AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  FEMALE                          50                            57
  MALE                           151                           150
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED   185   5
  AMP PEAK 13(7P21.1) WILD-TYPE 179  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED    185    5
  AMP PEAK 13(7P21.1) WILD-TYPE  179   14
     clus
vv    AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  NO                          185                           179
  YES                           5                            14
[1] 2 2
[1] FALSE
D13V9, continuous
D13V10, continuous
D13V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(7P21.1) MUTATED      11                        13   171
  AMP PEAK 13(7P21.1) WILD-TYPE    32                         9   156
D13V12, multiclass
                           clus
vv                          AMP PEAK 13(7P21.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             171
                           clus
vv                          AMP PEAK 13(7P21.1) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                               cls
clus                              0   1
  AMP PEAK 13(7P21.1) MUTATED     4 182
  AMP PEAK 13(7P21.1) WILD-TYPE   5 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED      4  182
  AMP PEAK 13(7P21.1) WILD-TYPE    5  187
                        clus
vv                       AMP PEAK 13(7P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         182
                        clus
vv                       AMP PEAK 13(7P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           187
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(7P11.2) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(7P11.2) MUTATED   103  87
  AMP PEAK 14(7P11.2) WILD-TYPE 126  90
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          190                           216 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                           87                            90 
$`AMP PEAK 14(7P11.2) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 
       16.27        16.77        27.62         0.62        41.75        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A5ZZ 
       10.22        47.80        29.65        40.08         2.66        12.39 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20W 
        6.58        19.04        26.14        12.16         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
        8.25        17.16        16.18        20.48        12.82        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI 
       36.43        28.41        23.01        12.56        12.13        12.16 
TCGA-CF-A5U8 TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A3 
       13.12        12.92         4.90        18.48        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 
        2.14        18.41       130.88       112.44        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       142.78        87.32         4.80        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        50.27        23.21         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6R 
       64.18        67.36        36.66        38.24        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4TZ 
      166.03        18.81        19.00        11.18        43.59        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
       22.16        25.58        24.03         0.92         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       12.95         8.09        32.02         8.94        33.04         4.01 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       22.52        24.30        46.78        19.79        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       27.35        20.91         3.62        26.73         5.36        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TD 
       18.08        58.92         7.10         6.28        13.35        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       12.36         2.27         3.06         9.67        10.65        17.23 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
        3.25        11.08        59.31        17.62        66.02        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       29.36        21.40        20.71        19.13        15.91        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       13.91         7.73        20.98         2.20        10.92        11.31 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JZ 
       20.05         5.62        32.98         7.00        21.34        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       20.28         8.48        27.35         8.58        19.07        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60         9.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LC-A66R 
       11.70         1.81        16.27        35.97         1.15        15.32 
TCGA-MV-A51V TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       13.48         1.84        12.43        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH 
       69.34         3.02         3.91        29.56         6.21        51.32 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ 
       97.45        97.12        15.35        48.62        79.66         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SY TCGA-XF-A9T3 
       15.98        34.45        14.93         5.98        21.04         2.24 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMX 
       66.64       110.60         7.63        71.57         2.96         6.77 
TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3M 
       98.99        56.48        61.45        75.39        18.15        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N 
       22.36        31.20        13.41        64.08        58.72         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA5H 
       59.38        63.02        56.35        19.17 

$`AMP PEAK 14(7P11.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 
       44.94        16.83        17.16        34.98        50.04        51.16 
TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX 
       66.54         2.50        17.42         7.33         6.74        13.15 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH 
       17.88        19.50         5.06        14.89        14.96         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C 
        9.96        17.56         8.98         1.94        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.59        13.08        10.95        12.66        12.46        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.62        12.26        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL 
       11.87        18.58        13.08        15.12         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        66.41        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       15.62        17.72        21.30        20.81        10.55       163.30 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q 
       53.29        76.60        15.68        50.70        52.01        13.58 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       13.64        15.35        13.64        56.15        12.03        20.32 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66        26.96        26.24         4.24        24.66        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.32        14.37        16.77        12.62        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S 
       23.41        17.98        29.16         5.52        25.74        14.96 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        53.88        11.01        19.33         5.69         8.25 
TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FD-A6TK 
        2.70        62.86        18.81         6.15         4.31        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       31.07        12.66         8.94        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO 
       26.93        33.01         7.23        20.12         6.94        15.81 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75        24.92         0.49         8.94         2.10         3.12 
TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO 
        7.36        18.97         7.63        32.78         4.73        10.65 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS 
       14.27        19.10        36.49         1.51        64.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB 
        3.45         2.76         9.14        27.68        17.72        15.42 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 
       11.80        52.73        50.56        46.98        44.38        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        12.23        16.67        14.24        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PF 
       17.62        37.05        78.25       112.83        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
       45.04         6.58       125.49         1.87        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ 
       66.41         4.21        12.76        11.90        23.64        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       26.27        18.90        16.27         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMZ 
       10.82        11.31        54.90        91.73         8.32        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        86.30        27.06         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        0.66        11.97        25.41        21.11        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RM 
       21.86        28.41        94.29         3.48        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA52 
       20.22        34.06        19.69         8.61        60.16        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        54.21         5.52        12.23 

  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                         0.62                          0.10 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                       166.03                        163.30 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                        18.03                         16.70 
[1] "0.6 - 166.0 (18.0)" "0.1 - 163.3 (16.7)"
[1] "hr=" "1"  
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 14(7P11.2) MUTATED         1       55        61       72
  AMP PEAK 14(7P11.2) WILD-TYPE       1       74        79       63
D14V3, multiclass
           clus
vv          AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           55                            74
  STAGE III                          61                            79
  STAGE IV                           72                            63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 14(7P11.2) MUTATED         54  94  28
  AMP PEAK 14(7P11.2) WILD-TYPE       69 101  30
D14V4, multiclass
          clus
vv         AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  T0+T1+T2                          54                            69
  T3                                94                           101
  T4                                28                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 14(7P11.2) MUTATED    97  23  41   8
  AMP PEAK 14(7P11.2) WILD-TYPE 138  24  34   1
D14V5, multiclass
    clus
vv   AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  N0                          97                           138
  N1                          23                            24
  N2                          41                            34
  N3                           8                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED    85   5
  AMP PEAK 14(7P11.2) WILD-TYPE 107   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED     85    5
  AMP PEAK 14(7P11.2) WILD-TYPE  107    6
   clus
vv  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  0                          85                           107
  1                           5                             6
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED    50 140
  AMP PEAK 14(7P11.2) WILD-TYPE  57 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED     50  140
  AMP PEAK 14(7P11.2) WILD-TYPE   57  161
        clus
vv       AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  FEMALE                          50                            57
  MALE                           140                           161
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED   174   6
  AMP PEAK 14(7P11.2) WILD-TYPE 190  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED    174    6
  AMP PEAK 14(7P11.2) WILD-TYPE  190   13
     clus
vv    AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  NO                          174                           190
  YES                           6                            13
[1] 2 2
[1] FALSE
D14V9, continuous
D14V10, continuous
D14V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(7P11.2) MUTATED      12                        11   160
  AMP PEAK 14(7P11.2) WILD-TYPE    31                        11   167
D14V12, multiclass
                           clus
vv                          AMP PEAK 14(7P11.2) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             160
                           clus
vv                          AMP PEAK 14(7P11.2) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                               cls
clus                              0   1
  AMP PEAK 14(7P11.2) MUTATED     5 168
  AMP PEAK 14(7P11.2) WILD-TYPE   4 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED      5  168
  AMP PEAK 14(7P11.2) WILD-TYPE    4  201
                        clus
vv                       AMP PEAK 14(7P11.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         168
                        clus
vv                       AMP PEAK 14(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           201
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(8P11.23) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(8P11.23) MUTATED    68  55
  AMP PEAK 15(8P11.23) WILD-TYPE 161 122
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           123                            283 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                            55                            122 
$`AMP PEAK 15(8P11.23) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-4Z-AA89 
       24.13        44.94        16.83        17.16        41.75        29.65 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LD 
        6.74        12.39        26.14         5.06        17.16        20.48 
TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MG TCGA-CU-A3QU TCGA-CU-A72E 
       36.43        23.01        13.97        12.13         5.19        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ 
        2.14       112.44        17.95        87.32         4.80        17.72 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6L 
       50.27        23.21        10.55        17.98        36.66        38.24 
TCGA-DK-AA6R TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ 
      165.73        13.64        56.15        43.59        29.72        22.16 
TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B7 
       26.96        24.03        13.68        12.95         8.09         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        24.30        17.98        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TD 
       27.35        20.91        53.88        58.92         7.10        12.69 
TCGA-FD-A6TI TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE 
        9.67        10.65         3.25        11.08        33.01        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I3 
       17.62        66.02        21.40        20.71        14.07        13.91 
TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         2.20         7.36         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5ND 
       19.10        36.49         8.58        22.72        38.60         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ 
       12.16         3.45        21.24        27.68        11.70         1.81 
TCGA-K4-A6MB TCGA-KQ-A41N TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-SY-A9G0 
       15.42        52.73         1.15        21.07        12.23        12.43 
TCGA-UY-A78N TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       86.83         3.02       112.83         6.21         3.85        45.04 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SK 
       97.45        97.12        15.35        48.62        64.80        15.98 
TCGA-XF-A9SU TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN7 
        5.98        66.64       110.60        71.57        98.99        18.15 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9RE TCGA-ZF-A9RG 
       13.64        22.36        21.11        31.20         3.48        58.72 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 
        2.89        34.06         8.61        63.02        56.35        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5P 
        8.52        54.21        12.23 

$`AMP PEAK 15(8P11.23) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 
       16.77        34.98        27.62        50.04         0.62        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       66.54        15.12        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         8.25        16.18         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR 
       17.56        28.70        28.41         8.98         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.56        12.59        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90        15.12        18.48        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       21.86        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        46.68         7.79       142.78 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58         8.15         8.22        21.30         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      163.30        66.05        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S 
       15.68        50.70        52.01        15.02        13.58       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 TCGA-DK-AA76 
       18.81        19.00        13.64        15.35        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       20.32        15.35        38.83         0.10         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
       25.58         0.56         0.66        26.24         4.24        24.66 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
        0.92         1.22        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94        33.04        12.62        22.52        27.98 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       23.41        29.16         5.52        25.74         7.56        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
        3.62        15.58        26.73        11.01        19.33         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P 
        5.69         8.25        27.45        18.08         2.70         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF 
       13.35        62.86        18.81         6.15        12.36         2.27 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        3.06         4.31        10.85        31.07        12.66        17.23 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
        7.23         6.94        70.32        29.36        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP 
       15.91        17.75        24.92         0.49         8.94         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98        10.92        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       32.78        20.05         5.62         4.73        10.65        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO 
       19.82        20.28         8.48        27.35        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH 
       19.40        64.01        25.02         2.76         9.14         9.07 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       17.72        16.27        11.80        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       44.38        15.32        15.58        13.48        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       76.01        78.25        69.34         3.91        29.56        17.82 
TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI 
       51.32         6.58       125.49         1.87        17.88        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        66.41        34.45        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
        2.24        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       11.31        54.90         7.63        91.73         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        6.77        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        25.41        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       94.29        13.41        64.08        88.87        47.84        20.22 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       19.69        59.38        60.16        35.41        19.40        19.17 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                          1.15                           0.10 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                        165.73                         166.03 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                         19.79                          16.27 
[1] "1.1 - 165.7 (19.8)" "0.1 - 166.0 (16.3)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 15(8P11.23) MUTATED         0       41        39       42
  AMP PEAK 15(8P11.23) WILD-TYPE       2       88       101       93
D15V3, multiclass
           clus
vv          AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            41                             88
  STAGE III                           39                            101
  STAGE IV                            42                             93
[1] 4 2
[1] 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(8P11.23) MUTATED         42  56  18
  AMP PEAK 15(8P11.23) WILD-TYPE       81 139  40
D15V4, multiclass
          clus
vv         AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  T0+T1+T2                           42                             81
  T3                                 56                            139
  T4                                 18                             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                              N0  N1  N2  N3
  AMP PEAK 15(8P11.23) MUTATED    63  20  18   3
  AMP PEAK 15(8P11.23) WILD-TYPE 172  27  57   6
D15V5, multiclass
    clus
vv   AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  N0                           63                            172
  N1                           20                             27
  N2                           18                             57
  N3                            3                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED    54   2
  AMP PEAK 15(8P11.23) WILD-TYPE 138   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED     54    2
  AMP PEAK 15(8P11.23) WILD-TYPE  138    9
   clus
vv  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  0                           54                            138
  1                            2                              9
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED    32  91
  AMP PEAK 15(8P11.23) WILD-TYPE  75 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED     32   91
  AMP PEAK 15(8P11.23) WILD-TYPE   75  210
        clus
vv       AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  FEMALE                           32                             75
  MALE                             91                            210
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED   113   6
  AMP PEAK 15(8P11.23) WILD-TYPE 251  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED    113    6
  AMP PEAK 15(8P11.23) WILD-TYPE  251   13
     clus
vv    AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  NO                           113                            251
  YES                            6                             13
[1] 2 2
[1] FALSE
D15V9, continuous
D15V10, continuous
D15V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(8P11.23) MUTATED       9                         8    98
  AMP PEAK 15(8P11.23) WILD-TYPE    34                        14   229
D15V12, multiclass
                           clus
vv                          AMP PEAK 15(8P11.23) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               98
                           clus
vv                          AMP PEAK 15(8P11.23) WILD-TYPE
  ASIAN                                                 34
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED     5 106
  AMP PEAK 15(8P11.23) WILD-TYPE   4 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED      5  106
  AMP PEAK 15(8P11.23) WILD-TYPE    4  263
                        clus
vv                       AMP PEAK 15(8P11.23) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          106
                        clus
vv                       AMP PEAK 15(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            263
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(8P11.21) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(8P11.21) MUTATED    86  54
  AMP PEAK 16(8P11.21) WILD-TYPE 143 123
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           140                            266 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                            54                            123 
$`AMP PEAK 16(8P11.21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       24.13        11.97       108.95        44.94        16.83        17.16 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13J TCGA-BL-A3JM 
       41.75        10.22        47.80        29.65         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PJ 
       12.39        26.14         8.35        17.16        20.48        12.82 
TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A47X TCGA-CU-A0YN 
       36.43        23.01        13.97        12.13        12.62        12.92 
TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 
        5.19        13.58        66.41        18.41       112.44        17.95 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
      142.78        87.32         4.80        17.72        50.27        23.21 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       10.55        17.98        36.66        38.24        52.01       165.73 
TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A677 
       19.00        13.64        56.15        43.59        22.16        26.96 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
       24.03         0.92         1.22        13.68        12.95         8.09 
TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       60.66        46.78        19.79        12.85         7.56        27.35 
TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TI 
       20.91        53.88        58.92         2.70         7.10         9.67 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 
        3.25        11.08        33.01        66.02        21.40        20.71 
TCGA-GC-A3RB TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-AATQ 
       19.13         0.49        20.98         2.20         7.36         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        19.10        19.82        20.28         8.48        36.49 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
        8.58        22.72        38.60        64.01         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41N TCGA-KQ-A41S 
        3.45        11.70         1.81        15.42        52.73         1.15 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78N TCGA-UY-A8OC 
       21.07        12.23        12.43        38.99        86.83         3.02 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD 
      112.83        17.82         6.21        51.32        45.04        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SU 
       97.12        15.35         1.87        48.62        64.80         5.98 
TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YC-A89H 
      110.60         7.63        71.57        98.99        18.15        18.84 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       13.64        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
        3.48        64.08        58.72         2.89        19.69         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        56.35        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.17        12.23 

$`AMP PEAK 16(8P11.21) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S 
       94.88       104.65         8.35        16.27        16.77        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       27.62        50.04         0.62        51.16        66.54        15.12 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX 
        2.50        17.42        40.08         7.33         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK 
       14.96         5.06         8.25        16.18         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR 
       17.56        28.70        28.41         8.98         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.56        12.59        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO 
       11.34        11.34        11.87        18.58        13.08         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
       15.12        18.48        29.79         1.84        21.86         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT 
       46.68         7.79        13.58         8.15         8.22        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
        9.67        20.81       163.30        66.05        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6Q 
       76.60        67.36        15.68        50.70        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 TCGA-DK-AA76 
      166.03        18.81        13.64        15.35        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       20.32        15.35        38.83        29.72         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD 
       16.70        25.58         0.56         0.66        26.24         4.24 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       24.66        14.07        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        23.41        17.98        29.16         5.52        25.74 
TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96         3.62        15.58        26.73        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P 
        5.36         5.69         8.25        27.45        18.08         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       13.35        62.86        18.81         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         3.06         4.31        10.85        31.07        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65        17.23         8.94        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C 
       26.93        59.31         7.23        20.12        17.62         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       70.32        29.36        15.81        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         8.94        13.91         7.73         2.10         3.12 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       10.92        11.31        18.97         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3QK 
        5.62         4.73        10.65        32.98        21.34        27.35 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB 
       19.07         1.51        19.40        12.16        21.24         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO 
        9.14        27.68         9.07        17.72        16.27        11.80 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
       50.56        35.97        46.98        44.38        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K 
       13.48        16.67        14.24         1.84        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA 
       37.05        22.68        76.01        78.25        69.34         3.91 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SI 
       29.56         3.85         6.58       125.49        17.88        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
        3.22        15.98        66.41        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       12.76        11.90        23.64        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       18.90         2.24        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMT 
       92.98        10.82        11.31        54.90        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32         6.77        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC 
       86.30        27.06        75.39         3.88         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       11.97        35.84        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W 
       88.87        47.84        20.22        34.06        59.38        60.16 
TCGA-ZF-AA52 TCGA-ZF-AA5N 
       35.41         5.52 

  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                        165.73                         166.03 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                        19.545                         15.965 
[1] "0.5 - 165.7 (19.5)" "0.1 - 166.0 (16.0)"
[1] "hr=" "1.4"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 16(8P11.21) MUTATED         0       46        49       44
  AMP PEAK 16(8P11.21) WILD-TYPE       2       83        91       91
D16V3, multiclass
           clus
vv          AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            46                             83
  STAGE III                           49                             91
  STAGE IV                            44                             91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 16(8P11.21) MUTATED         45  64  23
  AMP PEAK 16(8P11.21) WILD-TYPE       78 131  35
D16V4, multiclass
          clus
vv         AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  T0+T1+T2                           45                             78
  T3                                 64                            131
  T4                                 23                             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 16(8P11.21) MUTATED    75  19  20   5
  AMP PEAK 16(8P11.21) WILD-TYPE 160  28  55   4
D16V5, multiclass
    clus
vv   AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  N0                           75                            160
  N1                           19                             28
  N2                           20                             55
  N3                            5                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED    72   0
  AMP PEAK 16(8P11.21) WILD-TYPE 120  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED     72    0
  AMP PEAK 16(8P11.21) WILD-TYPE  120   11
   clus
vv  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  0                           72                            120
  1                            0                             11
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED    33 107
  AMP PEAK 16(8P11.21) WILD-TYPE  74 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED     33  107
  AMP PEAK 16(8P11.21) WILD-TYPE   74  194
        clus
vv       AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           33                             74
  MALE                            107                            194
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED   128   5
  AMP PEAK 16(8P11.21) WILD-TYPE 236  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED    128    5
  AMP PEAK 16(8P11.21) WILD-TYPE  236   14
     clus
vv    AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  NO                           128                            236
  YES                            5                             14
[1] 2 2
[1] FALSE
D16V9, continuous
D16V10, continuous
D16V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(8P11.21) MUTATED      10                         7   115
  AMP PEAK 16(8P11.21) WILD-TYPE    33                        15   212
D16V12, multiclass
                           clus
vv                          AMP PEAK 16(8P11.21) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              115
                           clus
vv                          AMP PEAK 16(8P11.21) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                                cls
clus                               0   1
  AMP PEAK 16(8P11.21) MUTATED     4 121
  AMP PEAK 16(8P11.21) WILD-TYPE   5 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED      4  121
  AMP PEAK 16(8P11.21) WILD-TYPE    5  248
                        clus
vv                       AMP PEAK 16(8P11.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          121
                        clus
vv                       AMP PEAK 16(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            248
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(8Q22.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(8Q22.3) MUTATED   146 118
  AMP PEAK 17(8Q22.3) WILD-TYPE  83  59
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          264                           142 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          118                            59 
$`AMP PEAK 17(8Q22.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        11.97       104.65         8.35        16.27        44.94 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       17.16        34.98         0.62        41.75        51.16        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        29.65        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W 
       12.39        19.04        26.14        14.89         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42B 
        8.25        17.16        16.18        20.48        12.82        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        36.43        28.41         8.98         1.94        23.01 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47X 
       12.56        13.97        12.13        13.08        10.95        12.62 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.00        11.34        11.87        12.92        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.19         1.84        13.58        21.86         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 
       18.41       130.88       112.44        16.14        17.95       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         4.80         8.15         8.22        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
       23.21        10.55        66.05        17.98        64.18        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U 
       36.66        52.01        15.02       165.73       166.03        19.00 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       13.64        13.64        56.15        11.18        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A541 
       43.59        15.35        38.83        22.16         2.24        25.58 
TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV 
        0.56        26.96         4.24        24.03         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 
       13.68        12.95        14.37         8.09         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ 
        4.01        27.98        60.66        24.30        25.74        46.78 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
        7.56        20.91        26.73        53.88        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        5.69        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       13.35        12.69        12.36         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EK 
       10.85        31.07        12.66        10.65         3.25        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D 
       59.31        33.01        20.12        17.62        66.02        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       29.36        21.40        20.71        19.13        14.07        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        8.94         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ 
       10.92        18.97         5.62         4.73        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       14.27        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       36.49         8.58        22.72         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       64.01         9.01        12.16        25.02         3.45         2.76 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14         9.07        11.70         1.81        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       52.73        35.97        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       21.07        13.48        12.23        16.67        14.24         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       12.43        38.99        17.62        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02       112.83        17.82         6.21         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       51.32        45.04        97.45        97.12        15.35         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       48.62        64.80        79.66         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T3 
       14.93         4.21         5.98        12.76        26.27         2.24 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        92.98       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 
       71.57         2.96         8.32        98.99        44.32        61.45 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.15        18.84        13.64        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       21.11        31.20        30.28        28.41        94.29         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       64.08        58.72        88.87        20.22         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        60.16        63.02        56.35        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21        19.17         5.52        12.23 

$`AMP PEAK 17(8Q22.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       94.88       108.95        16.83        16.77        27.62        50.04 
TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX 
       66.54         2.50        17.42         7.33         6.58        13.15 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH 
       12.16        17.88        19.50         5.06        14.96         4.67 
TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V 
        9.96        12.79        12.59        12.16        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FL 
       12.10        12.26        13.12        12.10        11.34        18.58 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF 
       13.08         4.90        29.79        19.00        16.70        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3IV 
       15.62        46.68         7.79        13.58        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 
       20.81       163.30        53.29        76.60        67.36        50.70 
TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E7-A3X6 TCGA-E7-A3Y1 
       38.24        13.58        18.81        15.35        29.72         0.10 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
       16.70         0.66        26.24        24.66        14.07        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SM 
       32.02        16.77        12.62        22.52        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S 
       29.16         5.52        19.79        12.85        27.35        14.96 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA 
        3.62        15.58        19.33         8.25         2.70        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P 
       18.81         6.15         2.27        17.23         8.94        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3OO 
       61.94        48.00        26.93         7.23         6.94        15.81 
TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GU-A42Q 
       15.91        24.92         0.49        13.91         7.73        11.31 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO TCGA-GV-A3QK TCGA-GV-A40G 
        7.63        32.78        20.05        10.65        27.35        19.07 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41Q 
       21.24        27.68        17.72        11.80        50.56        46.98 
TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HC 
       16.54        37.05        78.25         3.91        29.56         6.58 
TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
      125.49        17.88        66.41        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF 
       28.24        18.90        16.27        66.64        13.74        10.82 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
       91.73         6.77        56.48        30.94        86.30        27.06 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        3.88         9.63         0.66        11.97        35.84        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4V 
       13.41        47.84        34.06        59.38 

  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                         0.56                          0.10 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                       166.03                        163.30 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                        17.59                         16.80 
[1] "0.6 - 166.0 (17.6)" "0.1 - 163.3 (16.8)"
[1] "hr=" "1"  
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 17(8Q22.3) MUTATED         1       81        90       90
  AMP PEAK 17(8Q22.3) WILD-TYPE       1       48        50       45
D17V3, multiclass
           clus
vv          AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           81                            48
  STAGE III                          90                            50
  STAGE IV                           90                            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 17(8Q22.3) MUTATED         81 124  39
  AMP PEAK 17(8Q22.3) WILD-TYPE       42  71  19
D17V4, multiclass
          clus
vv         AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  T0+T1+T2                          81                            42
  T3                               124                            71
  T4                                39                            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 17(8Q22.3) MUTATED   145  35  46   6
  AMP PEAK 17(8Q22.3) WILD-TYPE  90  12  29   3
D17V5, multiclass
    clus
vv   AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  N0                         145                            90
  N1                          35                            12
  N2                          46                            29
  N3                           6                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                               cls
clus                              0   1
  AMP PEAK 17(8Q22.3) MUTATED   122   7
  AMP PEAK 17(8Q22.3) WILD-TYPE  70   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED    122    7
  AMP PEAK 17(8Q22.3) WILD-TYPE   70    4
   clus
vv  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  0                         122                            70
  1                           7                             4
[1] 2 2
[1] FALSE
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(8Q22.3) MUTATED    67 197
  AMP PEAK 17(8Q22.3) WILD-TYPE  40 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED     67  197
  AMP PEAK 17(8Q22.3) WILD-TYPE   40  104
        clus
vv       AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  FEMALE                          67                            40
  MALE                           197                           104
[1] 2 2
[1] FALSE
D17V8, binary
                               cls
clus                              0   1
  AMP PEAK 17(8Q22.3) MUTATED   236  13
  AMP PEAK 17(8Q22.3) WILD-TYPE 128   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED    236   13
  AMP PEAK 17(8Q22.3) WILD-TYPE  128    6
     clus
vv    AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  NO                          236                           128
  YES                          13                             6
[1] 2 2
[1] FALSE
D17V9, continuous
D17V10, continuous
D17V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(8Q22.3) MUTATED      23                        13   215
  AMP PEAK 17(8Q22.3) WILD-TYPE    20                         9   112
D17V12, multiclass
                           clus
vv                          AMP PEAK 17(8Q22.3) MUTATED
  ASIAN                                              23
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             215
                           clus
vv                          AMP PEAK 17(8Q22.3) WILD-TYPE
  ASIAN                                                20
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                               cls
clus                              0   1
  AMP PEAK 17(8Q22.3) MUTATED     5 235
  AMP PEAK 17(8Q22.3) WILD-TYPE   4 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED      5  235
  AMP PEAK 17(8Q22.3) WILD-TYPE    4  134
                        clus
vv                       AMP PEAK 17(8Q22.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         235
                        clus
vv                       AMP PEAK 17(8Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           134
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(9P24.1) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(9P24.1) MUTATED    50  38
  AMP PEAK 18(9P24.1) WILD-TYPE 179 139
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           88                           318 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                           38                           139 
$`AMP PEAK 18(9P24.1) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 
       24.13        16.77        15.12        47.80         6.74         6.58 
TCGA-BT-A20V TCGA-BT-A3PJ TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A5 TCGA-DK-A1AC 
        5.06        12.82        15.12         5.19         2.14       130.88 
TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A6B6 TCGA-DK-AA6R 
      112.44       142.78        87.32         8.15        36.66       165.73 
TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SL 
       12.95        32.02        33.04         4.01        22.52        23.41 
TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TD 
       27.35        11.01        19.33         5.69         2.70        12.69 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IE 
        2.27         4.31        31.07        61.94        48.00        20.12 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       21.40        20.71        15.91         0.49        13.91         7.73 
TCGA-GD-A3OP TCGA-GU-A763 TCGA-GU-A764 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
        2.10        32.78        20.05        19.82        20.28        36.49 
TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R TCGA-SY-A9G0 
        8.58        19.07        12.16         1.81        15.32        12.43 
TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG 
       17.62        78.25        29.56         6.58        97.12        15.35 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SY 
       48.62        79.66         3.22        34.45        14.93        21.04 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAN4 
       16.27        66.64       110.60         7.63         2.96        27.06 
TCGA-XF-AAN5 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RF 
       75.39        13.64        22.36        30.28        21.86        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89        19.69        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA58 
       60.16        63.02        57.90        54.21 

$`AMP PEAK 18(9P24.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 
        0.62        41.75        51.16        66.54        10.22        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ 
        2.50        17.42        40.08         7.33         2.66        12.39 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
        5.06        14.89        14.96         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       16.18        20.48         4.67         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         8.98         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL 
       18.58        13.08        12.92         4.90        18.48        29.79 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        1.84        13.58        21.86        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
       16.70        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        7.79         4.80        13.58         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       15.68        50.70        38.24        52.01        15.02        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       56.15        11.18        12.03        20.32        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       25.58         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       24.03        24.66         0.92         1.22        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       15.32        14.37         8.09        16.77         8.94        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        24.30        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S 
       25.74        46.78        19.79        12.85         7.56        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BV 
       20.91         3.62        15.58        26.73        53.88         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
       13.35        62.86        18.81         6.15        12.36         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        12.66        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        11.08        15.95        26.93        59.31        33.01 
TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
        7.23        17.62        66.02         6.94        70.32        29.36 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81        19.13        14.07        17.75        24.92         8.94 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       18.97         7.63         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QK 
        7.00        14.27        21.34        19.10         8.48        27.35 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       22.72         1.51        19.40        38.60        64.01         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        11.70        17.72        15.42        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       52.73        50.56        35.97        46.98        44.38         1.15 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
        1.84        16.54        38.99        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD 
       76.01        69.34         3.02       112.83         3.91        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE 
        6.21         3.85        51.32        45.04        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9ST 
        1.87        17.88        64.80        15.98        66.41         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
        5.98        12.76        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       11.31        54.90        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       25.41        21.11        31.20        35.84        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA51 
       13.41         3.48        88.87        34.06         8.61        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        19.40         8.52        19.17         5.52        12.23 

  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                         0.49                          0.10 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                       165.73                        166.03 
  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE 
                       20.170                        16.605 
[1] "0.5 - 165.7 (20.2)" "0.1 - 166.0 (16.6)"
[1] "hr=" "1.2"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 18(9P24.1) MUTATED         0       26        33       29
  AMP PEAK 18(9P24.1) WILD-TYPE       2      103       107      106
D18V3, multiclass
           clus
vv          AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           26                           103
  STAGE III                          33                           107
  STAGE IV                           29                           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"
                               vv
clus                            T0+T1+T2  T3  T4
  AMP PEAK 18(9P24.1) MUTATED         23  44  13
  AMP PEAK 18(9P24.1) WILD-TYPE      100 151  45
D18V4, multiclass
          clus
vv         AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  T0+T1+T2                          23                           100
  T3                                44                           151
  T4                                13                            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                             N0  N1  N2  N3
  AMP PEAK 18(9P24.1) MUTATED    45   9  19   2
  AMP PEAK 18(9P24.1) WILD-TYPE 190  38  56   7
D18V5, multiclass
    clus
vv   AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  N0                          45                           190
  N1                           9                            38
  N2                          19                            56
  N3                           2                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    34   3
  AMP PEAK 18(9P24.1) WILD-TYPE 158   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     34    3
  AMP PEAK 18(9P24.1) WILD-TYPE  158    8
   clus
vv  AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  0                          34                           158
  1                           3                             8
[1] 2 2
[1] FALSE
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    20  68
  AMP PEAK 18(9P24.1) WILD-TYPE  87 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     20   68
  AMP PEAK 18(9P24.1) WILD-TYPE   87  233
        clus
vv       AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  FEMALE                          20                            87
  MALE                            68                           233
[1] 2 2
[1] FALSE
D18V8, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED    80   1
  AMP PEAK 18(9P24.1) WILD-TYPE 284  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED     80    1
  AMP PEAK 18(9P24.1) WILD-TYPE  284   18
     clus
vv    AMP PEAK 18(9P24.1) MUTATED AMP PEAK 18(9P24.1) WILD-TYPE
  NO                           80                           284
  YES                           1                            18
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, continuous
D18V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(9P24.1) MUTATED       4                         7    74
  AMP PEAK 18(9P24.1) WILD-TYPE    39                        15   253
D18V12, multiclass
                           clus
vv                          AMP PEAK 18(9P24.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              74
                           clus
vv                          AMP PEAK 18(9P24.1) WILD-TYPE
  ASIAN                                                39
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                               cls
clus                              0   1
  AMP PEAK 18(9P24.1) MUTATED     3  79
  AMP PEAK 18(9P24.1) WILD-TYPE   6 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(9P24.1) MUTATED      3   79
  AMP PEAK 18(9P24.1) WILD-TYPE    6  290
                        clus
vv                       AMP PEAK 18(9P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          79
                        clus
vv                       AMP PEAK 18(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           290
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(10P14) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(10P14) MUTATED   100  82
  AMP PEAK 19(10P14) WILD-TYPE 129  95
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                         182                          224 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                          82                           95 
$`AMP PEAK 19(10P14) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 
       24.13        16.27        16.77        17.16        27.62         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J 
       41.75        15.12        47.80         2.50        40.08         2.66 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20W 
        6.58        26.14        19.50         5.06         5.06         8.35 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 
       16.18        20.48        12.82        36.43         8.98        23.01 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5UA TCGA-CF-A8HY 
       12.56        12.59        12.13        12.16        12.00        11.34 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A5 
       12.92        18.48         5.19         1.84        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 
       66.41       130.88       112.44        46.68        17.95        87.32 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 
       13.58         8.22         9.67        66.05        64.18        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U 
       15.68        36.66        15.02       165.73       166.03        19.00 
TCGA-DK-AA74 TCGA-E5-A4U1 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW 
       56.15        38.83         4.24        24.03         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       12.95        14.37         8.09        32.02         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       22.52        60.66        24.30        19.79        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BZ TCGA-FD-A5C0 
       27.35        15.58        26.73        53.88        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
       58.92        12.36         2.27         3.06         9.67        31.07 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.25        11.08        33.01        20.12        17.62        66.02 
TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       29.36        19.13        14.07         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A766 TCGA-GU-A767 
        7.73        20.98         2.20        10.92         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65        32.98         7.00        21.34        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.48         8.58        22.72        19.40        38.60        64.01 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
        9.01        12.16        25.02         9.14        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41P 
       11.70        17.72         1.81        16.27        11.80        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G0 
       46.98         1.15        15.32        15.58        13.48        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O 
       38.99        17.62        37.05        22.68        86.83        76.01 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF 
       69.34         3.91         6.21        51.32        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       15.35        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T6 TCGA-XF-AAMF 
       14.93         4.21        23.64        28.24         2.10        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX 
      110.60        11.31        54.90         7.63         2.96         6.77 
TCGA-XF-AAMZ TCGA-XF-AAN4 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       44.32        27.06        13.64        22.36        25.41        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN 
       30.28        28.41        94.29        64.08        47.84        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       34.06        19.69        59.38        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 
       57.90        19.40 

$`AMP PEAK 19(10P14) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       11.97        94.88       104.65       108.95         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       16.83        34.98        50.04        51.16        66.54        10.22 
TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       29.65        17.42         7.33         6.74        12.39        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X 
       19.04        12.16        17.88        14.89        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F 
       17.16         4.67         9.96        17.56        28.70        28.41 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
        1.94        12.79        13.97        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE 
       29.79        13.58        18.41        19.00        16.70        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
       17.62        15.62         7.79       142.78         4.80         8.15 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
       17.72        50.27        21.30        23.21        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L 
      163.30        17.98        53.29        76.60        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       52.01        13.58        18.81        13.64        15.35        13.64 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A3X6 
       11.18        12.03        20.32        43.59        15.35        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN 
        0.66        26.96        26.24        24.66         0.92        14.07 
TCGA-E7-A8O7 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SL 
       15.32        16.77         4.01        12.62        27.98        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S 
       17.98        29.16         5.52        25.74        46.78        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       20.91         3.62        11.01        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
        8.25         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 
       18.81         6.15        12.69         4.31        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65        17.23         8.94        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM 
       26.93        59.31         7.23         6.94        70.32        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP 
       20.71        15.81        15.91        17.75        24.92         2.10 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 
        3.12         7.36        11.31        18.97         7.63        32.78 
TCGA-GU-A764 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       20.05        14.27        19.10        36.49        27.35        19.07 
TCGA-H4-A2HO TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-KQ-A41N 
        1.51         3.45        21.24         2.76        15.42        52.73 
TCGA-KQ-A41O TCGA-KQ-A41R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       50.56        44.38        21.07        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB 
        1.84        16.54        78.25         3.02       112.83        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HH 
       17.82         3.85        45.04         6.58       125.49         1.87 
TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       17.88        66.41        34.45         5.98        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY 
       13.74        92.98        71.57        91.73         8.32        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        30.94        61.45        86.30        75.39        18.15 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R2 
        3.88        18.84         9.63         0.66        11.97        21.11 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL 
       35.84        21.86        13.41         3.48        58.72        88.87 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        2.89         8.61        60.16         8.52        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                        0.49                         0.10 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                      166.03                       163.30 
  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE 
                      18.740                       16.605 
[1] "0.5 - 166.0 (18.7)" "0.1 - 163.3 (16.6)"
[1] "hr=" "1"  
D19V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 19(10P14) MUTATED         1       53        61       66
  AMP PEAK 19(10P14) WILD-TYPE       1       76        79       69
D19V3, multiclass
           clus
vv          AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  STAGE I                            1                            1
  STAGE II                          53                           76
  STAGE III                         61                           79
  STAGE IV                          66                           69
[1] 4 2
[1] 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(10P14) MUTATED         53  88  28
  AMP PEAK 19(10P14) WILD-TYPE       70 107  30
D19V4, multiclass
          clus
vv         AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  T0+T1+T2                         53                           70
  T3                               88                          107
  T4                               28                           30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 19(10P14) MUTATED    88  26  34   6
  AMP PEAK 19(10P14) WILD-TYPE 147  21  41   3
D19V5, multiclass
    clus
vv   AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  N0                         88                          147
  N1                         26                           21
  N2                         34                           41
  N3                          6                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                              cls
clus                             0   1
  AMP PEAK 19(10P14) MUTATED    81   5
  AMP PEAK 19(10P14) WILD-TYPE 111   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(10P14) MUTATED     81    5
  AMP PEAK 19(10P14) WILD-TYPE  111    6
   clus
vv  AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  0                         81                          111
  1                          5                            6
[1] 2 2
[1] FALSE
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(10P14) MUTATED    44 138
  AMP PEAK 19(10P14) WILD-TYPE  63 163
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(10P14) MUTATED     44  138
  AMP PEAK 19(10P14) WILD-TYPE   63  163
        clus
vv       AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  FEMALE                         44                           63
  MALE                          138                          163
[1] 2 2
[1] FALSE
D19V8, binary
                              cls
clus                             0   1
  AMP PEAK 19(10P14) MUTATED   161   6
  AMP PEAK 19(10P14) WILD-TYPE 203  13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(10P14) MUTATED    161    6
  AMP PEAK 19(10P14) WILD-TYPE  203   13
     clus
vv    AMP PEAK 19(10P14) MUTATED AMP PEAK 19(10P14) WILD-TYPE
  NO                         161                          203
  YES                          6                           13
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
D19V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(10P14) MUTATED      16                         9   147
  AMP PEAK 19(10P14) WILD-TYPE    27                        13   180
D19V12, multiclass
                           clus
vv                          AMP PEAK 19(10P14) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            147
                           clus
vv                          AMP PEAK 19(10P14) WILD-TYPE
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                              cls
clus                             0   1
  AMP PEAK 19(10P14) MUTATED     4 159
  AMP PEAK 19(10P14) WILD-TYPE   5 210
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(10P14) MUTATED      4  159
  AMP PEAK 19(10P14) WILD-TYPE    5  210
                        clus
vv                       AMP PEAK 19(10P14) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        159
                        clus
vv                       AMP PEAK 19(10P14) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          210
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(11P13) MUTATION ANALYSIS
D20V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 20(11P13) MUTATED    28  23
  AMP PEAK 20(11P13) WILD-TYPE 201 154
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          51                          355 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                          23                          154 
$`AMP PEAK 20(11P13) MUTATED`
TCGA-4Z-AA7M TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-CU-A0YN 
       16.27         6.74         5.06        17.16        12.82        12.92 
TCGA-CU-A0YO TCGA-DK-A2I2 TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-AA6R TCGA-E5-A2PC 
        4.90         7.79         9.67        10.55       165.73        43.59 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A5BT TCGA-FD-A62N 
        0.56        24.03         1.22        33.04        11.01         2.70 
TCGA-FD-A62P TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-GC-A3RC TCGA-GU-A762 TCGA-GU-A766 
        6.28         9.67        31.07        15.91         7.63         5.62 
TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A3WS TCGA-K4-A4AC TCGA-KQ-A41P 
       19.82        36.49         8.58        25.02         9.14        35.97 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OD TCGA-UY-A9PB 
       15.32        12.23        17.62        22.68       112.83        29.56 
TCGA-UY-A9PF TCGA-XF-A9SP TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAMG 
        3.85        14.93        23.64        21.04         2.24       110.60 
TCGA-XF-AAMH TCGA-XF-AAMT TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9RD TCGA-ZF-AA4T 
       11.31         2.96        18.15        13.64        13.41        19.69 
TCGA-ZF-AA51 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       56.35        19.17        12.23 

$`AMP PEAK 20(11P13) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       50.04         0.62        41.75        51.16        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       10.22        47.80        29.65         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        7.33         2.66        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       26.14        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.35         8.25        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        1.94        23.01        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YR 
       11.34        11.34        11.87        18.58        13.08        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      142.78        87.32         4.80        13.58         8.15         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY 
       17.72        50.27        21.30        23.21        20.81       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       15.68        50.70        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       13.58       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        56.15        11.18        12.03        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
       25.58         0.66        26.96        26.24         4.24        24.66 
TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        0.92        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        32.02        16.77         8.94         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
        7.56        27.35        14.96        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       26.73        53.88        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA 
       27.45        18.08        58.92         7.10        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        4.31        10.85        12.66        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        11.08        61.94        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       59.31        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        70.32        29.36        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       19.13        14.07        17.75        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
        7.36        10.92        11.31        18.97        32.78        20.05 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       19.10        20.28         8.48        27.35        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60        64.01         9.01        12.16 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
        3.45        21.24         2.76        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT 
       50.56        46.98        44.38         1.15        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       13.48        16.67        14.24         1.84        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       38.99        37.05        86.83        76.01        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HB 
        3.02         3.91        17.82         6.21        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       66.41        34.45         4.21         5.98        12.76        11.90 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        92.98        10.82        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       91.73         8.32         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        31.20        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       94.29         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22         2.89        34.06         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        35.41        57.90        19.40         8.52        54.21 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                        0.56                         0.10 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                      165.73                       166.03 
  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE 
                       13.64                        17.72 
[1] "0.6 - 165.7 (13.6)" "0.1 - 166.0 (17.7)"
[1] "hr=" "1.3"
D20V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 20(11P13) MUTATED         0       13        13       25
  AMP PEAK 20(11P13) WILD-TYPE       2      116       127      110
D20V3, multiclass
           clus
vv          AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  STAGE I                            0                            2
  STAGE II                          13                          116
  STAGE III                         13                          127
  STAGE IV                          25                          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"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 20(11P13) MUTATED         14  25   9
  AMP PEAK 20(11P13) WILD-TYPE      109 170  49
D20V4, multiclass
          clus
vv         AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  T0+T1+T2                         14                          109
  T3                               25                          170
  T4                                9                           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                            N0  N1  N2  N3
  AMP PEAK 20(11P13) MUTATED    20   6  15   5
  AMP PEAK 20(11P13) WILD-TYPE 215  41  60   4
D20V5, multiclass
    clus
vv   AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  N0                         20                          215
  N1                          6                           41
  N2                         15                           60
  N3                          5                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                              cls
clus                             0   1
  AMP PEAK 20(11P13) MUTATED    16   1
  AMP PEAK 20(11P13) WILD-TYPE 176  10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(11P13) MUTATED     16    1
  AMP PEAK 20(11P13) WILD-TYPE  176   10
   clus
vv  AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  0                         16                          176
  1                          1                           10
[1] 2 2
[1] FALSE
D20V7, binary
                              cls
clus                             0   1
  AMP PEAK 20(11P13) MUTATED    14  37
  AMP PEAK 20(11P13) WILD-TYPE  93 264
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(11P13) MUTATED     14   37
  AMP PEAK 20(11P13) WILD-TYPE   93  264
        clus
vv       AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  FEMALE                         14                           93
  MALE                           37                          264
[1] 2 2
[1] FALSE
D20V8, binary
                              cls
clus                             0   1
  AMP PEAK 20(11P13) MUTATED    45   1
  AMP PEAK 20(11P13) WILD-TYPE 319  18
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(11P13) MUTATED     45    1
  AMP PEAK 20(11P13) WILD-TYPE  319   18
     clus
vv    AMP PEAK 20(11P13) MUTATED AMP PEAK 20(11P13) WILD-TYPE
  NO                          45                          319
  YES                          1                           18
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
D20V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(11P13) MUTATED       4                         1    45
  AMP PEAK 20(11P13) WILD-TYPE    39                        21   282
D20V12, multiclass
                           clus
vv                          AMP PEAK 20(11P13) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             45
                           clus
vv                          AMP PEAK 20(11P13) WILD-TYPE
  ASIAN                                               39
  BLACK OR AFRICAN AMERICAN                           21
  WHITE                                              282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                              cls
clus                             0   1
  AMP PEAK 20(11P13) MUTATED     2  48
  AMP PEAK 20(11P13) WILD-TYPE   7 321
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(11P13) MUTATED      2   48
  AMP PEAK 20(11P13) WILD-TYPE    7  321
                        clus
vv                       AMP PEAK 20(11P13) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         48
                        clus
vv                       AMP PEAK 20(11P13) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          321
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(11Q13.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(11Q13.3) MUTATED    77  58
  AMP PEAK 21(11Q13.3) WILD-TYPE 152 119
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                           135                            271 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                            58                            119 
$`AMP PEAK 21(11Q13.3) MUTATED`
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A2LA 
       16.83        34.98         0.62         2.66        26.14        17.16 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82        17.56        28.70        36.43        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A47V TCGA-CF-A8HX TCGA-CF-A8HY 
       23.01        12.56        12.13        12.46        11.34        11.34 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A3 
       12.92         4.90        15.12        18.48         1.84        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
        2.14        66.41        17.62        17.95         7.79        87.32 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       13.58         8.15        17.72        10.55        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 
       64.18        36.66        15.02        56.15        12.03        20.32 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7DV 
       43.59        38.83         0.56         0.66         4.24         1.22 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.09         8.94        33.04         4.01        60.66        24.30 
TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT 
        7.56        27.35        20.91        15.58        26.73        11.01 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
        5.36         2.70        13.35         3.06         9.67        31.07 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       33.01         7.23        20.12        66.02        70.32        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 
       21.40        20.71        15.91        14.07         8.94         7.73 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       20.98         2.20         7.63         5.62         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       14.27        21.34        19.82        20.28         8.48        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND 
       27.35         8.58        19.07        19.40        38.60         9.01 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       21.24         2.76         9.14        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX 
       46.98        15.32        21.07        12.23        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A8OD 
       16.54        12.43        22.68        76.01         3.02       112.83 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A9SV TCGA-XF-A9SY 
       29.56         3.85        51.32        97.12        12.76        21.04 
TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT 
       16.27         2.10        11.31         7.63        71.57         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YF-AA3M 
        8.32         6.77        44.32        27.06         3.88        13.64 
TCGA-ZF-A9R7 TCGA-ZF-AA51 TCGA-ZF-AA53 
       21.86        56.35        57.90 

$`AMP PEAK 21(11Q13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.27        44.94        16.77        17.16        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       41.75        51.16        66.54        15.12        10.22        47.80 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       29.65         2.50        17.42        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       19.50         5.06        14.89        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-C4-A0F0 
        8.25        16.18        20.48         9.96         8.98         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       12.79        13.97        12.59        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.10        11.87        18.58        13.08         5.19        29.79 
TCGA-CU-A72E TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       13.58        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IN 
       16.14        15.62        46.68       142.78         4.80         8.22 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        20.81       163.30 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       53.29        76.60        67.36        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       52.01        13.58       165.73       166.03        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A3X6 
       13.64        15.35        13.64        11.18        15.35        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A677 
        0.10        22.16         2.24        16.70        25.58        26.96 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
       26.24        24.03        24.66         0.92        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       12.95        15.32        14.37        32.02        16.77        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       22.52        27.98        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43X 
       25.74        46.78        19.79        12.85        14.96         3.62 
TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       53.88        19.33         5.69         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
       58.92         7.10         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z9 
       12.69        12.36         2.27         4.31        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3C 
       48.00        15.95        26.93        59.31        17.62         6.94 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 
       15.81        19.13        17.75        24.92         0.49        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12         7.36        10.92        11.31        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A6ZA 
       32.78        20.05        10.65        32.98        19.10        22.72 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R 
        1.51        64.01        12.16        25.02         3.45        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
       11.80        44.38         1.15        15.58        13.48        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB 
       38.99        17.62        37.05        86.83        78.25        69.34 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
        3.91        17.82         6.21        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
      125.49        15.35         1.87        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       79.66         3.22        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 
        4.21         5.98        11.90        23.64        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        66.64        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 
      110.60        54.90        91.73        98.99        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A8S6 
       61.45        86.30        75.39        18.15        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        35.84        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       64.08        58.72        88.87        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       35.41        19.40         8.52        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                          0.56                           0.10 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                        112.83                         166.03 
  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE 
                         16.27                          17.62 
[1] "0.6 - 112.8 (16.3)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.1"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 21(11Q13.3) MUTATED         0       47        38       49
  AMP PEAK 21(11Q13.3) WILD-TYPE       2       82       102       86
D21V3, multiclass
           clus
vv          AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            47                             82
  STAGE III                           38                            102
  STAGE IV                            49                             86
[1] 4 2
[1] 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(11Q13.3) MUTATED         46  58  20
  AMP PEAK 21(11Q13.3) WILD-TYPE       77 137  38
D21V4, multiclass
          clus
vv         AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  T0+T1+T2                           46                             77
  T3                                 58                            137
  T4                                 20                             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                              N0  N1  N2  N3
  AMP PEAK 21(11Q13.3) MUTATED    74  16  27   6
  AMP PEAK 21(11Q13.3) WILD-TYPE 161  31  48   3
D21V5, multiclass
    clus
vv   AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  N0                           74                            161
  N1                           16                             31
  N2                           27                             48
  N3                            6                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q13.3) MUTATED    59   3
  AMP PEAK 21(11Q13.3) WILD-TYPE 133   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q13.3) MUTATED     59    3
  AMP PEAK 21(11Q13.3) WILD-TYPE  133    8
   clus
vv  AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  0                           59                            133
  1                            3                              8
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q13.3) MUTATED    40  95
  AMP PEAK 21(11Q13.3) WILD-TYPE  67 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q13.3) MUTATED     40   95
  AMP PEAK 21(11Q13.3) WILD-TYPE   67  206
        clus
vv       AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  FEMALE                           40                             67
  MALE                             95                            206
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q13.3) MUTATED   121   4
  AMP PEAK 21(11Q13.3) WILD-TYPE 243  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q13.3) MUTATED    121    4
  AMP PEAK 21(11Q13.3) WILD-TYPE  243   15
     clus
vv    AMP PEAK 21(11Q13.3) MUTATED AMP PEAK 21(11Q13.3) WILD-TYPE
  NO                           121                            243
  YES                            4                             15
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
D21V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(11Q13.3) MUTATED      10                        12   106
  AMP PEAK 21(11Q13.3) WILD-TYPE    33                        10   221
D21V12, multiclass
                           clus
vv                          AMP PEAK 21(11Q13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              106
                           clus
vv                          AMP PEAK 21(11Q13.3) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                             10
  WHITE                                                221
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                                cls
clus                               0   1
  AMP PEAK 21(11Q13.3) MUTATED     2 124
  AMP PEAK 21(11Q13.3) WILD-TYPE   7 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(11Q13.3) MUTATED      2  124
  AMP PEAK 21(11Q13.3) WILD-TYPE    7  245
                        clus
vv                       AMP PEAK 21(11Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       AMP PEAK 21(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            245
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(11Q22.2) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(11Q22.2) MUTATED    45  26
  AMP PEAK 22(11Q22.2) WILD-TYPE 184 151
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            71                            335 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                            26                            151 
$`AMP PEAK 22(11Q22.2) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42E 
       24.13         0.62        15.12         8.35        12.82        36.43 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-DK-A1A3 
        1.94        23.01        11.34        15.12         1.84        21.86 
TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       17.95        87.32        13.58        10.55        66.05        17.98 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A5KF TCGA-E7-A7DV TCGA-E7-A97Q 
       12.03        20.32        43.59         0.66         1.22         8.09 
TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ 
       33.04        60.66        27.35        26.73        11.01        27.45 
TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3B TCGA-G2-AA3D 
       58.92         3.06         9.67        31.07        66.02        70.32 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3YS TCGA-GD-A3OS TCGA-GD-A6C6 
       29.36        20.71        15.91        24.92        20.98         2.20 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-K4-A4AB 
        7.63         5.62        20.28        36.49         8.58         2.76 
TCGA-K4-A4AC TCGA-K4-A6MB TCGA-KQ-A41N TCGA-KQ-A41P TCGA-LC-A66R TCGA-PQ-A6FI 
        9.14        15.42        52.73        35.97        15.32        12.23 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PF 
        1.84        12.43        22.68         3.02        29.56         3.85 
TCGA-XF-A8HF TCGA-XF-A9SY TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMX TCGA-YF-AA3M 
       97.12        21.04         2.10        11.31         6.77        13.64 
TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-AA51 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       21.86        64.08        56.35        19.17        12.23 

$`AMP PEAK 22(11Q22.2) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04        41.75        51.16        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       29.65         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06         8.25        17.16        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HR 
        9.96        17.56        28.70        28.41         8.98        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL 
       13.12        12.00        12.10        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       13.08        12.92         4.90        18.48         5.19        29.79 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62        46.68 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       142.78         4.80         8.15         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
       50.27        21.30        23.21         9.67        20.81       163.30 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       36.66        38.24        52.01        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
      166.03        18.81        19.00        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       56.15        11.18        15.35        38.83        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
       22.16         2.24        16.70        25.58         0.56        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
       26.24         4.24        24.03        24.66         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        12.95        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SJ 
        8.94         4.01        12.62        22.52        27.98        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       19.79        12.85         7.56        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        53.88        19.33         5.36         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       18.08         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         2.27         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        12.66        10.65        17.23         8.94         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
       11.08        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-GC-A3BM 
       33.01         7.23        20.12        17.62         6.94        21.40 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.81        19.13        14.07        17.75         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P 
       13.91         7.73         2.10         3.12         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO 
       11.31        18.97        32.78        20.05         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.98         7.00        14.27        21.34        19.10        19.82 
TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
        8.48        27.35        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       38.60        64.01         9.01        12.16        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       21.24        27.68         9.07        11.70        17.72         1.81 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       16.27        11.80        50.56        46.98        44.38         1.15 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        21.07        13.48        16.67        14.24        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       38.99        17.62        37.05        86.83        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH 
       69.34       112.83         3.91        17.82         6.21        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        23.64        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       16.27        66.64        13.74        92.98        10.82       110.60 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       54.90         7.63        71.57        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       98.99        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       30.28        35.84        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R 
       58.72        88.87        47.84        20.22         2.89        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       19.69         8.61        59.38        60.16        63.02        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       57.90        19.40         8.52        54.21         5.52 

  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                          0.62                           0.10 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                         97.12                         166.03 
  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE 
                         15.91                          17.23 
[1] "0.6 - 97.1 (15.9)"  "0.1 - 166.0 (17.2)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 22(11Q22.2) MUTATED         0       23        17       31
  AMP PEAK 22(11Q22.2) WILD-TYPE       2      106       123      104
D22V3, multiclass
           clus
vv          AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            23                            106
  STAGE III                           17                            123
  STAGE IV                            31                            104
[1] 4 2
[1] 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(11Q22.2) MUTATED         24  32  11
  AMP PEAK 22(11Q22.2) WILD-TYPE       99 163  47
D22V4, multiclass
          clus
vv         AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  T0+T1+T2                           24                             99
  T3                                 32                            163
  T4                                 11                             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                              N0  N1  N2  N3
  AMP PEAK 22(11Q22.2) MUTATED    33  11  17   4
  AMP PEAK 22(11Q22.2) WILD-TYPE 202  36  58   5
D22V5, multiclass
    clus
vv   AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  N0                           33                            202
  N1                           11                             36
  N2                           17                             58
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q22.2) MUTATED    33   2
  AMP PEAK 22(11Q22.2) WILD-TYPE 159   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q22.2) MUTATED     33    2
  AMP PEAK 22(11Q22.2) WILD-TYPE  159    9
   clus
vv  AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  0                           33                            159
  1                            2                              9
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q22.2) MUTATED    19  52
  AMP PEAK 22(11Q22.2) WILD-TYPE  88 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q22.2) MUTATED     19   52
  AMP PEAK 22(11Q22.2) WILD-TYPE   88  249
        clus
vv       AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  FEMALE                           19                             88
  MALE                             52                            249
[1] 2 2
[1] FALSE
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q22.2) MUTATED    63   1
  AMP PEAK 22(11Q22.2) WILD-TYPE 301  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q22.2) MUTATED     63    1
  AMP PEAK 22(11Q22.2) WILD-TYPE  301   18
     clus
vv    AMP PEAK 22(11Q22.2) MUTATED AMP PEAK 22(11Q22.2) WILD-TYPE
  NO                            63                            301
  YES                            1                             18
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
D22V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(11Q22.2) MUTATED       3                         3    62
  AMP PEAK 22(11Q22.2) WILD-TYPE    40                        19   265
D22V12, multiclass
                           clus
vv                          AMP PEAK 22(11Q22.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               62
                           clus
vv                          AMP PEAK 22(11Q22.2) WILD-TYPE
  ASIAN                                                 40
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q22.2) MUTATED     1  66
  AMP PEAK 22(11Q22.2) WILD-TYPE   8 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q22.2) MUTATED      1   66
  AMP PEAK 22(11Q22.2) WILD-TYPE    8  303
                        clus
vv                       AMP PEAK 22(11Q22.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       AMP PEAK 22(11Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            303
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(12P12.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(12P12.1) MUTATED    76  55
  AMP PEAK 23(12P12.1) WILD-TYPE 153 122
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                           131                            275 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                            55                            122 
$`AMP PEAK 23(12P12.1) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       24.13        27.62        41.75        15.12        10.22        47.80 
TCGA-BL-A0C8 TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20R 
       40.08         6.74        19.04        26.14        17.88         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06         8.25        16.18        20.48        12.82         9.96 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A5UA 
       36.43         1.94        12.13        13.08        12.16        12.00 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.34        11.34        12.92         4.90        15.12        18.48 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 
       66.41        18.41         8.15        50.27        10.55        66.05 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R 
       64.18        67.36        15.68        36.66        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 
      166.03        18.81        19.00        15.35        13.64        11.18 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3NA 
       22.16         0.56        24.03        32.02        33.04        60.66 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       12.85        27.35        53.88         5.36         5.69        27.45 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.28        13.35        18.81         2.27        31.07        12.66 
TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM 
       11.08        59.31        17.62        66.02        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A762 TCGA-GU-A764 
       20.71        15.81        14.07        13.91         7.63        20.05 
TCGA-GU-AATQ TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        7.00        19.82         8.48        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.07        38.60        64.01         9.01        12.16         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A83P TCGA-KQ-A41P 
       21.24         9.14         9.07        11.70        16.27        35.97 
TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78O 
       15.32        13.48        12.23        38.99        17.62        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PH TCGA-XF-A9SI 
       78.25         3.02         3.91        29.56        51.32        79.66 
TCGA-XF-A9SK TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX 
       15.98         5.98        12.76         7.63         2.96         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3M 
       98.99        44.32        86.30        75.39        18.15        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9RD TCGA-ZF-AA4N 
       25.41        21.11        31.20        30.28        13.41         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 
       59.38        60.16        56.35        57.90        19.40 

$`AMP PEAK 23(12P12.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
        0.62        51.16        66.54        29.65         2.50        17.42 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        7.33         2.66        12.39         6.58        13.15        12.16 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH 
       19.50        14.89        14.96         8.35        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        28.70        28.41         8.98        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.56        13.97        12.59        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.10        12.62        12.26        13.12        12.10        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       18.58        13.08         5.19        29.79         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       21.86         2.14        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
      142.78        87.32         4.80        13.58         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X2 
       21.30        23.21         9.67        20.81       163.30        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q 
       53.29        76.60        50.70        38.24        52.01        13.58 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
       13.64        56.15        12.03        20.32        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83        29.72         0.10         2.24        16.70        25.58 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        26.96        26.24         4.24        24.66         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        16.77         8.94         4.01        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       25.74        46.78        19.79         7.56        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BY 
        3.62        15.58        26.73        11.01        19.33         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TC 
       18.08        58.92         2.70         7.10        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK 
       12.69        12.36         3.06         4.31         9.67        10.85 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        33.01         7.23        20.12         6.94 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       70.32        19.13        15.91        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        8.94         7.73         2.10         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 
        7.36        10.92        11.31        18.97        32.78         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        4.73        10.65        32.98        14.27        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A4AB 
       20.28        22.72         1.51        19.40        25.02         2.76 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N 
       27.68        17.72         1.81        15.42        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT 
       50.56        46.98        44.38         1.15        15.58        21.07 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78L 
       16.67        14.24         1.84        16.54        12.43        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        86.83        69.34       112.83        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.85        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ 
       15.35         1.87        17.88        48.62        64.80         3.22 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX 
       66.41        34.45        14.93         4.21        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 
       11.31        54.90        71.57        91.73         8.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       30.94        61.45        27.06         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        0.66        11.97        22.36        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       94.29         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 
       20.22        34.06        19.69         8.61        63.02        35.41 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                          0.56                           0.10 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE 
                         17.88                          16.83 
[1] "0.6 - 166.0 (17.9)" "0.1 - 163.3 (16.8)"
[1] "hr=" "1.1"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 23(12P12.1) MUTATED         1       50        39       39
  AMP PEAK 23(12P12.1) WILD-TYPE       1       79       101       96
D23V3, multiclass
           clus
vv          AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            50                             79
  STAGE III                           39                            101
  STAGE IV                            39                             96
[1] 4 2
[1] 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(12P12.1) MUTATED         45  60  15
  AMP PEAK 23(12P12.1) WILD-TYPE       78 135  43
D23V4, multiclass
          clus
vv         AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  T0+T1+T2                           45                             78
  T3                                 60                            135
  T4                                 15                             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                              N0  N1  N2  N3
  AMP PEAK 23(12P12.1) MUTATED    76  18  19   4
  AMP PEAK 23(12P12.1) WILD-TYPE 159  29  56   5
D23V5, multiclass
    clus
vv   AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  N0                           76                            159
  N1                           18                             29
  N2                           19                             56
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED    66   4
  AMP PEAK 23(12P12.1) WILD-TYPE 126   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED     66    4
  AMP PEAK 23(12P12.1) WILD-TYPE  126    7
   clus
vv  AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  0                           66                            126
  1                            4                              7
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED    35  96
  AMP PEAK 23(12P12.1) WILD-TYPE  72 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED     35   96
  AMP PEAK 23(12P12.1) WILD-TYPE   72  205
        clus
vv       AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  FEMALE                           35                             72
  MALE                             96                            205
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED   122   5
  AMP PEAK 23(12P12.1) WILD-TYPE 242  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED    122    5
  AMP PEAK 23(12P12.1) WILD-TYPE  242   14
     clus
vv    AMP PEAK 23(12P12.1) MUTATED AMP PEAK 23(12P12.1) WILD-TYPE
  NO                           122                            242
  YES                            5                             14
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
D23V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(12P12.1) MUTATED      12                         7   105
  AMP PEAK 23(12P12.1) WILD-TYPE    31                        15   222
D23V12, multiclass
                           clus
vv                          AMP PEAK 23(12P12.1) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              105
                           clus
vv                          AMP PEAK 23(12P12.1) WILD-TYPE
  ASIAN                                                 31
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                                cls
clus                               0   1
  AMP PEAK 23(12P12.1) MUTATED     2 117
  AMP PEAK 23(12P12.1) WILD-TYPE   7 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(12P12.1) MUTATED      2  117
  AMP PEAK 23(12P12.1) WILD-TYPE    7  252
                        clus
vv                       AMP PEAK 23(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          117
                        clus
vv                       AMP PEAK 23(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            252
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(12Q15) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(12Q15) MUTATED    67  51
  AMP PEAK 24(12Q15) WILD-TYPE 162 126
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                         118                          288 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                          51                          126 
$`AMP PEAK 24(12Q15) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J 
       24.13        11.97         8.35         0.62        40.08         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V 
        6.74         6.58        19.04        17.88         5.06         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 
        8.25        16.18         9.96        28.70        36.43        23.01 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A5UA TCGA-CF-A7I0 
       12.59        12.13        13.08        12.16        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 
       11.34        11.34        18.58         4.90        15.12         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2I4 
       21.86         2.14        66.41        18.41       130.88       142.78 
TCGA-DK-A3WX TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6P TCGA-DK-AA6S 
       10.55        64.18        67.36        15.68        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 
       18.81        19.00        15.35        13.64        11.18        12.03 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
       25.58         0.56        24.03        13.68        12.95         8.09 
TCGA-FD-A43Y TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A62S 
       15.58         5.69        27.45        58.92         6.28        13.35 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EF 
       18.81         6.15         3.06        31.07        11.08        61.94 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 
       15.95        59.31        17.62        70.32        21.40        20.71 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI 
       14.07        13.91        18.97        21.34         8.48        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       27.35         8.58         1.51        19.40        38.60        64.01 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A83P TCGA-KQ-A41P TCGA-MV-A51V 
        3.45        21.24        11.70        16.27        35.97        13.48 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PE TCGA-XF-A9SH 
        1.84        12.43        38.99        76.01         6.21        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-AAMT 
       79.66         3.22         5.98        12.76        11.90         2.96 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
        6.77        98.99        44.32        61.45        86.30        27.06 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       18.15        13.64        25.41        21.11        30.28        94.29 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA53 
       20.22         8.61        59.38        57.90 

$`AMP PEAK 24(12Q15) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       94.88       104.65       108.95        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.77        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N 
        2.50        17.42         7.33        12.39        13.15        26.14 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA 
       12.16        19.50        14.89        14.96         8.35        17.16 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
       20.48         4.67        12.82        17.56        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A47T 
        1.94        12.79        12.56        13.97        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A9FF 
       12.46        12.10        12.62        12.26        13.12        11.87 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
       13.08        12.92        18.48         5.19        29.79        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       46.68        17.95         7.79        87.32         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67        20.81       163.30        66.05        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q 
       76.60        50.70        36.66        38.24        52.01        13.58 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ 
      165.73        13.64        56.15        20.32        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        26.96        26.24         4.24        24.66         0.92 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 
        1.22        14.07        15.32        14.37        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O 
       19.33         5.36         8.25        18.08         2.70         7.10 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI 
       62.86        12.69        12.36         2.27         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        12.66        10.65        17.23         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       48.00        26.93        33.01         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94        29.36        15.81        19.13        15.91        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       24.92         0.49         8.94         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 
       20.98         2.20         7.36        10.92        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       32.78        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40G 
        7.00        14.27        19.10        19.82        20.28        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        12.16        25.02         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
       27.68         9.07        17.72         1.81        15.42        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       52.73        50.56        46.98        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.58        21.07        12.23        16.67        14.24        16.54 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
        3.02       112.83         3.91        29.56        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SK TCGA-XF-A9SL 
       15.35         1.87        17.88        48.62        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       34.45        14.93         4.21        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
       13.74        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
        7.63        71.57        91.73         8.32        56.48        30.94 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       22.36        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N 
        3.48        64.08        58.72        88.87        47.84         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       34.06        19.69        60.16        63.02        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21        19.17         5.52        12.23 

  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                        0.56                         0.10 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                      166.03                       165.73 
  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE 
                      15.815                       17.590 
[1] "0.6 - 166.0 (15.8)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1"  
D24V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 24(12Q15) MUTATED         1       40        39       37
  AMP PEAK 24(12Q15) WILD-TYPE       1       89       101       98
D24V3, multiclass
           clus
vv          AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  STAGE I                            1                            1
  STAGE II                          40                           89
  STAGE III                         39                          101
  STAGE IV                          37                           98
[1] 4 2
[1] 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 24(12Q15) MUTATED         34  53  19
  AMP PEAK 24(12Q15) WILD-TYPE       89 142  39
D24V4, multiclass
          clus
vv         AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  T0+T1+T2                         34                           89
  T3                               53                          142
  T4                               19                           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                            N0  N1  N2  N3
  AMP PEAK 24(12Q15) MUTATED    68  12  23   2
  AMP PEAK 24(12Q15) WILD-TYPE 167  35  52   7
D24V5, multiclass
    clus
vv   AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  N0                         68                          167
  N1                         12                           35
  N2                         23                           52
  N3                          2                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED    65   3
  AMP PEAK 24(12Q15) WILD-TYPE 127   8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED     65    3
  AMP PEAK 24(12Q15) WILD-TYPE  127    8
   clus
vv  AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  0                         65                          127
  1                          3                            8
[1] 2 2
[1] FALSE
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED    34  84
  AMP PEAK 24(12Q15) WILD-TYPE  73 217
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED     34   84
  AMP PEAK 24(12Q15) WILD-TYPE   73  217
        clus
vv       AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  FEMALE                         34                           73
  MALE                           84                          217
[1] 2 2
[1] FALSE
D24V8, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED   110   6
  AMP PEAK 24(12Q15) WILD-TYPE 254  13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED    110    6
  AMP PEAK 24(12Q15) WILD-TYPE  254   13
     clus
vv    AMP PEAK 24(12Q15) MUTATED AMP PEAK 24(12Q15) WILD-TYPE
  NO                         110                          254
  YES                          6                           13
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
D24V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(12Q15) MUTATED      17                         5    92
  AMP PEAK 24(12Q15) WILD-TYPE    26                        17   235
D24V12, multiclass
                           clus
vv                          AMP PEAK 24(12Q15) MUTATED
  ASIAN                                             17
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             92
                           clus
vv                          AMP PEAK 24(12Q15) WILD-TYPE
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                           17
  WHITE                                              235
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                              cls
clus                             0   1
  AMP PEAK 24(12Q15) MUTATED     2 110
  AMP PEAK 24(12Q15) WILD-TYPE   7 259
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(12Q15) MUTATED      2  110
  AMP PEAK 24(12Q15) WILD-TYPE    7  259
                        clus
vv                       AMP PEAK 24(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        110
                        clus
vv                       AMP PEAK 24(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          259
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(13Q22.1) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(13Q22.1) MUTATED    75  53
  AMP PEAK 25(13Q22.1) WILD-TYPE 154 124
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                           128                            278 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                            53                            124 
$`AMP PEAK 25(13Q22.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA81 TCGA-4Z-AA87 
       24.13       108.95        16.83        16.77        41.75        47.80 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20U 
        6.74         6.58        19.04        26.14        19.50        14.96 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG 
       20.48        12.82         1.94        12.79        12.56        12.13 
TCGA-CF-A3MI TCGA-CF-A8HX TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A2HX 
       12.16        11.34        12.92        15.12        29.79        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         4.80        13.58        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       23.21        66.05        67.36        15.68        50.70        38.24 
TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA76 
       15.02       165.73       166.03        19.00        13.64        12.03 
TCGA-E5-A2PC TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 
       43.59        25.58         0.92         8.09         8.94        33.04 
TCGA-FD-A3N5 TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A62O TCGA-FD-A6TC 
       22.52        17.98         3.62        11.01         7.10         6.15 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EF 
       12.36         3.06         4.31        10.65        11.08        61.94 
TCGA-G2-A2EK TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       15.95        66.02        70.32        15.81        19.13        15.91 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A42R 
       17.75         0.49         2.10        20.98        10.92        18.97 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65         7.00        19.10        19.82        20.28         8.48 
TCGA-GV-A3QK TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
       27.35        19.40         9.01        12.16         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P 
        9.14         9.07        15.42        11.80        52.73        35.97 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-R3-A69X TCGA-SY-A9G5 TCGA-UY-A78K 
        1.15        15.32        13.48        14.24        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       37.05        86.83        78.25        69.34         3.02         3.91 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF 
       29.56        17.82        51.32         6.58        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9T0 TCGA-XF-A9T6 
       15.35        48.62        15.98        14.93        26.27         2.10 
TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
       10.82         7.63        71.57        91.73         6.77        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-AA4X 
       56.48        61.45        22.36        25.41        21.11        63.02 
TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.52        19.17 

$`AMP PEAK 25(13Q22.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        94.88       104.65         8.35        16.27        44.94 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 
       17.16        34.98        27.62        50.04         0.62        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       66.54        15.12        10.22        29.65         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33         2.66        12.39        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       17.88         5.06        14.89         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       17.16        16.18         4.67         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF 
       36.43        28.41         8.98        23.01        13.97        12.59 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       13.08        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       18.58        13.08         4.90        18.48         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IV 
       17.95         7.79       142.78         8.15         8.22         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       163.30        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W 
       76.60        36.66        52.01        13.58        18.81        13.64 
TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       15.35        56.15        11.18        20.32        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         0.10        22.16         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       32.02        16.77         4.01        12.62        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        23.41        29.16         5.52        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85         7.56        27.35        14.96        20.91 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX 
       15.58        26.73        53.88        19.33         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62P 
        8.25        27.45        18.08        58.92         2.70         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI 
       13.35        62.86        18.81        12.69         2.27         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
       10.85        31.07        12.66        17.23         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD 
       17.62         6.94        29.36        21.40        20.71        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 
       24.92         8.94        13.91         7.73         3.12         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        7.36        11.31         7.63        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI TCGA-GV-A40E 
        4.73        32.98        14.27        21.34        36.49         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS 
       19.07        22.72         1.51        38.60        64.01        25.02 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        2.76        27.68        11.70        17.72         1.81        16.27 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       50.56        46.98        44.38        15.58        21.07        12.23 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78O 
       16.67         1.84        16.54        12.43        22.68        76.01 
TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A8HH 
      112.83         6.21         3.85        45.04       125.49         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM 
       17.88        64.80        79.66         3.22        66.41        34.45 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 
       28.24        18.90         2.24        16.27        66.64        13.74 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW 
       92.98       110.60        11.31        54.90         2.96         8.32 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       44.32        30.94        86.30        27.06        75.39        18.15 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 
       60.16        56.35        35.41        57.90        19.40        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE 
                         17.67                          17.16 
[1] "0.5 - 166.0 (17.7)" "0.1 - 163.3 (17.2)"
[1] "hr=" "1.1"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 25(13Q22.1) MUTATED         0       36        46       46
  AMP PEAK 25(13Q22.1) WILD-TYPE       2       93        94       89
D25V3, multiclass
           clus
vv          AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            36                             93
  STAGE III                           46                             94
  STAGE IV                            46                             89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 25(13Q22.1) MUTATED         34  63  20
  AMP PEAK 25(13Q22.1) WILD-TYPE       89 132  38
D25V4, multiclass
          clus
vv         AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  T0+T1+T2                           34                             89
  T3                                 63                            132
  T4                                 20                             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                              N0  N1  N2  N3
  AMP PEAK 25(13Q22.1) MUTATED    75  17  24   5
  AMP PEAK 25(13Q22.1) WILD-TYPE 160  30  51   4
D25V5, multiclass
    clus
vv   AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  N0                           75                            160
  N1                           17                             30
  N2                           24                             51
  N3                            5                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q22.1) MUTATED    62   4
  AMP PEAK 25(13Q22.1) WILD-TYPE 130   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q22.1) MUTATED     62    4
  AMP PEAK 25(13Q22.1) WILD-TYPE  130    7
   clus
vv  AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  0                           62                            130
  1                            4                              7
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q22.1) MUTATED    26 102
  AMP PEAK 25(13Q22.1) WILD-TYPE  81 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q22.1) MUTATED     26  102
  AMP PEAK 25(13Q22.1) WILD-TYPE   81  199
        clus
vv       AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  FEMALE                           26                             81
  MALE                            102                            199
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q22.1) MUTATED   114   5
  AMP PEAK 25(13Q22.1) WILD-TYPE 250  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q22.1) MUTATED    114    5
  AMP PEAK 25(13Q22.1) WILD-TYPE  250   14
     clus
vv    AMP PEAK 25(13Q22.1) MUTATED AMP PEAK 25(13Q22.1) WILD-TYPE
  NO                           114                            250
  YES                            5                             14
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, continuous
D25V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(13Q22.1) MUTATED       6                         7   110
  AMP PEAK 25(13Q22.1) WILD-TYPE    37                        15   217
D25V12, multiclass
                           clus
vv                          AMP PEAK 25(13Q22.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              110
                           clus
vv                          AMP PEAK 25(13Q22.1) WILD-TYPE
  ASIAN                                                 37
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                217
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                                cls
clus                               0   1
  AMP PEAK 25(13Q22.1) MUTATED     3 116
  AMP PEAK 25(13Q22.1) WILD-TYPE   6 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(13Q22.1) MUTATED      3  116
  AMP PEAK 25(13Q22.1) WILD-TYPE    6  253
                        clus
vv                       AMP PEAK 25(13Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       AMP PEAK 25(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(16P13.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(16P13.2) MUTATED    43  44
  AMP PEAK 26(16P13.2) WILD-TYPE 186 133
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            87                            319 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                            44                            133 
$`AMP PEAK 26(16P13.2) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-5N-A9KI TCGA-BT-A0S7 
        8.35        16.27        17.16         0.62         2.50         6.58 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0EZ TCGA-CF-A47X TCGA-CU-A0YR 
        5.06         8.25        17.16         8.98        12.62        15.12 
TCGA-CU-A3QU TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
        5.19         7.79        13.58         8.15         8.22        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X 
        9.67        66.05        67.36       166.03        19.00        15.35 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A6ME 
       11.18        12.03        43.59        15.35        22.16        24.03 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A43U 
       12.95         8.09        60.66        24.30        19.79        20.91 
TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZE 
        8.25        12.69         2.27         3.06         9.67        10.65 
TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-GC-A3BM 
        3.25        59.31        20.12        17.62        66.02        21.40 
TCGA-GC-A3I6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV 
       20.71         7.36        10.92         5.62        32.98        14.27 
TCGA-GV-A3JZ TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU 
       19.82        19.40        38.60        64.01         9.01         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-LC-A66R TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 
        2.76        16.27        15.32        14.24         1.84        38.99 
TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SZ 
       17.82        51.32         3.22        34.45         5.98        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMR 
       26.27        66.64         2.10       110.60         7.63        91.73 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RF 
        6.77        44.32        18.15        22.36        13.41        64.08 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W 
       19.69        59.38        60.16 

$`AMP PEAK 26(16P13.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65       108.95        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.83        16.77        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        29.65 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       17.42        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD 
        5.06        14.89        14.96         8.35        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        4.67        12.82         9.96        17.56        28.70        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.41         1.94        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       11.34        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90        18.48        29.79         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
      142.78        87.32         4.80        17.72        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       163.30        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 
       15.02        13.58       165.73        18.81        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       56.15        20.32        38.83        29.72         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
        4.24        24.66         0.92         1.22        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.32        14.37        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.62        22.52        27.98        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N 
       29.16         5.52        25.74        46.78        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.36         5.69        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       18.81         6.15        12.36         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        17.23         8.94        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D 
       15.95        26.93        33.01         7.23         6.94        70.32 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       29.36        15.81        19.13        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       24.92         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW 
       32.78        20.05         4.73        10.65         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        20.28         8.48        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV 
       19.07        22.72         1.51        12.16        25.02        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       15.42        11.80        52.73        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       44.38         1.15        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        12.43        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       86.83        76.01        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
        3.91        29.56         6.21         3.85        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI 
       97.45       125.49        97.12        15.35         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP 
       48.62        64.80        79.66        15.98        66.41        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 
        4.21        12.76        11.90        23.64        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        16.27        13.74        92.98        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN0 
       54.90        71.57         2.96         8.32        98.99        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       30.94        61.45        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       21.11        31.20        30.28        35.84        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
       94.29         3.48        58.72        88.87        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89        34.06         8.61        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                          0.62                           0.10 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE 
                         15.35                          17.62 
[1] "0.6 - 166.0 (15.3)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1.3"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 26(16P13.2) MUTATED         0       20        31       35
  AMP PEAK 26(16P13.2) WILD-TYPE       2      109       109      100
D26V3, multiclass
           clus
vv          AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            20                            109
  STAGE III                           31                            109
  STAGE IV                            35                            100
[1] 4 2
[1] 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 26(16P13.2) MUTATED         20  38  21
  AMP PEAK 26(16P13.2) WILD-TYPE      103 157  37
D26V4, multiclass
          clus
vv         AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  T0+T1+T2                           20                            103
  T3                                 38                            157
  T4                                 21                             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                              N0  N1  N2  N3
  AMP PEAK 26(16P13.2) MUTATED    44  11  19   4
  AMP PEAK 26(16P13.2) WILD-TYPE 191  36  56   5
D26V5, multiclass
    clus
vv   AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  N0                           44                            191
  N1                           11                             36
  N2                           19                             56
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P13.2) MUTATED    37   4
  AMP PEAK 26(16P13.2) WILD-TYPE 155   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P13.2) MUTATED     37    4
  AMP PEAK 26(16P13.2) WILD-TYPE  155    7
   clus
vv  AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  0                           37                            155
  1                            4                              7
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P13.2) MUTATED    23  64
  AMP PEAK 26(16P13.2) WILD-TYPE  84 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P13.2) MUTATED     23   64
  AMP PEAK 26(16P13.2) WILD-TYPE   84  237
        clus
vv       AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  FEMALE                           23                             84
  MALE                             64                            237
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P13.2) MUTATED    79   3
  AMP PEAK 26(16P13.2) WILD-TYPE 285  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P13.2) MUTATED     79    3
  AMP PEAK 26(16P13.2) WILD-TYPE  285   16
     clus
vv    AMP PEAK 26(16P13.2) MUTATED AMP PEAK 26(16P13.2) WILD-TYPE
  NO                            79                            285
  YES                            3                             16
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
D26V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(16P13.2) MUTATED       5                         4    74
  AMP PEAK 26(16P13.2) WILD-TYPE    38                        18   253
D26V12, multiclass
                           clus
vv                          AMP PEAK 26(16P13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               74
                           clus
vv                          AMP PEAK 26(16P13.2) WILD-TYPE
  ASIAN                                                 38
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                                cls
clus                               0   1
  AMP PEAK 26(16P13.2) MUTATED     1  79
  AMP PEAK 26(16P13.2) WILD-TYPE   8 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(16P13.2) MUTATED      1   79
  AMP PEAK 26(16P13.2) WILD-TYPE    8  290
                        clus
vv                       AMP PEAK 26(16P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       AMP PEAK 26(16P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(16Q22.1) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(16Q22.1) MUTATED    57  51
  AMP PEAK 27(16Q22.1) WILD-TYPE 172 126
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                           108                            298 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                            51                            126 
$`AMP PEAK 27(16Q22.1) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-BL-A13J 
       11.97       108.95         8.35         0.62        47.80         2.66 
TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        6.58        26.14         5.06         5.06         8.25        17.16 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A47X 
       12.82        28.70        36.43         8.98        12.56        12.62 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS 
       18.48         2.14         7.79        13.58         8.15        50.27 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6S 
        9.67        66.05        64.18        15.68        38.24       166.03 
TCGA-DK-AA6X TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A7DV TCGA-E7-A7PW 
       15.35        11.18        43.59        38.83         1.22        13.68 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43Y 
        8.09        32.02        24.30        23.41        27.35        15.58 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P 
       11.01         5.36         8.25        27.45        18.08         6.28 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
       13.35         6.15         2.27         3.06         9.67        10.85 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3B 
       10.65         3.25        59.31        33.01        17.62        66.02 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       70.32        21.40        20.71        24.92         0.49         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATP 
        7.73        20.98         7.36         7.63        10.65        32.98 
TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       21.34        19.40        64.01         9.01        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-AAQO TCGA-LC-A66R TCGA-R3-A69X 
        3.45         2.76        15.42        11.80        15.32        14.24 
TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PE 
        1.84        38.99        22.68        69.34       112.83         6.21 
TCGA-UY-A9PH TCGA-XF-A9SG TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9T3 
       51.32        48.62        15.98        34.45         5.98         2.24 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R0 
       71.57        91.73         6.77        98.99        44.32        22.36 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA5H 
       21.86        94.29        13.41        60.16        19.40        19.17 

$`AMP PEAK 27(16Q22.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        94.88       104.65        16.27        44.94        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
       16.77        17.16        34.98        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI 
       51.16        66.54        15.12        10.22        29.65         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX 
       17.42        40.08         7.33         6.74        12.39        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       19.04        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.35        16.18        20.48         4.67         9.96        17.56 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       28.41         1.94        23.01        12.79        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.13        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.87        18.58        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       15.12         5.19        29.79         1.84        13.58        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       16.14        17.62        15.62        46.68        17.95       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         4.80         8.22        17.72        21.30        23.21 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       163.30        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q 
       67.36        50.70        36.66        52.01        15.02        13.58 
TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
      165.73        18.81        19.00        13.64        13.64        56.15 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        20.32        15.35        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66         0.92        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       12.95        15.32        14.37        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM 
        4.01        12.62        22.52        27.98        60.66        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
        7.56        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TA 
       19.33         5.69        58.92         2.70         7.10        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       18.81        12.69        12.36         4.31        31.07        12.66 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94        11.08        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       26.93         7.23        20.12         6.94        29.36        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A3OP 
       19.13        15.91        14.07        17.75        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
        3.12         2.20        10.92        11.31        18.97        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX 
       20.05         5.62         4.73         7.00        14.27        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC 
       19.07        22.72         1.51        38.60        21.24         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       27.68         9.07        11.70        17.72         1.81        16.27 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       52.73        50.56        35.97        46.98        44.38         1.15 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.58        21.07        13.48        12.23        16.67        16.54 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       12.43        17.62        37.05        86.83        76.01        78.25 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB 
        3.02         3.91        29.56        17.82         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SP 
       17.88        64.80        79.66         3.22        66.41        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        4.21        12.76        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.96         8.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        13.64        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       30.28        35.84        28.41         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
       88.87        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
        8.61        59.38        63.02        56.35        35.41        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21         5.52        12.23 

  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE 
                         15.50                          17.62 
[1] "0.5 - 166.0 (15.5)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1.2"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 27(16Q22.1) MUTATED         0       25        42       41
  AMP PEAK 27(16Q22.1) WILD-TYPE       2      104        98       94
D27V3, multiclass
           clus
vv          AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            25                            104
  STAGE III                           42                             98
  STAGE IV                            41                             94
[1] 4 2
[1] 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 27(16Q22.1) MUTATED         23  58  19
  AMP PEAK 27(16Q22.1) WILD-TYPE      100 137  39
D27V4, multiclass
          clus
vv         AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  T0+T1+T2                           23                            100
  T3                                 58                            137
  T4                                 19                             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                              N0  N1  N2  N3
  AMP PEAK 27(16Q22.1) MUTATED    58  13  23   5
  AMP PEAK 27(16Q22.1) WILD-TYPE 177  34  52   4
D27V5, multiclass
    clus
vv   AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  N0                           58                            177
  N1                           13                             34
  N2                           23                             52
  N3                            5                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED    43   5
  AMP PEAK 27(16Q22.1) WILD-TYPE 149   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED     43    5
  AMP PEAK 27(16Q22.1) WILD-TYPE  149    6
   clus
vv  AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  0                           43                            149
  1                            5                              6
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED    36  72
  AMP PEAK 27(16Q22.1) WILD-TYPE  71 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED     36   72
  AMP PEAK 27(16Q22.1) WILD-TYPE   71  229
        clus
vv       AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  FEMALE                           36                             71
  MALE                             72                            229
[1] 2 2
[1] FALSE
D27V8, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED    95   4
  AMP PEAK 27(16Q22.1) WILD-TYPE 269  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED     95    4
  AMP PEAK 27(16Q22.1) WILD-TYPE  269   15
     clus
vv    AMP PEAK 27(16Q22.1) MUTATED AMP PEAK 27(16Q22.1) WILD-TYPE
  NO                            95                            269
  YES                            4                             15
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
D27V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(16Q22.1) MUTATED       6                         7    88
  AMP PEAK 27(16Q22.1) WILD-TYPE    37                        15   239
D27V12, multiclass
                           clus
vv                          AMP PEAK 27(16Q22.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               88
                           clus
vv                          AMP PEAK 27(16Q22.1) WILD-TYPE
  ASIAN                                                 37
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                                cls
clus                               0   1
  AMP PEAK 27(16Q22.1) MUTATED     2  99
  AMP PEAK 27(16Q22.1) WILD-TYPE   7 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16Q22.1) MUTATED      2   99
  AMP PEAK 27(16Q22.1) WILD-TYPE    7  270
                        clus
vv                       AMP PEAK 27(16Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       AMP PEAK 27(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(17Q12) MUTATION ANALYSIS
D28V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 28(17Q12) MUTATED    87  78
  AMP PEAK 28(17Q12) WILD-TYPE 142  99
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                         165                          241 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                          78                           99 
$`AMP PEAK 28(17Q12) MUTATED`
TCGA-2F-A9KP TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 
       11.97        17.16        34.98         0.62        41.75        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        17.42        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       12.39         6.58        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
       14.96         8.35         8.25        20.48         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X 
        8.98        12.79        12.59        12.13        12.16        12.62 
TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 
       11.34        15.12        29.79         1.84         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM 
       18.41       112.44        17.95         7.79        87.32         8.15 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P 
       50.27        66.05        17.98        67.36        36.66        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E5-A2PC 
      166.03        19.00        15.35        13.64        11.18        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME 
       15.35        22.16        25.58         0.56        26.96        24.03 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       13.68        12.95         8.94        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X 
       24.30        25.74        46.78        27.35        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB 
       26.73         5.36        58.92         7.10        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3Z7 
        6.15        12.69        12.36         2.27         4.31        31.07 
TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
        3.25        20.12        66.02        70.32        29.36        21.40 
TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A767 
        0.49         2.10         7.36        10.92        18.97         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF 
       10.65        32.98         7.00        14.27        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        8.48        36.49        27.35         8.58        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.40        38.60        64.01         9.01        12.16         3.45 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41Q TCGA-KQ-A41S 
       21.24        11.70         1.81        11.80        46.98         1.15 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78N 
       13.48        12.23        14.24         1.84        38.99        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HC TCGA-XF-A8HD 
       76.01        69.34         3.02       112.83         6.58        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SJ 
       97.12        15.35         1.87        17.88        48.62         3.22 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9T0 TCGA-XF-AAMG TCGA-XF-AAMH 
       15.98        14.93         5.98        26.27       110.60        11.31 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
        7.63        71.57        91.73         2.96         8.32        56.48 
TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       86.30        11.97        13.64        30.28        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       13.41        47.84        20.22        19.69        59.38        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       35.41         8.52        19.17 

$`AMP PEAK 28(17Q12) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 
       44.94        16.83        16.77        27.62        50.04        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J 
       66.54        29.65         2.50         7.33        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       26.14        14.89         5.06        17.16        16.18         4.67 
TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82        17.56        36.43        28.41         1.94        23.01 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.56        13.97        13.08        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.10        12.26        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       11.87        18.58        13.08        12.92         4.90        18.48 
TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        5.19        13.58        21.86        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IK 
       16.14        17.62        15.62        46.68       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58         8.22        17.72        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       163.30        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R 
       15.68        50.70        38.24        52.01        13.58       165.73 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 
       18.81        13.64        56.15        12.03        20.32        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 
       29.72         0.10         2.24        16.70         0.66        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 
        4.24        24.66         0.92         1.22        14.07        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37         8.09        32.02        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR 
       27.98        23.41        17.98        29.16         5.52        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85         7.56        14.96        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
       19.33         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        6.28        13.35         3.06         9.67        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY 
       15.95        26.93        59.31        33.01         7.23        17.62 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        20.71        15.81        19.13        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       17.75        24.92         8.94        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
       20.98         2.20        11.31         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB 
        5.62        21.34        19.10        22.72        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14        27.68         9.07        17.72        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 
       52.73        50.56        35.97        44.38        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        16.67        16.54        12.43        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        78.25         3.91        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85        51.32        45.04       125.49        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       66.41        34.45         4.21        12.76        11.90        23.64 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       21.04        28.24        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMX 
        2.10        13.74        92.98        10.82        54.90         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        44.32        30.94        61.45        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 
       18.15         3.88        18.84         9.63         0.66        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RE 
       25.41        21.11        31.20        35.84        21.86         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4U 
       64.08        58.72        88.87         2.89        34.06         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       60.16        56.35        57.90        19.40        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                        0.49                         0.10 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                      166.03                       165.73 
  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE 
                       15.98                        17.56 
[1] "0.5 - 166.0 (16.0)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1.2"
D28V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 28(17Q12) MUTATED         1       48        54       62
  AMP PEAK 28(17Q12) WILD-TYPE       1       81        86       73
D28V3, multiclass
           clus
vv          AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  STAGE I                            1                            1
  STAGE II                          48                           81
  STAGE III                         54                           86
  STAGE IV                          62                           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"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 28(17Q12) MUTATED         52  75  30
  AMP PEAK 28(17Q12) WILD-TYPE       71 120  28
D28V4, multiclass
          clus
vv         AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  T0+T1+T2                         52                           71
  T3                               75                          120
  T4                               30                           28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 28(17Q12) MUTATED    91  18  40   2
  AMP PEAK 28(17Q12) WILD-TYPE 144  29  35   7
D28V5, multiclass
    clus
vv   AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  N0                         91                          144
  N1                         18                           29
  N2                         40                           35
  N3                          2                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED    72   4
  AMP PEAK 28(17Q12) WILD-TYPE 120   7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED     72    4
  AMP PEAK 28(17Q12) WILD-TYPE  120    7
   clus
vv  AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  0                         72                          120
  1                          4                            7
[1] 2 2
[1] FALSE
D28V7, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED    42 124
  AMP PEAK 28(17Q12) WILD-TYPE  65 177
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED     42  124
  AMP PEAK 28(17Q12) WILD-TYPE   65  177
        clus
vv       AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  FEMALE                         42                           65
  MALE                          124                          177
[1] 2 2
[1] FALSE
D28V8, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED   155   5
  AMP PEAK 28(17Q12) WILD-TYPE 209  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED    155    5
  AMP PEAK 28(17Q12) WILD-TYPE  209   14
     clus
vv    AMP PEAK 28(17Q12) MUTATED AMP PEAK 28(17Q12) WILD-TYPE
  NO                         155                          209
  YES                          5                           14
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
D28V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(17Q12) MUTATED      14                         9   135
  AMP PEAK 28(17Q12) WILD-TYPE    29                        13   192
D28V12, multiclass
                           clus
vv                          AMP PEAK 28(17Q12) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            135
                           clus
vv                          AMP PEAK 28(17Q12) WILD-TYPE
  ASIAN                                               29
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                              cls
clus                             0   1
  AMP PEAK 28(17Q12) MUTATED     6 145
  AMP PEAK 28(17Q12) WILD-TYPE   3 224
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(17Q12) MUTATED      6  145
  AMP PEAK 28(17Q12) WILD-TYPE    3  224
                        clus
vv                       AMP PEAK 28(17Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        145
                        clus
vv                       AMP PEAK 28(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          224
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(17Q23.3) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(17Q23.3) MUTATED   103  89
  AMP PEAK 29(17Q23.3) WILD-TYPE 126  88
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                           192                            214 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                            89                             88 
$`AMP PEAK 29(17Q23.3) MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
      104.65        16.27        16.77         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       15.12        47.80        17.42        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
        5.06        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS 
       17.16        20.48        28.70         8.98        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A8HY 
       13.97        12.59        12.13        12.16        12.62        11.34 
TCGA-CU-A0YN TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       12.92        29.79         1.84        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IM TCGA-DK-A3IQ 
       16.14        17.95         7.79        87.32         8.15        17.72 
TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
       50.27        10.55        66.05        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       36.66        15.02       165.73       166.03        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ 
       15.35        13.64        11.18        12.03        43.59        22.16 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW 
       25.58         0.56        26.96         4.24        24.03        13.68 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       16.77         8.94        33.04         4.01        60.66        24.30 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BV 
       25.74        46.78        20.91         3.62        26.73         5.36 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE 
       27.45        58.92         7.10        62.86        18.81        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        2.27         3.06         4.31         9.67        31.07        10.65 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3VY 
       17.23         3.25        11.08        48.00        59.31        17.62 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       70.32        29.36        21.40         7.73         2.10         2.20 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
        7.36        10.92        18.97        10.65        32.98         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
       14.27        21.34        19.82        20.28         8.48        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE 
        8.58        19.07        19.40        38.60         9.01        12.16 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
        3.45        21.24         9.07        11.70         1.81        15.42 
TCGA-K4-AAQO TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80        46.98         1.15        15.32        13.48        12.23 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       14.24         1.84        38.99        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC 
       76.01        69.34         3.02        17.82         6.21         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       97.45        97.12        15.35         1.87        17.88        48.62 
TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 
        3.22        14.93         5.98        21.04        26.27         2.24 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAML 
        2.10        13.74        10.82       110.60        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       71.57        91.73         2.96         8.32         6.77        56.48 
TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R9 
       86.30        11.97        13.64        31.20        30.28        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4R 
       94.29        13.41         3.48        64.08        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       19.69        59.38        63.02        35.41         8.52        19.17 

$`AMP PEAK 29(17Q23.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       108.95         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 
       16.83        17.16        34.98        27.62        50.04        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J 
       10.22        29.65         2.50         7.33        13.15        19.04 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E 
       16.18         4.67        12.82         9.96        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       28.41         1.94        23.01        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.48         5.19        13.58        21.86         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I4 
       16.70       130.88        17.62        15.62        46.68       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        4.80        13.58         8.22        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       20.81       163.30        53.29        76.60        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA74 TCGA-DK-AA77 
       38.24        52.01        13.58        18.81        56.15        20.32 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        29.72         0.10         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN 
        0.66        26.24        24.66         0.92         1.22        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B8 
       12.95        15.32        14.37         8.09        32.02        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       22.52        27.98        23.41        17.98        29.16         5.52 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43Y 
       19.79        12.85         7.56        27.35        14.96        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       53.88        11.01        19.33         5.69         8.25        18.08 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TK 
        2.70         6.28        13.35         6.15        12.69        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES 
       12.66         8.94        61.94        15.95        26.93        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12        66.02         6.94        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       19.13        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 
        8.94        13.91         3.12        20.98        11.31         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QI 
       32.78        20.05         5.62         4.73        19.10        36.49 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         1.51        64.01        25.02         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
       27.68        17.72        16.27        52.73        50.56        35.97 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 
       44.38        15.58        21.07        16.67        16.54        12.43 
TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF 
       17.62        78.25       112.83         3.91        29.56         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SK 
       51.32        45.04       125.49        64.80        79.66        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX 
       66.41        34.45         4.21        12.76        11.90        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-AAME TCGA-XF-AAMJ 
       28.24        18.90        16.27        66.64        92.98        54.90 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        44.32        30.94        61.45        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 
       18.15         3.88        18.84         9.63         0.66        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RG TCGA-ZF-A9RL 
       25.41        21.11        35.84        21.86        58.72        88.87 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 
       47.84         2.89         8.61        60.16        56.35        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40        54.21         5.52        12.23 

  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                          0.56                           0.10 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE 
                        16.205                         17.735 
[1] "0.6 - 166.0 (16.2)" "0.1 - 163.3 (17.7)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 29(17Q23.3) MUTATED         1       50        66       76
  AMP PEAK 29(17Q23.3) WILD-TYPE       1       79        74       59
D29V3, multiclass
           clus
vv          AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            50                             79
  STAGE III                           66                             74
  STAGE IV                            76                             59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 29(17Q23.3) MUTATED         53  94  32
  AMP PEAK 29(17Q23.3) WILD-TYPE       70 101  26
D29V4, multiclass
          clus
vv         AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  T0+T1+T2                           53                             70
  T3                                 94                            101
  T4                                 32                             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 29(17Q23.3) MUTATED    99  25  46   4
  AMP PEAK 29(17Q23.3) WILD-TYPE 136  22  29   5
D29V5, multiclass
    clus
vv   AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  N0                           99                            136
  N1                           25                             22
  N2                           46                             29
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q23.3) MUTATED    86   5
  AMP PEAK 29(17Q23.3) WILD-TYPE 106   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q23.3) MUTATED     86    5
  AMP PEAK 29(17Q23.3) WILD-TYPE  106    6
   clus
vv  AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  0                           86                            106
  1                            5                              6
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q23.3) MUTATED    55 139
  AMP PEAK 29(17Q23.3) WILD-TYPE  52 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q23.3) MUTATED     55  139
  AMP PEAK 29(17Q23.3) WILD-TYPE   52  162
        clus
vv       AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  FEMALE                           55                             52
  MALE                            139                            162
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q23.3) MUTATED   173  10
  AMP PEAK 29(17Q23.3) WILD-TYPE 191   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q23.3) MUTATED    173   10
  AMP PEAK 29(17Q23.3) WILD-TYPE  191    9
     clus
vv    AMP PEAK 29(17Q23.3) MUTATED AMP PEAK 29(17Q23.3) WILD-TYPE
  NO                           173                            191
  YES                           10                              9
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
D29V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(17Q23.3) MUTATED      18                         8   159
  AMP PEAK 29(17Q23.3) WILD-TYPE    25                        14   168
D29V12, multiclass
                           clus
vv                          AMP PEAK 29(17Q23.3) MUTATED
  ASIAN                                               18
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              159
                           clus
vv                          AMP PEAK 29(17Q23.3) WILD-TYPE
  ASIAN                                                 25
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                168
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                                cls
clus                               0   1
  AMP PEAK 29(17Q23.3) MUTATED     6 172
  AMP PEAK 29(17Q23.3) WILD-TYPE   3 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(17Q23.3) MUTATED      6  172
  AMP PEAK 29(17Q23.3) WILD-TYPE    3  197
                        clus
vv                       AMP PEAK 29(17Q23.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          172
                        clus
vv                       AMP PEAK 29(17Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            197
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(19Q12) MUTATION ANALYSIS
D30V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 30(19Q12) MUTATED    99  65
  AMP PEAK 30(19Q12) WILD-TYPE 130 112
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                         164                          242 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                          65                          112 
$`AMP PEAK 30(19Q12) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       16.27        16.77         0.62        41.75        51.16        15.12 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N 
       47.80         2.50        17.42         6.74        19.04        26.14 
TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       12.16         5.06         8.35         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       20.48        28.70        36.43         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY 
       12.56        12.59        12.13        12.62        12.00        11.34 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       12.92        18.48        29.79        21.86        66.41        18.41 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
       16.70       112.44        46.68       142.78        87.32        13.58 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L 
       66.05        64.18        67.36        15.68        36.66        38.24 
TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA76 
       15.02       166.03        19.00        13.64        11.18        12.03 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD 
       43.59        15.35        38.83        22.16         0.56         4.24 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3B8 
       24.03         0.92        13.68        12.95        32.02        12.62 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       24.30        23.41        19.79        12.85         7.56        27.35 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62P 
       20.91         3.62         8.25        27.45        18.08         6.28 
TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       18.81         3.06         4.31        10.85        31.07        17.23 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
        3.25        61.94        59.31        20.12        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS 
       70.32        29.36        19.13        15.91        14.07        24.92 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATP 
       13.91         7.73         7.36        18.97         4.73        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.07        19.40        38.60         9.01        12.16        25.02 
TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O 
        2.76         9.07        17.72        15.42        11.80        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G5 
       35.97        46.98        13.48        14.24         1.84        38.99 
TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PH 
       37.05        69.34         3.02         3.91        29.56        51.32 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
        6.58        97.12        15.35        79.66         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T3 
       14.93         5.98        12.76        21.04        28.24         2.24 
TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 
       71.57         6.77        98.99        44.32        56.48        86.30 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RF 
       75.39        18.15         9.63        13.64        21.11        64.08 
TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 
       88.87        20.22        19.69        59.38        56.35        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 
        8.52        54.21 

$`AMP PEAK 30(19Q12) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        29.65        40.08         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       12.39         6.58        13.15        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       14.89        14.96         4.67        12.82         9.96        17.56 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       28.41         8.98        13.97        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 
       12.66        12.46        12.10        12.26        13.12        12.10 
TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC 
        5.19         1.84        13.58         2.14        19.00       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       16.14        17.62        15.62        17.95         7.79         4.80 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        8.15         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67        20.81        10.55       163.30        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T 
       76.60        50.70        52.01        13.58       165.73        18.81 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       15.35        13.64        56.15        20.32        29.72         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70        25.58         0.66        26.96        26.24 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       24.66         1.22        14.07        15.32        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94        33.04         4.01        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       60.66        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        15.58        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        5.36         5.69        58.92         2.70         7.10        13.35 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI 
       62.86         6.15        12.69        12.36         2.27         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66        10.65         8.94        11.08        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 
       26.93        33.01         7.23         6.94        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81        17.75         0.49         8.94         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 
       20.98         2.20        10.92        11.31         7.63        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK 
       20.05         5.62        10.65        19.10        36.49        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A3WV 
        8.58        22.72         1.51        64.01         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41N 
        9.14        27.68        11.70         1.81        16.27        52.73 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       44.38         1.15        15.32        15.58        21.07        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N 
       16.67        16.54        12.43        17.62        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       76.01        78.25       112.83        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       45.04        97.45       125.49         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX 
       64.80        66.41        34.45         4.21        11.90        23.64 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90        16.27        66.64         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       92.98        10.82       110.60        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
       91.73         2.96         8.32        30.94        61.45        27.06 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       31.20        30.28        35.84        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R 
       13.41         3.48        58.72        47.84         2.89        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA5H 
        8.61        60.16        63.02        35.41        57.90        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                        0.56                         0.10 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                      166.03                       165.73 
  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE 
                      18.280                       16.405 
[1] "0.6 - 166.0 (18.3)" "0.1 - 165.7 (16.4)"
[1] "hr=" "1.2"
D30V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 30(19Q12) MUTATED         0       44        57       62
  AMP PEAK 30(19Q12) WILD-TYPE       2       85        83       73
D30V3, multiclass
           clus
vv          AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  STAGE I                            0                            2
  STAGE II                          44                           85
  STAGE III                         57                           83
  STAGE IV                          62                           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"
                              vv
clus                           T0+T1+T2  T3  T4
  AMP PEAK 30(19Q12) MUTATED         41  85  25
  AMP PEAK 30(19Q12) WILD-TYPE       82 110  33
D30V4, multiclass
          clus
vv         AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  T0+T1+T2                         41                           82
  T3                               85                          110
  T4                               25                           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                            N0  N1  N2  N3
  AMP PEAK 30(19Q12) MUTATED    85  22  37   3
  AMP PEAK 30(19Q12) WILD-TYPE 150  25  38   6
D30V5, multiclass
    clus
vv   AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  N0                         85                          150
  N1                         22                           25
  N2                         37                           38
  N3                          3                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED    76   5
  AMP PEAK 30(19Q12) WILD-TYPE 116   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED     76    5
  AMP PEAK 30(19Q12) WILD-TYPE  116    6
   clus
vv  AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  0                         76                          116
  1                          5                            6
[1] 2 2
[1] FALSE
D30V7, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED    39 125
  AMP PEAK 30(19Q12) WILD-TYPE  68 176
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED     39  125
  AMP PEAK 30(19Q12) WILD-TYPE   68  176
        clus
vv       AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  FEMALE                         39                           68
  MALE                          125                          176
[1] 2 2
[1] FALSE
D30V8, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED   146   5
  AMP PEAK 30(19Q12) WILD-TYPE 218  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED    146    5
  AMP PEAK 30(19Q12) WILD-TYPE  218   14
     clus
vv    AMP PEAK 30(19Q12) MUTATED AMP PEAK 30(19Q12) WILD-TYPE
  NO                         146                          218
  YES                          5                           14
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
D30V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(19Q12) MUTATED      16                         7   132
  AMP PEAK 30(19Q12) WILD-TYPE    27                        15   195
D30V12, multiclass
                           clus
vv                          AMP PEAK 30(19Q12) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          7
  WHITE                                            132
                           clus
vv                          AMP PEAK 30(19Q12) WILD-TYPE
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                              cls
clus                             0   1
  AMP PEAK 30(19Q12) MUTATED     3 145
  AMP PEAK 30(19Q12) WILD-TYPE   6 224
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 30(19Q12) MUTATED      3  145
  AMP PEAK 30(19Q12) WILD-TYPE    6  224
                        clus
vv                       AMP PEAK 30(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        145
                        clus
vv                       AMP PEAK 30(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          224
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(19Q13.43) MUTATION ANALYSIS
D31V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 31(19Q13.43) MUTATED    91  63
  AMP PEAK 31(19Q13.43) WILD-TYPE 138 114
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                            154                             252 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                             63                             114 
$`AMP PEAK 31(19Q13.43) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       16.27        16.77         0.62        41.75        51.16        15.12 
TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V 
       47.80        17.42         6.74        19.04        26.14         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E 
        8.25        16.18        20.48        12.82        28.70        36.43 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
        8.98         1.94        23.01        12.79        12.56        12.59 
TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3KJ 
       12.13        12.62        12.00        11.34        15.12        18.48 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC 
       29.79        21.86        66.41        18.41        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IV 
      112.44       142.78         4.80        13.58         8.15         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6P 
       17.98        64.18        67.36        15.68        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC 
      166.03        19.00        13.64        11.18        12.03        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME 
       15.35        22.16        25.58         0.56         4.24        24.03 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 
        0.92         1.22        12.95         8.09        32.02         8.94 
TCGA-FD-A3SL TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       23.41        12.85         7.56        20.91         3.62        15.58 
TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TH 
       11.01         8.25        27.45        18.81         2.27         4.31 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO 
       10.85        31.07        17.23         3.25        61.94        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I3 
       20.12        66.02        15.91        14.07        24.92        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A764 
        7.73         3.12        20.98         7.36        18.97        20.05 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ 
       10.65        32.98         7.00        14.27        21.34        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
       20.28         8.48        36.49        19.07        19.40        38.60 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41Q 
        9.01         2.76        15.42        11.80        50.56        46.98 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC 
        1.84        16.54        17.62        37.05        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HF TCGA-XF-A8HG 
        3.91        29.56        17.82        45.04        97.12        15.35 
TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T3 TCGA-XF-AAMG 
       79.66        15.98         5.98        23.64         2.24       110.60 
TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 
       71.57         6.77        98.99        44.32        56.48        86.30 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       75.39        18.15        18.84         9.63        21.11        30.28 
TCGA-ZF-A9R7 TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       21.86        88.87        20.22        34.06        19.69        59.38 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       56.35        19.40         8.52        54.21 

$`AMP PEAK 31(19Q13.43) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I 
       66.54        10.22        29.65         2.50        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66        12.39         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA 
       19.50         5.06        14.89        14.96         8.35        17.16 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A27C TCGA-CF-A3MH 
        4.67         9.96        17.56        28.41        13.97        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.16        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       13.12        12.10        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
       12.92         4.90         5.19         1.84        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
       19.00        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        7.79        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW 
       23.21        20.81        10.55       163.30        66.05        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R 
       76.60        50.70        36.66        52.01        13.58       165.73 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 
       18.81        13.64        15.35        56.15        20.32        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       29.72         0.10         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24        24.66        13.68        14.07        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        24.30        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        27.35        14.96        26.73        53.88 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       19.33         5.36         5.69        18.08        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        62.86         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       12.36         3.06         9.67        12.66        10.65         8.94 
TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IB 
       11.08        48.00        15.95        26.93        33.01         7.23 
TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       17.62         6.94        70.32        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP 
       15.81        19.13        17.75         0.49         8.94         2.10 
TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 
        2.20        10.92        11.31         7.63        32.78         5.62 
TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
        4.73        19.10        27.35         8.58        22.72         1.51 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
       64.01        12.16        25.02         3.45        21.24         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       27.68         9.07        11.70        17.72         1.81        16.27 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       52.73        35.97        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 
       21.07        13.48        12.23        16.67        14.24        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD 
       38.99        22.68        86.83        76.01        78.25       112.83 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        6.21         3.85        51.32         6.58        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80         3.22        66.41 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45        14.93         4.21        12.76        11.90        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       28.24        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98        10.82        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
       91.73         2.96         8.32        30.94        61.45        27.06 
TCGA-XF-AAN8 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 
        3.88         0.66        11.97        13.64        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       31.20        35.84        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       64.08        58.72        47.84         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       63.02        35.41        57.90        19.17         5.52        12.23 

  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                           0.56                            0.10 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                         166.03                          165.73 
  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE 
                         18.065                          16.685 
[1] "0.6 - 166.0 (18.1)" "0.1 - 165.7 (16.7)"
[1] "hr=" "1.2"
D31V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 31(19Q13.43) MUTATED         0       41        52       60
  AMP PEAK 31(19Q13.43) WILD-TYPE       2       88        88       75
D31V3, multiclass
           clus
vv          AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  STAGE I                               0                               2
  STAGE II                             41                              88
  STAGE III                            52                              88
  STAGE IV                             60                              75
[1] 4 2
[1] 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 31(19Q13.43) MUTATED         36  75  27
  AMP PEAK 31(19Q13.43) WILD-TYPE       87 120  31
D31V4, multiclass
          clus
vv         AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  T0+T1+T2                            36                              87
  T3                                  75                             120
  T4                                  27                              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                               N0  N1  N2  N3
  AMP PEAK 31(19Q13.43) MUTATED    77  24  32   5
  AMP PEAK 31(19Q13.43) WILD-TYPE 158  23  43   4
D31V5, multiclass
    clus
vv   AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  N0                            77                             158
  N1                            24                              23
  N2                            32                              43
  N3                             5                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                                 cls
clus                                0   1
  AMP PEAK 31(19Q13.43) MUTATED    69   5
  AMP PEAK 31(19Q13.43) WILD-TYPE 123   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(19Q13.43) MUTATED     69    5
  AMP PEAK 31(19Q13.43) WILD-TYPE  123    6
   clus
vv  AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  0                            69                             123
  1                             5                               6
[1] 2 2
[1] FALSE
D31V7, binary
                                 cls
clus                                0   1
  AMP PEAK 31(19Q13.43) MUTATED    43 111
  AMP PEAK 31(19Q13.43) WILD-TYPE  64 190
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(19Q13.43) MUTATED     43  111
  AMP PEAK 31(19Q13.43) WILD-TYPE   64  190
        clus
vv       AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  FEMALE                            43                              64
  MALE                             111                             190
[1] 2 2
[1] FALSE
D31V8, binary
                                 cls
clus                                0   1
  AMP PEAK 31(19Q13.43) MUTATED   135   4
  AMP PEAK 31(19Q13.43) WILD-TYPE 229  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(19Q13.43) MUTATED    135    4
  AMP PEAK 31(19Q13.43) WILD-TYPE  229   15
     clus
vv    AMP PEAK 31(19Q13.43) MUTATED AMP PEAK 31(19Q13.43) WILD-TYPE
  NO                            135                             229
  YES                             4                              15
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
D31V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(19Q13.43) MUTATED      13                         8   125
  AMP PEAK 31(19Q13.43) WILD-TYPE    30                        14   202
D31V12, multiclass
                           clus
vv                          AMP PEAK 31(19Q13.43) MUTATED
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               125
                           clus
vv                          AMP PEAK 31(19Q13.43) WILD-TYPE
  ASIAN                                                  30
  BLACK OR AFRICAN AMERICAN                              14
  WHITE                                                 202
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                                 cls
clus                                0   1
  AMP PEAK 31(19Q13.43) MUTATED     3 134
  AMP PEAK 31(19Q13.43) WILD-TYPE   6 235
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(19Q13.43) MUTATED      3  134
  AMP PEAK 31(19Q13.43) WILD-TYPE    6  235
                        clus
vv                       AMP PEAK 31(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           134
                        clus
vv                       AMP PEAK 31(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             235
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(20Q11.21) MUTATION ANALYSIS
D32V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 32(20Q11.21) MUTATED   145 116
  AMP PEAK 32(20Q11.21) WILD-TYPE  84  61
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                            261                             145 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                            116                              61 
$`AMP PEAK 32(20Q11.21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        11.97       104.65       108.95        16.27        44.94 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A3JM 
       10.22        47.80         2.50        17.42        40.08         6.74 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        19.04        26.14        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK 
       14.89         5.06         8.35         8.25        20.48         9.96 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        36.43        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S 
       12.79        12.56        12.59        12.13        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A0YO 
       12.66        12.62        11.34        11.34        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
       15.12        18.48         1.84         2.14        66.41        18.41 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
      130.88       112.44        46.68        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         4.80        13.58         8.15         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        23.21         9.67        10.55        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       64.18        67.36        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W 
       52.01        15.02       165.73       166.03        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4TZ 
       15.35        13.64        56.15        11.18        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME 
       38.83        22.16        25.58         0.56         4.24        24.03 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B6 
        1.22        13.68        12.95         8.09        32.02        33.04 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SP 
        4.01        22.52        60.66        24.30        23.41        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43X 
       46.78        19.79        12.85         7.56        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O 
       26.73        11.01        27.45        18.08        58.92         7.10 
TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       13.35        18.81         6.15        12.69        12.36         2.27 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE 
        4.31         9.67        10.85        31.07        10.65         3.25 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3VY 
       11.08        61.94        48.00        15.95        59.31        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       66.02        70.32        29.36        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       19.13        15.91        14.07        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         2.10        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP 
       11.31        18.97        20.05         5.62        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
        7.00        14.27        21.34        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE 
        8.48        36.49         8.58        19.07        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
       64.01        12.16        25.02         3.45        21.24         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P 
        9.07        11.70         1.81        11.80        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       46.98         1.15        15.58        13.48        12.23        16.67 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        12.43        38.99        17.62        37.05        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        76.01        69.34         3.02         3.91        29.56 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF 
        6.21         3.85        51.32        45.04        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       15.35         1.87        79.66         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 
       14.93         5.98        12.76        23.64        21.04         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ 
       16.27        66.64         2.10        10.82         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       91.73         2.96         6.77        98.99        44.32        30.94 
TCGA-YC-A89H TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
       18.84        13.64        22.36        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RG 
       30.28        21.86        28.41        94.29        13.41        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       88.87        47.84        20.22         2.89        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
       59.38        63.02        56.35        35.41        19.40        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.17         5.52        12.23 

$`AMP PEAK 32(20Q11.21) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7Y 
       94.88         8.35        16.83        16.77        17.16        50.04 
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A0YX 
       15.12        29.65         7.33         2.66        12.39        13.15 
TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ 
       12.16        14.96        17.16        16.18         4.67        12.82 
TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       17.56        13.97        13.08        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       13.12        12.00        12.10        11.87        18.58        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB 
        5.19        29.79        13.58        21.86        19.00        16.70 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WY 
       16.14        17.62        15.62        21.30        20.81       163.30 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-DK-AA77 
       53.29        76.60        13.58        18.81        12.03        20.32 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       29.72         0.10         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24        24.66         0.92        14.07        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SN 
       16.77         8.94        12.62        27.98        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BU 
        5.52        14.96        20.91        15.58        53.88        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TA 
        5.36         5.69         8.25         2.70         6.28        62.86 
TCGA-FD-A6TG TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-G2-A2EL TCGA-G2-A2ES 
        3.06        12.66        17.23         8.94        26.93        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GU-A42P 
        7.23        20.12         6.94        17.75         3.12        10.92 
TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.63        32.78         4.73        27.35        22.72         1.51 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P 
        9.01         2.76        27.68        17.72        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-AA26 
       52.73        44.38        15.32        21.07        14.24        16.54 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI 
       78.25       112.83        17.82         6.58       125.49        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SZ 
       48.62        64.80        66.41         4.21        11.90        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH 
       26.27        18.90        13.74        92.98       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       54.90         8.32        56.48        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39        18.15         3.88         9.63         0.66        11.97 
TCGA-ZF-A9R5 TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA4W TCGA-ZF-AA53 
       35.84         3.48        64.08        34.06        60.16        57.90 
TCGA-ZF-AA56 
        8.52 

  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                           0.49                            0.10 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                         166.03                          163.30 
  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE 
                          18.08                           16.54 
[1] "0.5 - 166.0 (18.1)" "0.1 - 163.3 (16.5)"
[1] "hr=" "1"  
D32V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 32(20Q11.21) MUTATED         1       80        86       94
  AMP PEAK 32(20Q11.21) WILD-TYPE       1       49        54       41
D32V3, multiclass
           clus
vv          AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  STAGE I                               1                               1
  STAGE II                             80                              49
  STAGE III                            86                              54
  STAGE IV                             94                              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                              T0+T1+T2  T3  T4
  AMP PEAK 32(20Q11.21) MUTATED         77 125  38
  AMP PEAK 32(20Q11.21) WILD-TYPE       46  70  20
D32V4, multiclass
          clus
vv         AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  T0+T1+T2                            77                              46
  T3                                 125                              70
  T4                                  38                              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 32(20Q11.21) MUTATED   139  32  53   8
  AMP PEAK 32(20Q11.21) WILD-TYPE  96  15  22   1
D32V5, multiclass
    clus
vv   AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  N0                           139                              96
  N1                            32                              15
  N2                            53                              22
  N3                             8                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                                 cls
clus                                0   1
  AMP PEAK 32(20Q11.21) MUTATED   119   8
  AMP PEAK 32(20Q11.21) WILD-TYPE  73   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(20Q11.21) MUTATED    119    8
  AMP PEAK 32(20Q11.21) WILD-TYPE   73    3
   clus
vv  AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  0                           119                              73
  1                             8                               3
[1] 2 2
[1] FALSE
D32V7, binary
                                 cls
clus                                0   1
  AMP PEAK 32(20Q11.21) MUTATED    74 188
  AMP PEAK 32(20Q11.21) WILD-TYPE  33 113
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(20Q11.21) MUTATED     74  188
  AMP PEAK 32(20Q11.21) WILD-TYPE   33  113
        clus
vv       AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  FEMALE                            74                              33
  MALE                             188                             113
[1] 2 2
[1] FALSE
D32V8, binary
                                 cls
clus                                0   1
  AMP PEAK 32(20Q11.21) MUTATED   233  11
  AMP PEAK 32(20Q11.21) WILD-TYPE 131   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(20Q11.21) MUTATED    233   11
  AMP PEAK 32(20Q11.21) WILD-TYPE  131    8
     clus
vv    AMP PEAK 32(20Q11.21) MUTATED AMP PEAK 32(20Q11.21) WILD-TYPE
  NO                            233                             131
  YES                            11                               8
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
D32V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(20Q11.21) MUTATED      19                        12   218
  AMP PEAK 32(20Q11.21) WILD-TYPE    24                        10   109
D32V12, multiclass
                           clus
vv                          AMP PEAK 32(20Q11.21) MUTATED
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               218
                           clus
vv                          AMP PEAK 32(20Q11.21) WILD-TYPE
  ASIAN                                                  24
  BLACK OR AFRICAN AMERICAN                              10
  WHITE                                                 109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                                 cls
clus                                0   1
  AMP PEAK 32(20Q11.21) MUTATED     4 235
  AMP PEAK 32(20Q11.21) WILD-TYPE   5 134
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 32(20Q11.21) MUTATED      4  235
  AMP PEAK 32(20Q11.21) WILD-TYPE    5  134
                        clus
vv                       AMP PEAK 32(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           235
                        clus
vv                       AMP PEAK 32(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             134
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(22Q12.2) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 33(22Q12.2) MUTATED    51  36
  AMP PEAK 33(22Q12.2) WILD-TYPE 178 141
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            87                            319 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                            36                            141 
$`AMP PEAK 33(22Q12.2) MUTATED`
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA86 TCGA-4Z-AA87 
      104.65         8.35        44.94        34.98        10.22        47.80 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-C4-A0F6 
       17.42        40.08         8.35        16.18        12.82        23.01 
TCGA-CF-A3MF TCGA-CF-A8HY TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I6 
       12.59        11.34        66.41        18.41       112.44        87.32 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3WX TCGA-DK-AA6L TCGA-DK-AA6P 
        8.22        50.27        23.21        10.55        38.24        15.02 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA77 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
      166.03        19.00        20.32        22.16        25.58         0.56 
TCGA-E7-A85H TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43P 
       12.95        33.04         4.01        23.41        29.16        27.35 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A62O TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A2ES 
       11.01         5.36         7.10        61.94        59.31        33.01 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A4ZW 
       66.02        70.32        21.40        20.71        14.07         0.49 
TCGA-GD-A2C5 TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QH 
        7.73        20.05         4.73        14.27        19.82         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A2OE TCGA-KQ-A41P 
       36.49        27.35         8.58        19.07        38.60        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78L 
       46.98        44.38        15.58         1.84        12.43        37.05 
TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SM 
       76.01       112.83         6.21        48.62        79.66        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAML 
       14.93         4.21        26.27         2.10       110.60         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-ZF-A9R0 
       71.57        91.73         8.32         6.77        98.99        22.36 
TCGA-ZF-A9R4 TCGA-ZF-A9RF TCGA-ZF-AA4R 
       30.28        64.08        34.06 

$`AMP PEAK 33(22Q12.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7O 
       24.13        11.97        94.88       108.95        16.27        16.83 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.77        17.16        27.62        50.04         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A13I 
       51.16        66.54        15.12        29.65         2.50         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
        2.66         6.74        12.39         6.58        13.15        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       26.14        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.96         5.06         8.25        17.16        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH 
        1.94        12.79        12.56        13.97        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        5.19        29.79         1.84        13.58        21.86         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00        16.70       130.88        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       46.68        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY 
        8.15        17.72        21.30         9.67        20.81       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R 
       15.68        50.70        36.66        52.01        13.58       165.73 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       18.81        13.64        15.35        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       12.03        43.59        15.35        38.83        29.72         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
        2.24        16.70         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       24.03        24.66         0.92         1.22        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       15.32        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        24.30        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
        5.52        25.74        46.78        19.79        12.85         7.56 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       19.33         5.69         8.25        27.45        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         6.28        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
       12.69        12.36         2.27         3.06         4.31         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07        12.66        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        11.08        48.00        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12        17.62         6.94        29.36        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP 
       15.91        17.75        24.92         8.94        13.91         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP 
       18.97         7.63        32.78         5.62        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A6ZA TCGA-H4-A2HO 
        7.00        21.34        19.10        20.28        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        64.01         9.01        12.16        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI 
       21.24         2.76         9.14        27.68         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41O TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
       50.56         1.15        15.32        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       16.67        14.24        16.54        38.99        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       86.83        78.25        69.34         3.02         3.91        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       17.82         3.85        51.32        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
      125.49        97.12        15.35         1.87        17.88        64.80 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
        3.22        15.98        66.41         5.98        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        28.24        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64        13.74        92.98        10.82        11.31        54.90 
TCGA-XF-AAMT TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.96        44.32        56.48        30.94        61.45        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        13.64        25.41        21.11        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE 
       35.84        21.86        28.41        94.29        13.41         3.48 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T 
       58.72        88.87        47.84        20.22         2.89        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       57.90        19.40         8.52        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                          0.49                           0.10 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE 
                         22.36                          16.27 
[1] "0.5 - 166.0 (22.4)" "0.1 - 165.7 (16.3)"
[1] "hr=" "1.4"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 33(22Q12.2) MUTATED         1       30        34       21
  AMP PEAK 33(22Q12.2) WILD-TYPE       1       99       106      114
D33V3, multiclass
           clus
vv          AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            30                             99
  STAGE III                           34                            106
  STAGE IV                            21                            114
[1] 4 2
[1] 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 33(22Q12.2) MUTATED         29  41  10
  AMP PEAK 33(22Q12.2) WILD-TYPE       94 154  48
D33V4, multiclass
          clus
vv         AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  T0+T1+T2                           29                             94
  T3                                 41                            154
  T4                                 10                             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                              N0  N1  N2  N3
  AMP PEAK 33(22Q12.2) MUTATED    57   8  11   3
  AMP PEAK 33(22Q12.2) WILD-TYPE 178  39  64   6
D33V5, multiclass
    clus
vv   AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  N0                           57                            178
  N1                            8                             39
  N2                           11                             64
  N3                            3                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                                cls
clus                               0   1
  AMP PEAK 33(22Q12.2) MUTATED    41   2
  AMP PEAK 33(22Q12.2) WILD-TYPE 151   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(22Q12.2) MUTATED     41    2
  AMP PEAK 33(22Q12.2) WILD-TYPE  151    9
   clus
vv  AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  0                           41                            151
  1                            2                              9
[1] 2 2
[1] FALSE
D33V7, binary
                                cls
clus                               0   1
  AMP PEAK 33(22Q12.2) MUTATED    22  65
  AMP PEAK 33(22Q12.2) WILD-TYPE  85 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(22Q12.2) MUTATED     22   65
  AMP PEAK 33(22Q12.2) WILD-TYPE   85  236
        clus
vv       AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  FEMALE                           22                             85
  MALE                             65                            236
[1] 2 2
[1] FALSE
D33V8, binary
                                cls
clus                               0   1
  AMP PEAK 33(22Q12.2) MUTATED    79   4
  AMP PEAK 33(22Q12.2) WILD-TYPE 285  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(22Q12.2) MUTATED     79    4
  AMP PEAK 33(22Q12.2) WILD-TYPE  285   15
     clus
vv    AMP PEAK 33(22Q12.2) MUTATED AMP PEAK 33(22Q12.2) WILD-TYPE
  NO                            79                            285
  YES                            4                             15
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
D33V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 33(22Q12.2) MUTATED       6                         7    70
  AMP PEAK 33(22Q12.2) WILD-TYPE    37                        15   257
D33V12, multiclass
                           clus
vv                          AMP PEAK 33(22Q12.2) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               70
                           clus
vv                          AMP PEAK 33(22Q12.2) WILD-TYPE
  ASIAN                                                 37
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                                cls
clus                               0   1
  AMP PEAK 33(22Q12.2) MUTATED     3  75
  AMP PEAK 33(22Q12.2) WILD-TYPE   6 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(22Q12.2) MUTATED      3   75
  AMP PEAK 33(22Q12.2) WILD-TYPE    6  294
                        clus
vv                       AMP PEAK 33(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       AMP PEAK 33(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            294
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    48  42
  DEL PEAK  1(1P36.11) WILD-TYPE 181 135
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            90                            316 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            42                            135 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 
       24.13         8.35        16.77        17.16        34.98         0.62 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20W 
       15.12        10.22         6.58        19.04        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS 
       20.48         9.96        17.56        36.43        12.79        12.56 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-DK-A1A7 
       12.16        12.62        15.12        18.48         1.84        18.41 
TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A6B6 
       16.14         7.79        17.72        21.30        10.55        36.66 
TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        19.00        15.35        56.15        12.03        43.59 
TCGA-FD-A3B5 TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BU TCGA-FD-A5C1 TCGA-FD-A6TE 
        8.94         5.52        15.58        19.33        58.92        12.36 
TCGA-FD-A6TG TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GU-A763 
        3.06        10.65        26.93        70.32        29.36        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A6ZA 
       20.05         5.62        32.98        14.27        36.49        22.72 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6MB 
       64.01        25.02        21.24         9.14        17.72        15.42 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       35.97        46.98        44.38        15.58        13.48        12.23 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        76.01        69.34       112.83        29.56        17.82 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SU 
       97.12        15.35         3.22        15.98         4.21         5.98 
TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN2 
       12.76        23.64       110.60         6.77        30.94        61.45 
TCGA-XF-AAN5 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA54 
       75.39        31.20        30.28        88.87        57.90        19.40 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        94.88       104.65       108.95        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       16.83        27.62        50.04        41.75        51.16        66.54 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        2.66         6.74        12.39        13.15        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42F 
       17.16        16.18         4.67        12.82        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        8.98         1.94        23.01        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       13.08        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL 
       18.58        13.08        12.92         4.90         5.19        29.79 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58        21.86         2.14        66.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        17.62        15.62        46.68        17.95 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      142.78        87.32         4.80        13.58         8.15         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       50.27        23.21         9.67        20.81       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        38.24        52.01        15.02       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       18.81        13.64        13.64        11.18        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD 
       25.58         0.56         0.66        26.96        26.24         4.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN 
       24.03        24.66         0.92         1.22        13.68        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       12.95        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA 
       33.04         4.01        12.62        22.52        27.98        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        23.41        17.98        29.16        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       19.79        12.85         7.56        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BX 
        3.62        26.73        53.88        11.01         5.36         5.69 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        18.08         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
       13.35        62.86        18.81         6.15        12.69         2.27 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
        4.31         9.67        10.85        31.07        12.66        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        8.94         3.25        11.08        61.94        48.00        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       59.31        33.01         7.23        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        21.40        20.71        15.81        19.13        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       14.07        17.75        24.92         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
        7.73         2.10         3.12        20.98         2.20         7.36 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO 
       10.92        11.31        18.97         7.63         4.73        10.65 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       27.35         8.58        19.07         1.51        19.40        38.60 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH 
        9.01        12.16         3.45         2.76        27.68         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       11.70         1.81        16.27        11.80        52.73        50.56 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
        1.15        15.32        21.07        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N 
       16.54        12.43        38.99        17.62        37.05        86.83 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
       78.25         3.02         3.91         6.21         3.85        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       45.04         6.58        97.45       125.49         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       48.62        64.80        79.66        66.41        34.45        14.93 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       11.90        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT 
       11.31        54.90         7.63        71.57        91.73         2.96 
TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN4 
        8.32        98.99        44.32        56.48        86.30        27.06 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       13.64        22.36        25.41        21.11        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 
       59.38        60.16        63.02        56.35        35.41         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.62                           0.10 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        112.83                         166.03 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        17.770                         16.735 
[1] "0.6 - 112.8 (17.8)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1"  
D34V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.11) MUTATED         0       28        32       31
  DEL PEAK  1(1P36.11) WILD-TYPE       2      101       108      104
D34V3, multiclass
           clus
vv          DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            28                            101
  STAGE III                           32                            108
  STAGE IV                            31                            104
[1] 4 2
[1] 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         26  48   9
  DEL PEAK  1(1P36.11) WILD-TYPE       97 147  49
D34V4, multiclass
          clus
vv         DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1+T2                           26                             97
  T3                                 48                            147
  T4                                  9                             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                              N0  N1  N2  N3
  DEL PEAK  1(1P36.11) MUTATED    53  15  11   4
  DEL PEAK  1(1P36.11) WILD-TYPE 182  32  64   5
D34V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           53                            182
  N1                           15                             32
  N2                           11                             64
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    39   4
  DEL PEAK  1(1P36.11) WILD-TYPE 153   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     39    4
  DEL PEAK  1(1P36.11) WILD-TYPE  153    7
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                           39                            153
  1                            4                              7
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    23  68
  DEL PEAK  1(1P36.11) WILD-TYPE  84 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     23   68
  DEL PEAK  1(1P36.11) WILD-TYPE   84  233
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           23                             84
  MALE                             68                            233
[1] 2 2
[1] FALSE
D34V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    85   3
  DEL PEAK  1(1P36.11) WILD-TYPE 279  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     85    3
  DEL PEAK  1(1P36.11) WILD-TYPE  279   16
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                            85                            279
  YES                            3                             16
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
D34V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       5                         7    77
  DEL PEAK  1(1P36.11) WILD-TYPE    38                        15   250
D34V12, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               77
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                 38
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     3  81
  DEL PEAK  1(1P36.11) WILD-TYPE   6 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      3   81
  DEL PEAK  1(1P36.11) WILD-TYPE    6  288
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            288
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  2(1Q32.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1Q32.1) MUTATED    38  33
  DEL PEAK  2(1Q32.1) WILD-TYPE 191 144
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           71                           335 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           33                           144 
$`DEL PEAK  2(1Q32.1) MUTATED`
TCGA-2F-A9KO TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
       24.13        16.77        15.12        26.14        14.89         8.35 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A1HS TCGA-CU-A0YO TCGA-CU-A3YL TCGA-DK-A2HX 
       12.82         9.96        12.56         4.90        29.79        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 
       87.32         4.80         8.15        17.72        50.27        66.05 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA76 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A85H 
       15.68        36.66        12.03        22.16         2.24        12.95 
TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TE 
       23.41        19.79        18.08         6.28        13.35        12.36 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31        31.07        15.95        20.12        17.62        70.32 
TCGA-GC-A3RC TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QH 
       15.91        20.05         5.62        21.34        19.82         8.48 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-MV-A51V 
        8.58        22.72         3.45        11.80        15.58        13.48 
TCGA-S5-A6DX TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HF 
        1.84        17.62        76.01         6.21         6.58        97.12 
TCGA-XF-A8HH TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMQ TCGA-XF-AAMX 
        1.87         2.10        10.82       110.60        71.57         6.77 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R3 
       44.32        61.45        18.15        11.97        13.64        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-AA5H 
       30.28        94.29        64.08        88.87        19.17 

$`DEL PEAK  2(1Q32.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
        0.62        41.75        51.16        66.54        10.22        47.80 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       29.65         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       17.88        19.50         5.06        14.96         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
       17.16        16.18        20.48         4.67        17.56        28.70 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       36.43        28.41         8.98         1.94        23.01        12.79 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL 
       12.00        12.10        11.34        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       13.08        12.92        15.12        18.48         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       13.58        21.86         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       16.70       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT 
       17.95         7.79       142.78        13.58         8.22        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 
       23.21         9.67        20.81        10.55       163.30        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        53.29        76.60        67.36        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       52.01        15.02        13.58       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       19.00        13.64        15.35        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       20.32        43.59        15.35        38.83        29.72         0.10 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        4.24        24.03        24.66         0.92         1.22        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.94        33.04         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        24.30        17.98        29.16         5.52        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
       46.78        12.85         7.56        27.35        14.96        20.91 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
        3.62        15.58        26.73        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N 
        5.36         5.69         8.25        27.45        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TF 
        7.10        62.86        18.81         6.15        12.69         2.27 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        3.06         9.67        10.85        12.66        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
        8.94         3.25        11.08        61.94        48.00        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31        33.01         7.23        66.02         6.94        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
       21.40        20.71        15.81        19.13        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       24.92         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       18.97         7.63        32.78         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK 
        7.00        14.27        19.10        20.28        36.49        27.35 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07         1.51        19.40        38.60        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       12.16        25.02        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.07        11.70        17.72         1.81        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       52.73        50.56        35.97        46.98        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-AA26 
       15.32        21.07        12.23        16.67        14.24        16.54 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P 
       12.43        38.99        37.05        22.68        86.83        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       69.34         3.02       112.83         3.91        29.56        17.82 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        3.85        51.32        45.04        97.45       125.49        15.35 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
       11.90        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
        2.24        16.27        66.64        13.74        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY 
       54.90         7.63        91.73         2.96         8.32        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       56.48        30.94        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       18.84         9.63         0.66        22.36        25.41        21.11 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41         3.48        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U 
       47.84        20.22         2.89        34.06        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 
       59.38        60.16        63.02        56.35        35.41        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21         5.52        12.23 

  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                         1.84                          0.10 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                       110.60                        166.03 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                        16.77                         17.23 
[1] "1.8 - 110.6 (16.8)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.1"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1Q32.1) MUTATED         0       28        18       25
  DEL PEAK  2(1Q32.1) WILD-TYPE       2      101       122      110
D35V3, multiclass
           clus
vv          DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           28                           101
  STAGE III                          18                           122
  STAGE IV                           25                           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"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  2(1Q32.1) MUTATED         21  31   9
  DEL PEAK  2(1Q32.1) WILD-TYPE      102 164  49
D35V4, multiclass
          clus
vv         DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  T0+T1+T2                          21                           102
  T3                                31                           164
  T4                                 9                            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                             N0  N1  N2  N3
  DEL PEAK  2(1Q32.1) MUTATED    31   5  19   2
  DEL PEAK  2(1Q32.1) WILD-TYPE 204  42  56   7
D35V5, multiclass
    clus
vv   DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  N0                          31                           204
  N1                           5                            42
  N2                          19                            56
  N3                           2                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    29   2
  DEL PEAK  2(1Q32.1) WILD-TYPE 163   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     29    2
  DEL PEAK  2(1Q32.1) WILD-TYPE  163    9
   clus
vv  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  0                          29                           163
  1                           2                             9
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    14  57
  DEL PEAK  2(1Q32.1) WILD-TYPE  93 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     14   57
  DEL PEAK  2(1Q32.1) WILD-TYPE   93  244
        clus
vv       DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          14                            93
  MALE                            57                           244
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    64   1
  DEL PEAK  2(1Q32.1) WILD-TYPE 300  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     64    1
  DEL PEAK  2(1Q32.1) WILD-TYPE  300   18
     clus
vv    DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  NO                           64                           300
  YES                           1                            18
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, continuous
D35V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q32.1) MUTATED       6                         2    60
  DEL PEAK  2(1Q32.1) WILD-TYPE    37                        20   267
D35V12, multiclass
                           clus
vv                          DEL PEAK  2(1Q32.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              60
                           clus
vv                          DEL PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                37
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED     3  65
  DEL PEAK  2(1Q32.1) WILD-TYPE   6 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED      3   65
  DEL PEAK  2(1Q32.1) WILD-TYPE    6  304
                        clus
vv                       DEL PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       DEL PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           304
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    72  62
  DEL PEAK  3(2Q22.1) WILD-TYPE 157 115
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          134                           272 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           62                           115 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7S 
       24.13        94.88       104.65         8.35        16.27        34.98 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BT-A20P TCGA-BT-A20T 
       15.12        47.80         2.50         7.33        17.88        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-C4-A0EZ 
        5.06         8.35        17.16         4.67        12.82         8.98 
TCGA-C4-A0F6 TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CU-A0YN 
       23.01        12.59        12.16        12.62        12.10        12.92 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I1 
       18.48         5.19        21.86        18.41        46.68        17.95 
TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        4.80        50.27         9.67        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6U TCGA-DK-AA77 TCGA-E5-A4U1 
       36.66        15.02       165.73        19.00        20.32        38.83 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 
       25.58         0.92        13.68        14.37         8.09         8.94 
TCGA-FD-A3N6 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       27.98        24.30        19.79        26.73         5.36        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.08         2.70        12.36         2.27         3.06         4.31 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3VY 
       17.23        11.08        61.94        48.00        26.93        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       66.02         6.94        15.81        14.07         0.49         8.94 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A767 
        2.10        20.98         2.20        11.31        32.78         4.73 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-HQ-A5NE 
       10.65        14.27        21.34        19.82        27.35        12.16 
TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41P 
        3.45         9.14        17.72         1.81        11.80        35.97 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78M 
       44.38         1.15        15.58        13.48        16.54        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HG 
       86.83        76.01        69.34        17.82         6.58        15.35 
TCGA-XF-A8HH TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T0 
        1.87        15.98        14.93         4.21        12.76        26.27 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       66.64        13.74        10.82       110.60         2.96         6.77 
TCGA-XF-AAN2 TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       61.45        75.39         0.66        11.97        13.64        22.36 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.11        31.20        28.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 
       20.22        34.06         8.61        63.02        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.52        19.17 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       11.97       108.95        44.94        16.83        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        29.65        17.42        40.08         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        26.14        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25        16.18        20.48 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        9.96        17.56        28.70        36.43        28.41         1.94 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       12.79        12.56        13.97        12.13        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO 
       11.34        11.34        11.87        18.58        13.08         4.90 
TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
       15.12        29.79         1.84        13.58         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62         7.79       142.78        87.32        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        17.72        21.30        23.21        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
      163.30        66.05        53.29        76.60        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W 
       38.24        52.01        13.58       166.03        18.81        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC 
       15.35        13.64        56.15        11.18        12.03        43.59 
TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 
       24.66         1.22        14.07        12.95        15.32        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
       16.77        33.04         4.01        12.62        22.52        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       23.41        17.98        29.16         5.52        25.74        46.78 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85         7.56        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        53.88        11.01        19.33         5.69         8.25 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        6.15        12.69         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
       10.65         8.94         3.25        15.95        59.31        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
        7.23        20.12        70.32        29.36        21.40        20.71 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 
       19.13        15.91        17.75        24.92        13.91         7.73 
TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        3.12         7.36        10.92        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH 
        5.62        32.98         7.00        19.10        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ 
       36.49         8.58        19.07        22.72         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60        64.01         9.01        25.02        21.24         2.76 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N 
       27.68         9.07        11.70        15.42        16.27        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       50.56        46.98        15.32        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        38.99        17.62        37.05 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       78.25         3.02       112.83         3.91        29.56         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        3.85        51.32        45.04        97.45       125.49        97.12 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL 
       17.88        48.62        64.80        79.66         3.22        66.41 
TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       34.45         5.98        11.90        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMH 
       18.90         2.24        16.27         2.10        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY 
       54.90         7.63        71.57        91.73         8.32        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN7 
       44.32        56.48        30.94        86.30        27.06        18.15 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        3.88        18.84         9.63        25.41        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4N 
       21.86        94.29        13.41         3.48        88.87         2.89 
TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 
       19.69        59.38        60.16        56.35        35.41        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       165.73                        166.03 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       16.405                        17.590 
[1] "0.5 - 165.7 (16.4)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.2"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED         0       41        47       46
  DEL PEAK  3(2Q22.1) WILD-TYPE       2       88        93       89
D36V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           41                            88
  STAGE III                          47                            93
  STAGE IV                           46                            89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  3(2Q22.1) MUTATED         36  67  19
  DEL PEAK  3(2Q22.1) WILD-TYPE       87 128  39
D36V4, multiclass
          clus
vv         DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T0+T1+T2                          36                            87
  T3                                67                           128
  T4                                19                            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                             N0  N1  N2  N3
  DEL PEAK  3(2Q22.1) MUTATED    68  14  28   4
  DEL PEAK  3(2Q22.1) WILD-TYPE 167  33  47   5
D36V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                          68                           167
  N1                          14                            33
  N2                          28                            47
  N3                           4                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    62   6
  DEL PEAK  3(2Q22.1) WILD-TYPE 130   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     62    6
  DEL PEAK  3(2Q22.1) WILD-TYPE  130    5
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          62                           130
  1                           6                             5
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    41  93
  DEL PEAK  3(2Q22.1) WILD-TYPE  66 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     41   93
  DEL PEAK  3(2Q22.1) WILD-TYPE   66  208
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          41                            66
  MALE                            93                           208
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED   115   7
  DEL PEAK  3(2Q22.1) WILD-TYPE 249  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED    115    7
  DEL PEAK  3(2Q22.1) WILD-TYPE  249   12
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                          115                           249
  YES                           7                            12
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
D36V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED      11                         7   109
  DEL PEAK  3(2Q22.1) WILD-TYPE    32                        15   218
D36V12, multiclass
                           clus
vv                          DEL PEAK  3(2Q22.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             109
                           clus
vv                          DEL PEAK  3(2Q22.1) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               218
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     4 121
  DEL PEAK  3(2Q22.1) WILD-TYPE   5 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      4  121
  DEL PEAK  3(2Q22.1) WILD-TYPE    5  248
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         121
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  4(2Q34) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2Q34) MUTATED    98  76
  DEL PEAK  4(2Q34) WILD-TYPE 131 101
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        174                         232 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                         76                         101 
$`DEL PEAK  4(2Q34) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       108.95         8.35        16.27 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       17.16        34.98         0.62        15.12        10.22        47.80 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T 
        2.50        17.42         2.66        19.04        26.14        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42C TCGA-BT-A42E 
        5.06         8.35        17.16         4.67        28.70        36.43 
TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 
        8.98        12.56        12.59        12.16        12.62        12.10 
TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A5 
       11.87        12.92        18.48         5.19        29.79         2.14 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
      130.88        46.68        17.95         7.79         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV 
        8.15        50.27        21.30         9.67        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R 
       53.29        67.36        50.70        36.66        15.02       165.73 
TCGA-DK-AA6U TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A3X6 TCGA-E7-A4IJ 
       19.00        12.03        20.32        15.35        29.72        22.16 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q 
       25.58         0.92         1.22        13.68        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SR 
       16.77         8.94        22.52        24.30        29.16        19.79 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
       26.73         5.36         8.25        27.45        18.08         2.70 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF 
       12.69        12.36         2.27         3.06         4.31        17.23 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3VY TCGA-G2-AA3B 
       11.08        61.94        15.95        26.93        17.62        66.02 
TCGA-G2-AA3D TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       70.32        15.81        19.13        14.07        17.75        24.92 
TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A767 TCGA-GU-AATO TCGA-GV-A3JV 
        0.49         2.10        10.92         4.73        10.65        14.27 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA 
       21.34         8.48        36.49        27.35        19.07        22.72 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC 
       38.60        12.16        25.02         3.45        21.24         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41O 
       27.68         9.07        17.72         1.81        11.80        50.56 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       35.97        44.38         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB 
       16.67        16.54        17.62        22.68        86.83        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
        3.91        29.56        17.82         6.21         3.85        51.32 
TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       15.35         1.87         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMT 
       26.27         2.24        13.74        10.82       110.60         2.96 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R2 
       44.32        61.45        18.15        11.97        22.36        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       31.20        28.41        94.29         3.48        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA5H 
       47.84        34.06        59.38        63.02        57.90        19.17 

$`DEL PEAK  4(2Q34) WILD-TYPE`
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y 
      104.65        44.94        16.83        16.77        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-BL-A0C8 TCGA-BL-A13I 
       41.75        51.16        66.54        29.65        40.08         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       19.50         5.06        14.96         8.25        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82         9.96        17.56        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       12.79        13.97        12.13        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HX 
       12.46        12.10        12.26        13.12        12.00        11.34 
TCGA-CF-A8HY TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 
       11.34        18.58        13.08         4.90        15.12         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       13.58        21.86        66.41        18.41        19.00        16.70 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A2I6 
      112.44        16.14        17.62        15.62       142.78        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        8.22        17.72        23.21        20.81        10.55       163.30 
TCGA-DK-A3X1 TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q 
       66.05        76.60        15.68        38.24        52.01        13.58 
TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
      166.03        18.81        13.64        15.35        13.64        56.15 
TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       11.18        43.59        38.83         0.10         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B6 
       24.66        14.07        12.95        15.32        32.02        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.62        27.98        60.66        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        46.78        12.85         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       19.33         5.69        58.92         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 
       62.86        18.81         6.15         9.67        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO 
       12.66        10.65         8.94         3.25        48.00        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       33.01         7.23        20.12         6.94        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       20.71        15.91         8.94        13.91         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         2.20         7.36        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JX 
       32.78        20.05         5.62        32.98         7.00        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
       19.82        20.28         8.58         1.51        19.40        64.01 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N 
        9.01         2.76        11.70        15.42        16.27        52.73 
TCGA-KQ-A41Q TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       46.98        21.07        12.23        14.24         1.84        12.43 
TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       38.99        37.05        76.01        78.25         3.02       112.83 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI 
       45.04         6.58        97.45       125.49        97.12        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SZ TCGA-XF-A9T2 
       48.62        64.80        79.66        66.41        28.24        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY 
        7.63        71.57        91.73         8.32         6.77        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       56.48        30.94        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R4 
       18.84         9.63         0.66        13.64        25.41        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N 
       35.84        21.86        13.41        88.87        20.22         2.89 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
       19.69         8.61        60.16        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21         5.52        12.23 

  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                       0.49                        0.10 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                     165.73                      166.03 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                      17.16                       17.59 
[1] "0.5 - 165.7 (17.2)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.1"
D37V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q34) MUTATED         0       53        56       64
  DEL PEAK  4(2Q34) WILD-TYPE       2       76        84       71
D37V3, multiclass
           clus
vv          DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  STAGE I                           0                           2
  STAGE II                         53                          76
  STAGE III                        56                          84
  STAGE IV                         64                          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"
                             vv
clus                          T0+T1+T2  T3  T4
  DEL PEAK  4(2Q34) MUTATED         47  88  24
  DEL PEAK  4(2Q34) WILD-TYPE       76 107  34
D37V4, multiclass
          clus
vv         DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  T0+T1+T2                        47                          76
  T3                              88                         107
  T4                              24                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  4(2Q34) MUTATED    92  18  42   4
  DEL PEAK  4(2Q34) WILD-TYPE 143  29  33   5
D37V5, multiclass
    clus
vv   DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  N0                        92                         143
  N1                        18                          29
  N2                        42                          33
  N3                         4                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED    76   5
  DEL PEAK  4(2Q34) WILD-TYPE 116   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED     76    5
  DEL PEAK  4(2Q34) WILD-TYPE  116    6
   clus
vv  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  0                        76                         116
  1                         5                           6
[1] 2 2
[1] FALSE
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED    42 132
  DEL PEAK  4(2Q34) WILD-TYPE  65 169
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED     42  132
  DEL PEAK  4(2Q34) WILD-TYPE   65  169
        clus
vv       DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  FEMALE                        42                          65
  MALE                         132                         169
[1] 2 2
[1] FALSE
D37V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED   154   7
  DEL PEAK  4(2Q34) WILD-TYPE 210  12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED    154    7
  DEL PEAK  4(2Q34) WILD-TYPE  210   12
     clus
vv    DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  NO                        154                         210
  YES                         7                          12
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, continuous
D37V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q34) MUTATED      13                         9   146
  DEL PEAK  4(2Q34) WILD-TYPE    30                        13   181
D37V12, multiclass
                           clus
vv                          DEL PEAK  4(2Q34) MUTATED
  ASIAN                                            13
  BLACK OR AFRICAN AMERICAN                         9
  WHITE                                           146
                           clus
vv                          DEL PEAK  4(2Q34) WILD-TYPE
  ASIAN                                              30
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED     5 155
  DEL PEAK  4(2Q34) WILD-TYPE   4 214
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED      5  155
  DEL PEAK  4(2Q34) WILD-TYPE    4  214
                        clus
vv                       DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  HISPANIC OR LATINO                             5                           4
  NOT HISPANIC OR LATINO                       155                         214
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  5(2Q37.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.1) MUTATED   119  89
  DEL PEAK  5(2Q37.1) WILD-TYPE 110  88
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          208                           198 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                           89                            88 
$`DEL PEAK  5(2Q37.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       108.95         8.35        16.27 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 
       17.16        34.98         0.62        15.12        10.22        47.80 
TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q 
        2.50        40.08         2.66        19.04        26.14        19.50 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
       14.89         5.06         8.35         8.25        17.16         4.67 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS 
       17.56        28.70        36.43         8.98        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.59        12.13        12.16        12.62        12.10        11.34 
TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       11.87        12.92        15.12        18.48         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2HX 
        1.84         2.14       130.88       112.44        15.62        46.68 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IS TCGA-DK-A3IT 
       17.95         4.80        13.58         8.15        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 
       23.21         9.67        17.98        64.18        53.29        67.36 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S 
       50.70        36.66        38.24        15.02       165.73       166.03 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ 
       19.00        15.35        13.64        12.03        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A7DU 
       38.83        29.72        22.16        25.58         0.56         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 
        1.22        13.68        14.37         8.09        16.77         8.94 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X 
       22.52        24.30        29.16        19.79        12.85         3.62 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
       26.73         5.36         8.25        27.45        18.08         2.70 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3VY 
       17.23        11.08        61.94        15.95        26.93        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       66.02        70.32        29.36        15.81        19.13        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GU-A42P 
       14.07        17.75        24.92         0.49         2.10        10.92 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW 
        7.63         4.73        10.65        32.98        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G 
       19.10        20.28         8.48        36.49        27.35        19.07 
TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       22.72        38.60         9.01        12.16        25.02         3.45 
TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
       21.24         9.14        27.68         9.07        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S 
       15.42        11.80        50.56        35.97        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 
       15.32        15.58        13.48        16.67         1.84        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        22.68        86.83        76.01        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
        3.91        29.56        17.82         6.21         3.85        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SJ TCGA-XF-A9SK 
       45.04         6.58        15.35         1.87         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       14.93         4.21        12.76        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMT 
       26.27         2.24        13.74        10.82       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M 
        8.32        30.94        61.45        18.15        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       22.36        21.11        31.20        28.41        94.29         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22        34.06         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA5H 
       59.38        63.02        57.90        19.17 

$`DEL PEAK  5(2Q37.1) WILD-TYPE`
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA7Y 
      104.65        44.94        16.83        16.77        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I 
       41.75        51.16        66.54        29.65        17.42         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        6.74        12.39         6.58        13.15        12.16        17.88 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
        5.06        14.96        16.18        20.48        12.82         9.96 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S 
       28.41         1.94        23.01        13.97        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A8HY TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A3 
       11.34        18.58        13.08         4.90        13.58        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        18.41        19.00        16.70        16.14        17.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3WW 
        7.79       142.78        87.32         8.22        17.72        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA6M 
       10.55       163.30        66.05        76.60        15.68        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A2PC 
       13.58        18.81        13.64        56.15        11.18        43.59 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
        4.24        24.03        24.66        14.07        12.95        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       32.02        33.04         4.01        12.62        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N 
       23.41        17.98         5.52        25.74        46.78         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35        14.96        20.91        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       19.33         5.69        58.92         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       62.86        18.81         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
       10.65         8.94         3.25        48.00        59.31        33.01 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A6I1 
        7.23        20.12         6.94        21.40        20.71         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B 
       13.91         7.73         3.12        20.98         2.20         7.36 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ 
       11.31        18.97        32.78        20.05         5.62         7.00 
TCGA-GV-A3JZ TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A4AB 
       19.82         8.58         1.51        19.40        64.01         2.76 
TCGA-K4-A5RI TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-LT-A8JT TCGA-PQ-A6FI 
       11.70        16.27        52.73        46.98        21.07        12.23 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       14.24        12.43        37.05        78.25         3.02       112.83 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       97.45       125.49        97.12        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T2 
       79.66        66.41        34.45         5.98        28.24        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ 
       16.27        66.64         2.10        92.98        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
        7.63        71.57        91.73         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        86.30        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        9.63         0.66        25.41        30.28        35.84        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA51 
       13.41        88.87         2.89        19.69        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41        19.40         8.52        54.21         5.52        12.23 

  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                       166.03                        163.30 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                       16.605                        17.880 
[1] "0.5 - 166.0 (16.6)" "0.1 - 163.3 (17.9)"
[1] "hr=" "1.1"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(2Q37.1) MUTATED         1       65        64       77
  DEL PEAK  5(2Q37.1) WILD-TYPE       1       64        76       58
D38V3, multiclass
           clus
vv          DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           65                            64
  STAGE III                          64                            76
  STAGE IV                           77                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2 T3 T4
  DEL PEAK  5(2Q37.1) MUTATED         62 98 32
  DEL PEAK  5(2Q37.1) WILD-TYPE       61 97 26
D38V4, multiclass
          clus
vv         DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  T0+T1+T2                          62                            61
  T3                                98                            97
  T4                                32                            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  5(2Q37.1) MUTATED   110  22  50   4
  DEL PEAK  5(2Q37.1) WILD-TYPE 125  25  25   5
D38V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  N0                         110                           125
  N1                          22                            25
  N2                          50                            25
  N3                           4                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.1) MUTATED   97  5
  DEL PEAK  5(2Q37.1) WILD-TYPE 95  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     97    5
  DEL PEAK  5(2Q37.1) WILD-TYPE   95    6
   clus
vv  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  0                          97                            95
  1                           5                             6
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED    46 162
  DEL PEAK  5(2Q37.1) WILD-TYPE  61 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     46  162
  DEL PEAK  5(2Q37.1) WILD-TYPE   61  139
        clus
vv       DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  FEMALE                          46                            61
  MALE                           162                           139
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED   187   8
  DEL PEAK  5(2Q37.1) WILD-TYPE 177  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED    187    8
  DEL PEAK  5(2Q37.1) WILD-TYPE  177   11
     clus
vv    DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  NO                          187                           177
  YES                           8                            11
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
D38V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.1) MUTATED      18                         9   170
  DEL PEAK  5(2Q37.1) WILD-TYPE    25                        13   157
D38V12, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.1) MUTATED
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             170
                           clus
vv                          DEL PEAK  5(2Q37.1) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED     7 185
  DEL PEAK  5(2Q37.1) WILD-TYPE   2 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      7  185
  DEL PEAK  5(2Q37.1) WILD-TYPE    2  184
                        clus
vv                       DEL PEAK  5(2Q37.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         185
                        clus
vv                       DEL PEAK  5(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           184
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    59  57
  DEL PEAK  6(3P14.2) WILD-TYPE 170 120
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          116                           290 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           57                           120 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA82 
       24.13       104.65         8.35        16.77        27.62        51.16 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42C 
       14.89         5.06         8.35         8.25        17.56        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YR 
       36.43         8.98         1.94        12.56        12.92        15.12 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A2I2 TCGA-DK-A3IM 
       18.48        29.79        66.41        16.70         7.79         8.15 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A6B5 TCGA-DK-AA6L 
       17.72        50.27        10.55        66.05        50.70        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.58       165.73        13.64        11.18        20.32        43.59 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B6 
       25.58         1.22        12.95         8.09        16.77        33.04 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BV 
       22.52        24.30        29.16         7.56        15.58         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TF TCGA-FD-A6TG 
        8.25        27.45        58.92         6.28         2.27         3.06 
TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       10.65        61.94        48.00        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3WC 
       17.62        66.02        29.36        20.71        19.13        17.75 
TCGA-GC-A3YS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW 
       24.92         2.20        11.31         4.73         7.00        21.34 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV 
       22.72        19.40        38.60         9.01        25.02        21.24 
TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A6MB TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-PQ-A6FI 
        9.14        11.70        15.42        35.97        46.98        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       16.67        38.99        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-XF-A8HD TCGA-XF-A8HI TCGA-XF-A9SK TCGA-XF-A9SU 
      112.83        29.56        97.45        17.88        15.98         5.98 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAMQ 
       26.27        66.64         2.10        13.74       110.60        71.57 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R9 TCGA-ZF-A9RD 
        2.96         8.32        86.30        13.64        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA4W TCGA-ZF-AA53 
        3.48        64.08        58.72        34.06        60.16        57.90 
TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.52        19.17 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       108.95        16.27        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 
       17.16        34.98        50.04         0.62        41.75        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       15.12        10.22        47.80        29.65         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       13.15        19.04        26.14        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.96        17.16        16.18        20.48         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       12.82         9.96        28.41        23.01        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.59        12.13        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90         5.19         1.84        13.58        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       18.41        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62        46.68        17.95       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       13.58         8.22        21.30        23.21         9.67        20.81 
TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
      163.30        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        36.66        52.01        15.02       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4TZ 
       19.00        15.35        13.64        56.15        12.03        15.35 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         0.10        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66         0.92        13.68        14.07        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA 
       32.02         8.94         4.01        12.62        27.98        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       23.41        17.98         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR 
       12.85        27.35        14.96        20.91         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62N 
       53.88        11.01        19.33         5.69        18.08         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10        13.35        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.36         4.31         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL 
       17.23         8.94         3.25        11.08        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
       59.31         6.94        70.32        21.40        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         7.36        10.92        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV 
       32.78        20.05         5.62        10.65        32.98        14.27 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        36.49        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU 
        8.58        19.07         1.51        64.01        12.16         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        2.76        27.68         9.07        17.72         1.81        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       11.80        52.73        50.56        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       15.58        21.07        13.48        14.24         1.84        16.54 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PA 
       12.43        17.62        37.05        22.68        86.83         3.91 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       17.82         6.21         3.85        51.32        45.04         6.58 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH 
      125.49        97.12        15.35         1.87        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       79.66         3.22        66.41        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 
       12.76        11.90        23.64        21.04        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        16.27        92.98        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
        7.63        91.73         6.77        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        27.06        75.39        18.15         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       21.11        31.20        30.28        35.84        21.86        94.29 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       88.87        47.84        20.22         2.89        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
       59.38        63.02        56.35        35.41        19.40        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         1.22                          0.10 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       165.73                        166.03 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       18.805                        16.270 
[1] "1.2 - 165.7 (18.8)" "0.1 - 166.0 (16.3)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P14.2) MUTATED         0       31        41       44
  DEL PEAK  6(3P14.2) WILD-TYPE       2       98        99       91
D39V3, multiclass
           clus
vv          DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           31                            98
  STAGE III                          41                            99
  STAGE IV                           44                            91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  6(3P14.2) MUTATED         31  63  14
  DEL PEAK  6(3P14.2) WILD-TYPE       92 132  44
D39V4, multiclass
          clus
vv         DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  T0+T1+T2                          31                            92
  T3                                63                           132
  T4                                14                            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                             N0  N1  N2  N3
  DEL PEAK  6(3P14.2) MUTATED    64  21  16   6
  DEL PEAK  6(3P14.2) WILD-TYPE 171  26  59   3
D39V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  N0                          64                           171
  N1                          21                            26
  N2                          16                            59
  N3                           6                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    45   5
  DEL PEAK  6(3P14.2) WILD-TYPE 147   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     45    5
  DEL PEAK  6(3P14.2) WILD-TYPE  147    6
   clus
vv  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  0                          45                           147
  1                           5                             6
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    40  77
  DEL PEAK  6(3P14.2) WILD-TYPE  67 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     40   77
  DEL PEAK  6(3P14.2) WILD-TYPE   67  224
        clus
vv       DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  FEMALE                          40                            67
  MALE                            77                           224
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED   108   5
  DEL PEAK  6(3P14.2) WILD-TYPE 256  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED    108    5
  DEL PEAK  6(3P14.2) WILD-TYPE  256   14
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NO                          108                           256
  YES                           5                            14
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
D39V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P14.2) MUTATED       3                         7   101
  DEL PEAK  6(3P14.2) WILD-TYPE    40                        15   226
D39V12, multiclass
                           clus
vv                          DEL PEAK  6(3P14.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             101
                           clus
vv                          DEL PEAK  6(3P14.2) WILD-TYPE
  ASIAN                                                40
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED     5 103
  DEL PEAK  6(3P14.2) WILD-TYPE   4 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      5  103
  DEL PEAK  6(3P14.2) WILD-TYPE    4  266
                        clus
vv                       DEL PEAK  6(3P14.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         103
                        clus
vv                       DEL PEAK  6(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           266
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK  7(4Q22.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q22.1) MUTATED    83  79
  DEL PEAK  7(4Q22.1) WILD-TYPE 146  98
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          162                           244 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           79                            98 
$`DEL PEAK  7(4Q22.1) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA82 
      108.95         8.35        16.77        17.16         0.62        51.16 
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       10.22         2.50         7.33         5.06        14.96         5.06 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C 
       16.18        20.48         4.67        12.82        17.56        28.70 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG 
       28.41         1.94        23.01        12.79        12.56        12.13 
TCGA-CF-A3MI TCGA-CF-A47V TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A3 
       12.16        12.46        12.92         4.90        15.12        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       18.41       112.44        46.68        17.95         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X2 
        4.80         8.15         8.22        17.72        21.30        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q 
       64.18        15.68        50.70        36.66        38.24        13.58 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
      165.73        13.64        43.59        15.35        38.83        29.72 
TCGA-E7-A541 TCGA-E7-A6MD TCGA-E7-A7DU TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 
       25.58         4.24         0.92        32.02        33.04         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY 
       24.30        23.41         5.52        15.58        26.73         8.25 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC 
       58.92         2.70         7.10         6.28        13.35         6.15 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EF 
        3.06         4.31        10.85        31.07        17.23        61.94 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3D TCGA-GC-A3BM 
       26.93        59.31        33.01         7.23        70.32        21.40 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        19.13         0.49         8.94        13.91         7.73 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JV 
        2.20        11.31         7.63        20.05        32.98        14.27 
TCGA-GV-A3QH TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV 
        8.48        22.72        19.40        64.01        25.02        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.42        50.56        46.98         1.15        12.23        16.67 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78N 
       14.24        12.43        38.99        17.62        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE 
       76.01        69.34       112.83         3.91        29.56         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG 
        3.85        51.32         6.58        97.12        15.35        48.62 
TCGA-XF-A9SK TCGA-XF-A9SX TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMG 
       15.98        23.64        26.27        66.64        13.74       110.60 
TCGA-XF-AAMJ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       54.90         2.96         8.32        98.99        44.32        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R4 
       61.45        86.30        18.15        13.64        22.36        30.28 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 
       88.87        20.22         2.89         8.61        63.02        19.40 

$`DEL PEAK  7(4Q22.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       16.83        34.98        27.62        50.04        41.75        66.54 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J 
       15.12        47.80        29.65        17.42        40.08         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A20X 
       12.16        17.88        19.50        14.89         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0EZ TCGA-CF-A27C TCGA-CF-A3MF 
       17.16         9.96        36.43         8.98        13.97        12.59 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       13.08        10.95        12.66        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       18.58        13.08        18.48         5.19        29.79         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       13.58         2.14        66.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IS 
       16.14        17.62        15.62       142.78        13.58        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       163.30        66.05 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6S 
       53.29        76.60        67.36        52.01        15.02       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       18.81        19.00        15.35        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        20.32         0.10        22.16         2.24        16.70 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        0.56         0.66        26.96        26.24        24.03        24.66 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
        1.22        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       60.66        17.98        29.16        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
       12.85         7.56        27.35        14.96        20.91         3.62 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ 
       53.88        11.01        19.33         5.36         5.69        27.45 
TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF 
       18.08        62.86        18.81        12.69        12.36         2.27 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        9.67        12.66        10.65         8.94         3.25        11.08 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       48.00        15.95        20.12        17.62        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       29.36        20.71        15.91        14.07        17.75        24.92 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R 
        2.10         3.12        20.98         7.36        10.92        18.97 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JW 
       32.78         5.62         4.73        10.65         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82        20.28        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       19.07         1.51        38.60         9.01        12.16         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41R 
        2.76        16.27        11.80        52.73        35.97        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-A6DX TCGA-S5-AA26 
       15.32        15.58        21.07        13.48         1.84        16.54 
TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HD 
       37.05        78.25         3.02        17.82        45.04        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
      125.49         1.87        17.88        64.80        79.66         3.22 
TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       66.41        34.45        14.93         4.21         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       11.90        21.04        28.24        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        92.98        10.82        11.31         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       91.73         6.77        30.94        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       18.84         9.63         0.66        11.97        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T 
       31.20        35.84        28.41        47.84        34.06        19.69 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 
       59.38        60.16        56.35        35.41        57.90         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                       165.73                        166.03 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                        17.59                         16.80 
[1] "0.5 - 165.7 (17.6)" "0.1 - 166.0 (16.8)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(4Q22.1) MUTATED         0       45        56       61
  DEL PEAK  7(4Q22.1) WILD-TYPE       2       84        84       74
D40V3, multiclass
           clus
vv          DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           45                            84
  STAGE III                          56                            84
  STAGE IV                           61                            74
[1] 4 2
[1] 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(4Q22.1) MUTATED         44  85  20
  DEL PEAK  7(4Q22.1) WILD-TYPE       79 110  38
D40V4, multiclass
          clus
vv         DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T0+T1+T2                          44                            79
  T3                                85                           110
  T4                                20                            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                             N0  N1  N2  N3
  DEL PEAK  7(4Q22.1) MUTATED    83  24  33   2
  DEL PEAK  7(4Q22.1) WILD-TYPE 152  23  42   7
D40V5, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  N0                          83                           152
  N1                          24                            23
  N2                          33                            42
  N3                           2                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    71   2
  DEL PEAK  7(4Q22.1) WILD-TYPE 121   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     71    2
  DEL PEAK  7(4Q22.1) WILD-TYPE  121    9
   clus
vv  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  0                          71                           121
  1                           2                             9
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    45 117
  DEL PEAK  7(4Q22.1) WILD-TYPE  62 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     45  117
  DEL PEAK  7(4Q22.1) WILD-TYPE   62  184
        clus
vv       DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  FEMALE                          45                            62
  MALE                           117                           184
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED   141   6
  DEL PEAK  7(4Q22.1) WILD-TYPE 223  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED    141    6
  DEL PEAK  7(4Q22.1) WILD-TYPE  223   13
     clus
vv    DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  NO                          141                           223
  YES                           6                            13
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
D40V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4Q22.1) MUTATED      10                        10   135
  DEL PEAK  7(4Q22.1) WILD-TYPE    33                        12   192
D40V12, multiclass
                           clus
vv                          DEL PEAK  7(4Q22.1) MUTATED
  ASIAN                                              10
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             135
                           clus
vv                          DEL PEAK  7(4Q22.1) WILD-TYPE
  ASIAN                                                33
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED     5 146
  DEL PEAK  7(4Q22.1) WILD-TYPE   4 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED      5  146
  DEL PEAK  7(4Q22.1) WILD-TYPE    4  223
                        clus
vv                       DEL PEAK  7(4Q22.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         146
                        clus
vv                       DEL PEAK  7(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           223
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK  8(4Q34.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q34.2) MUTATED    98  79
  DEL PEAK  8(4Q34.2) WILD-TYPE 131  98
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          177                           229 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                           79                            98 
$`DEL PEAK  8(4Q34.2) MUTATED`
TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA82 
      108.95         8.35        16.77        17.16         0.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20R 
       15.12        10.22         2.50         2.66        26.14         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89         5.06         8.35        16.18        20.48         4.67 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
       17.56        28.70        36.43        28.41         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-CU-A0YN TCGA-CU-A0YO 
       12.56        12.13        12.16        10.95        12.92         4.90 
TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX 
       15.12        21.86        18.41       112.44        16.14        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
       17.95         7.79        87.32         4.80         8.15         8.22 
TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       21.30        64.18        15.68        50.70        36.66        38.24 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 
       13.58       165.73       166.03        13.64        11.18        20.32 
TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A85H TCGA-FD-A3B3 
       43.59        15.35        25.58         0.92        12.95        32.02 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A43N 
       33.04         4.01        23.41        29.16         5.52         7.56 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
       15.58        26.73         8.25        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        62.86         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        2.27         3.06         4.31        10.85        31.07        17.23 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       61.94        26.93         7.23        20.12        17.62        66.02 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       70.32        29.36        21.40        15.81        19.13        15.91 
TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
       17.75        13.91         7.73         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A40G 
       20.05        32.98        14.27        21.34         8.48        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WV 
       22.72        19.40        38.60        64.01        25.02        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        9.14        27.68         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V 
       15.42        50.56        46.98         1.15        15.58        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       16.67        14.24        12.43        38.99        17.62        22.68 
TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA 
       86.83        76.01        78.25        69.34       112.83         3.91 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56         6.21         3.85        51.32        45.04         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SY 
       97.12        15.35         3.22         4.21        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMT 
       26.27        66.64        10.82       110.60        54.90         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 
        8.32         6.77        98.99        56.48        61.45        86.30 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC 
       18.15        13.64        22.36        30.28        21.86        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       13.41         3.48        58.72         2.89        19.69         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA5H 
       63.02        19.40        19.17 

$`DEL PEAK  8(4Q34.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       16.83        34.98        27.62        50.04        41.75        66.54 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       47.80        29.65        17.42        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A3PK 
       19.50        14.96         8.25        17.16        12.82         9.96 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47T 
        8.98        23.01        13.97        12.59        13.08        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.46        12.10        12.62        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
       18.48         5.19        29.79         1.84        13.58         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        19.00        16.70       130.88        17.62        15.62 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
      142.78        13.58        17.72        50.27        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
       20.81        10.55       163.30        66.05        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       76.60        67.36        52.01        15.02        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.35        13.64        56.15        12.03        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        0.10        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV 
       26.96        26.24         4.24        24.03        24.66         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       13.68        14.07        15.32        14.37         8.09        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       17.98        25.74        46.78        19.79        12.85        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       14.96        20.91         3.62        53.88        11.01        19.33 
TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-FD-A6TI 
        5.36         5.69        27.45        18.08        18.81         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        11.08        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RD 
       15.95        59.31        33.01         6.94        20.71        14.07 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92         0.49         8.94         2.10         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 
        7.36        10.92        18.97        32.78         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
       10.65         7.00        19.10        19.82        20.28        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU 
       27.35         8.58         1.51         9.01        12.16         3.45 
TCGA-K4-A4AB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41R 
        2.76        16.27        11.80        52.73        35.97        44.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78L 
       15.32        21.07        12.23         1.84        16.54        37.05 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
        3.02        17.82        97.45       125.49         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       48.62        64.80        79.66        15.98        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T2 
       14.93         5.98        12.76        11.90        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
        2.24        16.27         2.10        13.74        92.98        11.31 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN4 
        7.63        71.57        91.73        44.32        30.94        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       75.39         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
       25.41        21.11        31.20        35.84        28.41        64.08 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4W 
       88.87        47.84        20.22        34.06        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        35.41        57.90         8.52        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                         0.62                          0.10 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                       166.03                        163.30 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                        17.23                         17.16 
[1] "0.6 - 166.0 (17.2)" "0.1 - 163.3 (17.2)"
[1] "hr=" "1"  
D41V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(4Q34.2) MUTATED         0       48        60       68
  DEL PEAK  8(4Q34.2) WILD-TYPE       2       81        80       67
D41V3, multiclass
           clus
vv          DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           48                            81
  STAGE III                          60                            80
  STAGE IV                           68                            67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  8(4Q34.2) MUTATED         46  94  22
  DEL PEAK  8(4Q34.2) WILD-TYPE       77 101  36
D41V4, multiclass
          clus
vv         DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  T0+T1+T2                          46                            77
  T3                                94                           101
  T4                                22                            36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  8(4Q34.2) MUTATED    91  24  41   1
  DEL PEAK  8(4Q34.2) WILD-TYPE 144  23  34   8
D41V5, multiclass
    clus
vv   DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  N0                          91                           144
  N1                          24                            23
  N2                          41                            34
  N3                           1                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED    71   4
  DEL PEAK  8(4Q34.2) WILD-TYPE 121   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED     71    4
  DEL PEAK  8(4Q34.2) WILD-TYPE  121    7
   clus
vv  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  0                          71                           121
  1                           4                             7
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED    47 130
  DEL PEAK  8(4Q34.2) WILD-TYPE  60 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED     47  130
  DEL PEAK  8(4Q34.2) WILD-TYPE   60  171
        clus
vv       DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  FEMALE                          47                            60
  MALE                           130                           171
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED   157   8
  DEL PEAK  8(4Q34.2) WILD-TYPE 207  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED    157    8
  DEL PEAK  8(4Q34.2) WILD-TYPE  207   11
     clus
vv    DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  NO                          157                           207
  YES                           8                            11
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
D41V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q34.2) MUTATED      12                        11   147
  DEL PEAK  8(4Q34.2) WILD-TYPE    31                        11   180
D41V12, multiclass
                           clus
vv                          DEL PEAK  8(4Q34.2) MUTATED
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             147
                           clus
vv                          DEL PEAK  8(4Q34.2) WILD-TYPE
  ASIAN                                                31
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               180
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED     6 158
  DEL PEAK  8(4Q34.2) WILD-TYPE   3 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED      6  158
  DEL PEAK  8(4Q34.2) WILD-TYPE    3  211
                        clus
vv                       DEL PEAK  8(4Q34.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         158
                        clus
vv                       DEL PEAK  8(4Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           211
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED   105  96
  DEL PEAK  9(5Q12.1) WILD-TYPE 124  81
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          201                           205 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           96                            81 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       24.13        11.97       108.95         8.35        16.83        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM 
       17.16        27.62        15.12        10.22         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20R 
       40.08         7.33         6.58        19.04        26.14         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD 
       14.89         5.06         8.35        17.16        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR 
        4.67        12.82        17.56        36.43        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A8HY TCGA-CU-A3QU TCGA-DK-A1A5 
       12.56        12.13        13.08        11.34         5.19         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       18.41       112.44        17.95       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       13.58         8.15         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       23.21         9.67        10.55        66.05        17.98        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       15.68        50.70        38.24        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 TCGA-E5-A2PC 
      166.03        19.00        13.64        15.35        11.18        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6MD 
       15.35        38.83        29.72        22.16        25.58         4.24 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 
       24.03         0.92         1.22        13.68         8.09         8.94 
TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP 
       33.04        22.52        24.30        23.41        17.98        25.74 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43U TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY 
       19.79        12.85        20.91        26.73         5.36         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB 
       27.45        18.08         2.70         7.10        13.35        18.81 
TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        6.15         2.27         3.06        10.85        31.07        10.65 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY 
       17.23        11.08        61.94        26.93         7.23        17.62 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       66.02        29.36        15.81        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
       13.91         7.73         2.10         2.20         7.36        10.92 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW 
        7.63         4.73        10.65        32.98         7.00        21.34 
TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G 
       19.10        20.28         8.48        36.49         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       22.72        19.40        38.60        64.01         9.01        12.16 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RI 
        3.45        21.24         2.76         9.14        27.68        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        1.81        15.42        11.80        50.56        35.97        46.98 
TCGA-KQ-A41R TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G5 TCGA-UY-A78K 
       44.38        13.48        16.67        14.24        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD 
       37.05        22.68        69.34       112.83        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
        6.21         3.85         6.58        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SZ 
       15.98        34.45        14.93        12.76        23.64        28.24 
TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMZ 
        2.24        54.90         7.63         2.96         6.77        44.32 
TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       56.48        11.97        13.64        22.36        25.41        31.20 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        28.41        88.87        47.84        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       34.06        19.69        59.38        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       57.90         8.52        19.17 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       94.88       104.65        16.27        44.94        34.98        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 
        0.62        41.75        51.16        66.54        47.80        29.65 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74        12.39        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42F 
       19.50        14.96         8.25         9.96        28.70        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47S 
        8.98         1.94        13.97        12.59        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 
       12.66        12.46        12.10        12.62        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.00        12.10        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       12.92         4.90        15.12        18.48        29.79         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       13.58        21.86        66.41        19.00        16.70       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3WW 
       16.14        17.62        15.62        46.68         7.79        20.81 
TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M 
      163.30        53.29        76.60        67.36        36.66        52.01 
TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E7-A3Y1 
       18.81        13.64        56.15        12.03        20.32         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
       24.66        14.07        12.95        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN 
       16.77         4.01        12.62        27.98        60.66        29.16 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X 
        5.52        46.78         7.56        27.35        14.96         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 
       15.58        53.88        11.01        19.33         5.69        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
        6.28        62.86        12.69        12.36         4.31         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
       12.66         8.94         3.25        48.00        15.95        59.31 
TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 
       33.01        20.12         6.94        70.32        21.40        20.71 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS 
       19.13        15.91        14.07        17.75         3.12        20.98 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV 
       11.31        18.97        32.78        20.05         5.62        14.27 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A5RH TCGA-K4-A5RJ 
       19.82        27.35         1.51        25.02         9.07        17.72 
TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       16.27        52.73         1.15        15.32        15.58        21.07 
TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A78O 
       12.23         1.84        16.54        12.43        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD 
       78.25         3.02         3.91        51.32        45.04        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
      125.49         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       66.41         4.21         5.98        11.90        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
       10.82       110.60        11.31        71.57        91.73         8.32 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R2 
       18.15         3.88        18.84         9.63         0.66        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       30.28        35.84        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       58.72         8.61        60.16        19.40        54.21         5.52 
TCGA-ZF-AA5P 
       12.23 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                       166.03                        163.30 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                        17.23                         16.77 
[1] "0.5 - 166.0 (17.2)" "0.1 - 163.3 (16.8)"
[1] "hr=" "1.3"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(5Q12.1) MUTATED         1       55        64       81
  DEL PEAK  9(5Q12.1) WILD-TYPE       1       74        76       54
D42V3, multiclass
           clus
vv          DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           55                            74
  STAGE III                          64                            76
  STAGE IV                           81                            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK  9(5Q12.1) MUTATED         52 104  28
  DEL PEAK  9(5Q12.1) WILD-TYPE       71  91  30
D42V4, multiclass
          clus
vv         DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  T0+T1+T2                          52                            71
  T3                               104                            91
  T4                                28                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  9(5Q12.1) MUTATED    96  28  46   7
  DEL PEAK  9(5Q12.1) WILD-TYPE 139  19  29   2
D42V5, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  N0                          96                           139
  N1                          28                            19
  N2                          46                            29
  N3                           7                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    89   8
  DEL PEAK  9(5Q12.1) WILD-TYPE 103   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     89    8
  DEL PEAK  9(5Q12.1) WILD-TYPE  103    3
   clus
vv  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  0                          89                           103
  1                           8                             3
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED    53 149
  DEL PEAK  9(5Q12.1) WILD-TYPE  54 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED     53  149
  DEL PEAK  9(5Q12.1) WILD-TYPE   54  152
        clus
vv       DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  FEMALE                          53                            54
  MALE                           149                           152
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED   180   8
  DEL PEAK  9(5Q12.1) WILD-TYPE 184  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED    180    8
  DEL PEAK  9(5Q12.1) WILD-TYPE  184   11
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                          180                           184
  YES                           8                            11
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
D42V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q12.1) MUTATED      14                        12   166
  DEL PEAK  9(5Q12.1) WILD-TYPE    29                        10   161
D42V12, multiclass
                           clus
vv                          DEL PEAK  9(5Q12.1) MUTATED
  ASIAN                                              14
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             166
                           clus
vv                          DEL PEAK  9(5Q12.1) WILD-TYPE
  ASIAN                                                29
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED     4 184
  DEL PEAK  9(5Q12.1) WILD-TYPE   5 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED      4  184
  DEL PEAK  9(5Q12.1) WILD-TYPE    5  185
                        clus
vv                       DEL PEAK  9(5Q12.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         184
                        clus
vv                       DEL PEAK  9(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           185
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 10(6P25.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(6P25.3) MUTATED    58  48
  DEL PEAK 10(6P25.3) WILD-TYPE 171 129
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                          106                           300 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           48                           129 
$`DEL PEAK 10(6P25.3) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-BT-A20V TCGA-BT-A20X 
        8.35        16.77        17.16        51.16         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-CF-A3MG TCGA-CU-A0YR 
       17.16        16.18        20.48         4.67        12.13        15.12 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
        1.84        13.58        66.41        16.70       130.88        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3X1 
       17.95         7.79       142.78        13.58        21.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6U 
       17.98        67.36        36.66        15.02       165.73        19.00 
TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6MD 
       13.64        12.03        15.35        38.83        22.16         4.24 
TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
       13.68        14.37         8.09        16.77        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O 
       60.66        23.41        29.16        20.91         5.36         7.10 
TCGA-FD-A62P TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-GC-A6I3 TCGA-GD-A3OP 
        6.28        31.07        17.23        59.31        13.91         2.10 
TCGA-GD-A3OS TCGA-GU-A764 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       20.98        20.05        19.82        20.28         8.48        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A4AB TCGA-K4-A5RI 
       27.35         8.58        19.40        64.01         2.76        11.70 
TCGA-K4-A6FZ TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
        1.81        52.73        35.97        46.98        44.38         1.15 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-UY-A78K TCGA-UY-A78N 
       15.58        13.48        12.23        14.24        17.62        86.83 
TCGA-UY-A8OD TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9ST 
      112.83        15.35         1.87        48.62        34.45         4.21 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML 
       28.24        26.27        10.82       110.60        54.90         7.63 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 
        8.32         6.77        98.99        44.32        56.48        86.30 
TCGA-XF-AAN5 TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       75.39        13.64        22.36        25.41        21.11        94.29 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA53 
        2.89        59.38        56.35        57.90 

$`DEL PEAK 10(6P25.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       24.13        11.97        94.88       104.65       108.95        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        16.83        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       41.75        66.54        15.12        10.22        47.80        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        2.50        17.42        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
       12.82         9.96        17.56        28.70        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        8.98         1.94        23.01        12.79        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.59        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       11.34        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 
        4.90        18.48         5.19        29.79        21.86         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       18.41        19.00       112.44        16.14        17.62        15.62 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         4.80         8.15         8.22        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AV 
       23.21         9.67        20.81        10.55       163.30        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        76.60        15.68        50.70        38.24        52.01 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA74 
       13.58       166.03        18.81        13.64        15.35        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       11.18        20.32        43.59        29.72         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A85H 
       24.03        24.66         0.92         1.22        14.07        12.95 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       15.32        32.02         8.94        12.62        22.52        27.98 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        17.98         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y 
       12.85         7.56        27.35        14.96         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       26.73        53.88        11.01        19.33         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TA 
       27.45        18.08        58.92         2.70        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG 
       18.81         6.15        12.69        12.36         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        4.31         9.67        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        3.25        11.08        61.94        48.00        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       33.01         7.23        20.12        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       70.32        29.36        21.40        20.71        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       15.91        14.07        17.75        24.92         0.49         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        7.73         3.12         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       18.97         7.63        32.78         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A40G 
       32.98         7.00        14.27        21.34        19.10        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
       22.72         1.51        38.60         9.01        12.16        25.02 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ 
        3.45        21.24         9.14        27.68         9.07        17.72 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O TCGA-LC-A66R TCGA-LT-A8JT 
       15.42        16.27        11.80        50.56        15.32        21.07 
TCGA-PQ-A6FN TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L 
       16.67         1.84        16.54        12.43        38.99        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       22.68        76.01        78.25        69.34         3.02         3.91 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
       29.56        17.82         6.21         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SH 
        6.58        97.45       125.49        97.12        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU 
       79.66         3.22        15.98        66.41        14.93         5.98 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        23.64        21.04        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
       16.27        66.64         2.10        13.74        92.98        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
       71.57        91.73         2.96        30.94        61.45        27.06 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       31.20        30.28        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN 
        3.48        64.08        58.72        88.87        47.84        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
       34.06        19.69         8.61        60.16        63.02        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21        19.17         5.52        12.23 

  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                         1.15                          0.10 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                       165.73                        166.03 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                       18.490                        16.405 
[1] "1.1 - 165.7 (18.5)" "0.1 - 166.0 (16.4)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6P25.3) MUTATED         0       29        38       39
  DEL PEAK 10(6P25.3) WILD-TYPE       2      100       102       96
D43V3, multiclass
           clus
vv          DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           29                           100
  STAGE III                          38                           102
  STAGE IV                           39                            96
[1] 4 2
[1] 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(6P25.3) MUTATED         25  48  21
  DEL PEAK 10(6P25.3) WILD-TYPE       98 147  37
D43V4, multiclass
          clus
vv         DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  T0+T1+T2                          25                            98
  T3                                48                           147
  T4                                21                            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                             N0  N1  N2  N3
  DEL PEAK 10(6P25.3) MUTATED    54   8  24   4
  DEL PEAK 10(6P25.3) WILD-TYPE 181  39  51   5
D43V5, multiclass
    clus
vv   DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  N0                          54                           181
  N1                           8                            39
  N2                          24                            51
  N3                           4                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    50   3
  DEL PEAK 10(6P25.3) WILD-TYPE 142   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     50    3
  DEL PEAK 10(6P25.3) WILD-TYPE  142    8
   clus
vv  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  0                          50                           142
  1                           3                             8
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    32  74
  DEL PEAK 10(6P25.3) WILD-TYPE  75 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     32   74
  DEL PEAK 10(6P25.3) WILD-TYPE   75  227
        clus
vv       DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  FEMALE                          32                            75
  MALE                            74                           227
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    99   2
  DEL PEAK 10(6P25.3) WILD-TYPE 265  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     99    2
  DEL PEAK 10(6P25.3) WILD-TYPE  265   17
     clus
vv    DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  NO                           99                           265
  YES                           2                            17
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
D43V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6P25.3) MUTATED       5                        10    87
  DEL PEAK 10(6P25.3) WILD-TYPE    38                        12   240
D43V12, multiclass
                           clus
vv                          DEL PEAK 10(6P25.3) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              87
                           clus
vv                          DEL PEAK 10(6P25.3) WILD-TYPE
  ASIAN                                                38
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED     4  95
  DEL PEAK 10(6P25.3) WILD-TYPE   5 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED      4   95
  DEL PEAK 10(6P25.3) WILD-TYPE    5  274
                        clus
vv                       DEL PEAK 10(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK 10(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           274
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 11(6Q21) MUTATION ANALYSIS
D44V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(6Q21) MUTATED   100  90
  DEL PEAK 11(6Q21) WILD-TYPE 129  87
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        190                         216 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                         90                          87 
$`DEL PEAK 11(6Q21) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       16.77        27.62         0.62        41.75        51.16        10.22 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD 
       19.04        26.14        14.89         5.06        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR 
        4.67         9.96        17.56        28.70         1.94        12.79 
TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 
       13.97        12.13        12.16        12.62         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I1 
       21.86        66.41        18.41        16.70        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IQ 
        7.79       142.78        87.32         4.80        13.58        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       50.27        21.30        66.05        17.98        64.18        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       36.66        38.24        15.02        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ 
       18.81        13.64        13.64        12.03        43.59        15.35 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME 
       38.83        22.16        25.58         0.56         4.24        24.03 
TCGA-E7-A7DV TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        1.22         8.09         8.94        24.30        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35        20.91        26.73 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.36         8.25        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TE 
       58.92         7.10         6.28        13.35         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES 
        3.06         4.31        31.07        11.08        59.31        33.01 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
       20.12        17.62        66.02        70.32        29.36        20.71 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R 
       14.07         0.49         8.94         2.10        10.92        18.97 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
        7.63         4.73        32.98         7.00        21.34        19.10 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
       20.28         8.48         8.58        19.07        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6FZ 
       38.60        64.01        21.24         2.76        11.70         1.81 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
       52.73        50.56        44.38        15.58        13.48        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        12.43        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       22.68        69.34       112.83        29.56        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58        97.45        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP 
       17.88        48.62        79.66         3.22        15.98        14.93 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 
        4.21        11.90        28.24        26.27         2.24         2.10 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ 
       54.90         7.63        91.73         8.32         6.77        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 
       56.48        86.30        75.39        11.97        13.64        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RN 
       25.41        21.11        21.86        28.41        94.29        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89        34.06        19.69        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       57.90        19.40        54.21        19.17 

$`DEL PEAK 11(6Q21) WILD-TYPE`
TCGA-2F-A9KP TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       11.97        44.94        16.83        17.16        34.98        50.04 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       66.54        15.12        47.80        29.65         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       13.15        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42E TCGA-BT-A42F 
        8.35         8.25        17.16        12.82        36.43        28.41 
TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
        8.98        23.01        12.56        12.59        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E 
       12.92         4.90        15.12        18.48        29.79        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        2.14        19.00       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       15.62         8.15         8.22        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       10.55       163.30        53.29        76.60        67.36        15.68 
TCGA-DK-AA6M TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
       52.01        19.00        15.35        56.15        11.18        20.32 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       29.72         0.10         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       26.24        24.66         0.92        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.32        14.37        32.02        16.77        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO 
       12.62        22.52        27.98        60.66        17.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS 
       25.74         7.56        14.96         3.62        15.58        53.88 
TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF 
        5.69         2.70        62.86        18.81        12.69         2.27 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        12.66        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94        21.40        15.81        19.13        15.91        17.75 
TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       24.92        13.91         7.73         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
        7.36        11.31        32.78        20.05         5.62        10.65 
TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND 
       14.27        19.82        36.49        27.35         1.51         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       12.16        25.02         3.45         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41P TCGA-KQ-A41Q 
       17.72        15.42        16.27        11.80        35.97        46.98 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78N 
        1.15        15.32        21.07        12.23        16.54        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PH 
       76.01        78.25         3.02         3.91         6.21        51.32 
TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SV 
      125.49        64.80        66.41        34.45         5.98        12.76 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 
       23.64        21.04        18.90        16.27        66.64        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMT 
       92.98        10.82       110.60        11.31        71.57         2.96 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        30.94        61.45        27.06        18.15         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       18.84         9.63         0.66        31.20        30.28        35.84 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM 
       13.41         3.48        64.08        58.72        88.87        47.84 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.61        59.38        60.16         8.52         5.52        12.23 

  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                       0.49                        0.10 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                     166.03                      163.30 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                     19.085                      15.600 
[1] "0.5 - 166.0 (19.1)" "0.1 - 163.3 (15.6)"
[1] "hr=" "1"  
D44V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q21) MUTATED         0       55        55       79
  DEL PEAK 11(6Q21) WILD-TYPE       2       74        85       56
D44V3, multiclass
           clus
vv          DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  STAGE I                           0                           2
  STAGE II                         55                          74
  STAGE III                        55                          85
  STAGE IV                         79                          56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 11(6Q21) MUTATED         54 97 24
  DEL PEAK 11(6Q21) WILD-TYPE       69 98 34
D44V4, multiclass
          clus
vv         DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                        54                          69
  T3                              97                          98
  T4                              24                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 11(6Q21) MUTATED    91  25  49   4
  DEL PEAK 11(6Q21) WILD-TYPE 144  22  26   5
D44V5, multiclass
    clus
vv   DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  N0                        91                         144
  N1                        25                          22
  N2                        49                          26
  N3                         4                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    84   2
  DEL PEAK 11(6Q21) WILD-TYPE 108   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     84    2
  DEL PEAK 11(6Q21) WILD-TYPE  108    9
   clus
vv  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  0                        84                         108
  1                         2                           9
[1] 2 2
[1] FALSE
D44V7, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    55 135
  DEL PEAK 11(6Q21) WILD-TYPE  52 166
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     55  135
  DEL PEAK 11(6Q21) WILD-TYPE   52  166
        clus
vv       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  FEMALE                        55                          52
  MALE                         135                         166
[1] 2 2
[1] FALSE
D44V8, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED   168   8
  DEL PEAK 11(6Q21) WILD-TYPE 196  11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED    168    8
  DEL PEAK 11(6Q21) WILD-TYPE  196   11
     clus
vv    DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  NO                        168                         196
  YES                         8                          11
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
D44V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q21) MUTATED      14                        11   154
  DEL PEAK 11(6Q21) WILD-TYPE    29                        11   173
D44V12, multiclass
                           clus
vv                          DEL PEAK 11(6Q21) MUTATED
  ASIAN                                            14
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                           154
                           clus
vv                          DEL PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              29
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED     7 169
  DEL PEAK 11(6Q21) WILD-TYPE   2 200
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED      7  169
  DEL PEAK 11(6Q21) WILD-TYPE    2  200
                        clus
vv                       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  HISPANIC OR LATINO                             7                           2
  NOT HISPANIC OR LATINO                       169                         200
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 12(6Q27) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q27) MUTATED   101  89
  DEL PEAK 12(6Q27) WILD-TYPE 128  88
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        190                         216 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                         89                          88 
$`DEL PEAK 12(6Q27) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q 
       24.13       104.65       108.95         8.35        16.27        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       17.16        27.62         0.62        41.75        51.16        10.22 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       19.04        26.14         5.06        16.18        20.48         4.67 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A3MI 
        9.96        28.70         1.94        12.79        12.13        12.16 
TCGA-CF-A47X TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 
       12.62        18.58        15.12         5.19         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       66.41        16.70       112.44        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ 
      142.78        87.32         4.80        13.58         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       50.27        21.30        66.05        17.98        64.18        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       36.66        38.24        15.02        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC 
       18.81        19.00        13.64        13.64        12.03        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DV 
       15.35        22.16         0.56         4.24        24.03         1.22 
TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       12.95         8.94        23.41        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       12.85        15.58        26.73        11.01        19.33         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        18.08        58.92         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       13.35        62.86         6.15        12.36         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY 
       31.07        11.08        59.31        33.01        20.12        17.62 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A4ZW 
       70.32        29.36        20.71        19.13        14.07         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 
        8.94         7.73         2.10        10.92        18.97         7.63 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        4.73        32.98         7.00        21.34        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       20.28         8.48        36.49         8.58        19.07        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R 
       19.40        38.60        64.01        25.02         2.76        27.68 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R 
       11.70         1.81        52.73        50.56        35.97        44.38 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       15.58        13.48        16.67        14.24         1.84        12.43 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD 
       38.99        17.62        37.05        22.68        69.34       112.83 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       29.56        17.82         6.21         3.85        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       97.45        97.12        15.35         1.87        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       79.66         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML 
       11.90        28.24        26.27         2.24        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN3 
       91.73         8.32         6.77        44.32        56.48        86.30 
TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
       75.39        11.97        13.64        22.36        25.41        21.11 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4X 
       21.86        28.41         2.89        34.06        19.69        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       35.41        57.90        19.40        19.17 

$`DEL PEAK 12(6Q27) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       11.97        94.88        44.94        16.83        34.98        50.04 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       66.54        15.12        47.80        29.65         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       40.08         7.33         2.66         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       13.15        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ TCGA-BT-A42B 
       14.96         8.35         8.25        17.16        12.82        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C 
       36.43        28.41         8.98        23.01        12.56        13.97 
TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.59        13.08        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL 
       11.87        13.08        12.92         4.90        18.48        29.79 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE 
       13.58         2.14        18.41        19.00       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.62        15.62         8.15        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       10.55       163.30        53.29        76.60        67.36        15.68 
TCGA-DK-AA6M TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4U1 
       52.01        15.35        56.15        11.18        20.32        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KF 
       29.72         0.10         2.24        16.70        25.58         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A7XN 
       26.96        26.24        24.66         0.92        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
       15.32        14.37         8.09        32.02        16.77        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43S 
       17.98         5.52        25.74         7.56        27.35        14.96 
TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A6TB 
       20.91         3.62        53.88         5.69         2.70        18.81 
TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.69         2.27         9.67        10.85        12.66        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       17.23         8.94         3.25        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3OO 
       26.93         7.23        66.02         6.94        21.40        15.81 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75        24.92        13.91         3.12        20.98 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        2.20         7.36        11.31        32.78        20.05         5.62 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE 
       10.65        14.27        27.35         1.51         9.01        12.16 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
        3.45        21.24         9.14         9.07        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       16.27        11.80        46.98         1.15        15.32        21.07 
TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       12.23        16.54        86.83        76.01        78.25         3.02 
TCGA-UY-A9PA TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU 
        3.91        51.32       125.49        64.80        66.41         5.98 
TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 
       12.76        23.64        21.04        18.90        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 
       71.57         2.96        98.99        30.94        61.45        27.06 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R3 
       18.15         3.88        18.84         9.63         0.66        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF 
       30.28        35.84        94.29        13.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        88.87        47.84        20.22         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       60.16        56.35         8.52        54.21         5.52        12.23 

  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                       0.49                        0.10 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                     166.03                      163.30 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                     18.985                      15.745 
[1] "0.5 - 166.0 (19.0)" "0.1 - 163.3 (15.7)"
[1] "hr=" "1"  
D45V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(6Q27) MUTATED         0       51        58       80
  DEL PEAK 12(6Q27) WILD-TYPE       2       78        82       55
D45V3, multiclass
           clus
vv          DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  STAGE I                           0                           2
  STAGE II                         51                          78
  STAGE III                        58                          82
  STAGE IV                         80                          55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2 T3 T4
  DEL PEAK 12(6Q27) MUTATED         50 98 26
  DEL PEAK 12(6Q27) WILD-TYPE       73 97 32
D45V4, multiclass
          clus
vv         DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  T0+T1+T2                        50                          73
  T3                              98                          97
  T4                              26                          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                           N0  N1  N2  N3
  DEL PEAK 12(6Q27) MUTATED    93  23  50   5
  DEL PEAK 12(6Q27) WILD-TYPE 142  24  25   4
D45V5, multiclass
    clus
vv   DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  N0                        93                         142
  N1                        23                          24
  N2                        50                          25
  N3                         5                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED    84   3
  DEL PEAK 12(6Q27) WILD-TYPE 108   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED     84    3
  DEL PEAK 12(6Q27) WILD-TYPE  108    8
   clus
vv  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  0                        84                         108
  1                         3                           8
[1] 2 2
[1] FALSE
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED    48 142
  DEL PEAK 12(6Q27) WILD-TYPE  59 159
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED     48  142
  DEL PEAK 12(6Q27) WILD-TYPE   59  159
        clus
vv       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  FEMALE                        48                          59
  MALE                         142                         159
[1] 2 2
[1] FALSE
D45V8, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED   169   7
  DEL PEAK 12(6Q27) WILD-TYPE 195  12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED    169    7
  DEL PEAK 12(6Q27) WILD-TYPE  195   12
     clus
vv    DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  NO                        169                         195
  YES                         7                          12
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, continuous
D45V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q27) MUTATED      15                        11   154
  DEL PEAK 12(6Q27) WILD-TYPE    28                        11   173
D45V12, multiclass
                           clus
vv                          DEL PEAK 12(6Q27) MUTATED
  ASIAN                                            15
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                           154
                           clus
vv                          DEL PEAK 12(6Q27) WILD-TYPE
  ASIAN                                              28
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             173
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED     6 168
  DEL PEAK 12(6Q27) WILD-TYPE   3 201
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED      6  168
  DEL PEAK 12(6Q27) WILD-TYPE    3  201
                        clus
vv                       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             6                           3
  NOT HISPANIC OR LATINO                       168                         201
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 13(7Q36.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7Q36.3) MUTATED    39  21
  DEL PEAK 13(7Q36.3) WILD-TYPE 190 156
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           60                           346 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           21                           156 
$`DEL PEAK 13(7Q36.3) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-BL-A13J TCGA-BT-A20N TCGA-BT-A20X TCGA-CF-A1HS 
        8.35        17.16         2.66        26.14         8.25        12.56 
TCGA-CF-A47X TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA77 
       12.62       142.78         4.80         8.15        15.02        20.32 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A97P TCGA-FD-A3N6 TCGA-FD-A3NA 
       15.35        38.83        24.03        14.37        27.98        60.66 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TE TCGA-FD-A6TF 
        8.25        27.45        18.08        62.86        12.36         2.27 
TCGA-FJ-A3ZF TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW 
       17.23        20.71        19.13        14.07        24.92         0.49 
TCGA-GC-A6I1 TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ 
        8.94         7.63         5.62        10.65        32.98         7.00 
TCGA-GV-A3QI TCGA-K4-A3WS TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-KQ-A41N 
       36.49        25.02         9.07        11.70        15.42        52.73 
TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A8OB 
       46.98        15.32        15.58        12.23        16.67        69.34 
TCGA-XF-A8HD TCGA-XF-A9SM TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMZ 
       97.45        34.45       110.60         7.63         2.96        44.32 
TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4W 
       13.64        94.29        64.08        88.87        47.84        60.16 

$`DEL PEAK 13(7Q36.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       24.13        11.97        94.88       104.65       108.95        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        16.77        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        40.08         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35        17.16        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
        9.96        17.56        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
        1.94        23.01        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       13.08        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
       18.48         5.19        29.79         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        7.79        87.32        13.58         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        23.21         9.67        20.81        10.55       163.30 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       66.05        17.98        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q 
       15.68        50.70        36.66        38.24        52.01        13.58 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
      165.73       166.03        18.81        19.00        13.64        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
       13.64        56.15        11.18        12.03        43.59        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU 
        0.66        26.96        26.24         4.24        24.66         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97Q 
        1.22        13.68        14.07        12.95        15.32         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       22.52        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
       25.74        46.78        19.79        12.85         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62N 
       11.01        19.33         5.36         5.69        58.92         2.70 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        7.10         6.28        13.35        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65         8.94         3.25        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       17.62        66.02         6.94        70.32        29.36        21.40 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.81        15.91        17.75        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q 
        3.12        20.98         2.20         7.36        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
       18.97        32.78        20.05         4.73        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40E 
       19.10        19.82        20.28         8.48        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.07        22.72         1.51        19.40        38.60        64.01 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01        12.16         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O 
       27.68        17.72         1.81        16.27        11.80        50.56 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT TCGA-MV-A51V TCGA-R3-A69X 
       35.97        44.38         1.15        21.07        13.48        14.24 
TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
        1.84        16.54        12.43        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       22.68        86.83        76.01        78.25         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
        3.91        29.56        17.82         6.21         3.85        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
       45.04         6.58       125.49        97.12        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
       17.88        48.62        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       66.41        14.93         4.21         5.98        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       16.27        66.64         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
       11.31        54.90        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        56.48        30.94        61.45        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.15         3.88        18.84         9.63         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
       11.97        22.36        25.41        21.11        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41         3.48        58.72 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       63.02        56.35        35.41        57.90        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       54.21        19.17         5.52        12.23 

  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       142.78                        166.03 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       16.915                        17.490 
[1] "0.5 - 142.8 (16.9)" "0.1 - 166.0 (17.5)"
[1] "hr=" "1.4"
D46V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(7Q36.3) MUTATED         0       17        24       19
  DEL PEAK 13(7Q36.3) WILD-TYPE       2      112       116      116
D46V3, multiclass
           clus
vv          DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           17                           112
  STAGE III                          24                           116
  STAGE IV                           19                           116
[1] 4 2
[1] 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(7Q36.3) MUTATED         15  33   8
  DEL PEAK 13(7Q36.3) WILD-TYPE      108 162  50
D46V4, multiclass
          clus
vv         DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  T0+T1+T2                          15                           108
  T3                                33                           162
  T4                                 8                            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                             N0  N1  N2  N3
  DEL PEAK 13(7Q36.3) MUTATED    36   4  14   0
  DEL PEAK 13(7Q36.3) WILD-TYPE 199  43  61   9
D46V5, multiclass
    clus
vv   DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  N0                          36                           199
  N1                           4                            43
  N2                          14                            61
  N3                           0                             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"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    20   1
  DEL PEAK 13(7Q36.3) WILD-TYPE 172  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     20    1
  DEL PEAK 13(7Q36.3) WILD-TYPE  172   10
   clus
vv  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  0                          20                           172
  1                           1                            10
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    13  47
  DEL PEAK 13(7Q36.3) WILD-TYPE  94 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     13   47
  DEL PEAK 13(7Q36.3) WILD-TYPE   94  254
        clus
vv       DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  FEMALE                          13                            94
  MALE                            47                           254
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    56   1
  DEL PEAK 13(7Q36.3) WILD-TYPE 308  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     56    1
  DEL PEAK 13(7Q36.3) WILD-TYPE  308   18
     clus
vv    DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  NO                           56                           308
  YES                           1                            18
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
D46V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q36.3) MUTATED       4                         3    50
  DEL PEAK 13(7Q36.3) WILD-TYPE    39                        19   277
D46V12, multiclass
                           clus
vv                          DEL PEAK 13(7Q36.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              50
                           clus
vv                          DEL PEAK 13(7Q36.3) WILD-TYPE
  ASIAN                                                39
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               277
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED     3  55
  DEL PEAK 13(7Q36.3) WILD-TYPE   6 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED      3   55
  DEL PEAK 13(7Q36.3) WILD-TYPE    6  314
                        clus
vv                       DEL PEAK 13(7Q36.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          55
                        clus
vv                       DEL PEAK 13(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           314
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED   139 102
  DEL PEAK 14(8P23.3) WILD-TYPE  90  75
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          241                           165 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          102                            75 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        16.77        17.16        27.62         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J 
       51.16        10.22        47.80         2.50        40.08         2.66 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PJ TCGA-BT-A3PK 
       19.04         5.06         8.35        16.18        12.82         9.96 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HS 
       28.70        36.43        28.41         8.98         1.94        12.56 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR 
       13.97        10.95        11.34        11.87        12.92        15.12 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC 
       18.48         5.19        21.86         2.14        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
      112.44        46.68        17.95       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.15         8.22        17.72        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
        9.67        64.18        15.68        50.70        38.24        52.01 
TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 
       15.02       165.73       166.03        19.00        13.64        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ 
       12.03        20.32        15.35        38.83        29.72        22.16 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7DU TCGA-E7-A7DV 
       25.58         0.56        26.96         4.24         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       13.68        14.37         8.09        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
        4.01        22.52        24.30        23.41        17.98         5.52 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
       25.74        19.79         7.56        27.35        15.58        26.73 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N 
       19.33         5.69         8.25        27.45        18.08         2.70 
TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        6.28        13.35        62.86         6.15        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.27         4.31        10.85        31.07        12.66        10.65 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-A3VY 
       17.23        11.08        61.94        15.95        20.12        17.62 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        70.32        29.36        19.13        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       17.75        24.92         0.49        13.91         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 
        3.12        20.98         2.20         7.36        10.92         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX 
       20.05         5.62         4.73        10.65        32.98        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ 
       19.82         8.48         8.58        19.07        22.72        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       64.01         9.01        12.16        25.02         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76         9.14        27.68        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R 
       16.27        11.80        52.73        35.97        46.98        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X 
       15.32        15.58        21.07        13.48        16.67        14.24 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        38.99        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD 
       76.01        69.34         3.02       112.83        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HG 
        6.21         3.85        51.32        45.04         6.58        15.35 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
        1.87        48.62        79.66         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 
       14.93         4.21         5.98        12.76        11.90        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
        2.24        66.64       110.60        54.90         7.63        71.57 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 
        2.96         8.32         6.77        98.99        56.48        61.45 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R4 
       75.39        18.15        18.84        22.36        25.41        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN 
       94.29        13.41         3.48        64.08        88.87        20.22 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       34.06        19.69         8.61        59.38        60.16        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        57.90         8.52        54.21        19.17 
TCGA-ZF-AA5P 
       12.23 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA84 
       94.88        44.94        34.98        50.04        66.54        15.12 
TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 
       29.65        17.42         7.33         6.74        12.39         6.58 
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       13.15        26.14        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.25        17.16        20.48         4.67 
TCGA-BT-A42B TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       17.56        23.01        12.79        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       12.16        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FL TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA 
        4.90        29.79         1.84        13.58        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IS 
       16.70        16.14        17.62        15.62         7.79        50.27 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW 
       20.81        10.55       163.30        66.05        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       76.60        67.36        36.66        13.58        18.81        15.35 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       13.64        56.15        43.59         0.10         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
        0.66        26.24        24.03        24.66        14.07        12.95 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SN 
       15.32        32.02        12.62        27.98        60.66        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS 
       46.78        12.85        14.96        20.91         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TG 
       11.01         5.36        58.92         7.10        18.81         3.06 
TCGA-FD-A6TI TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        9.67         8.94         3.25        48.00        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       33.01         7.23        66.02        21.40        20.71        15.81 
TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3JV 
        8.94        11.31        18.97        32.78         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE 
       21.34        20.28        36.49        27.35         1.51        38.60 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-KQ-A41O TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-S5-A6DX 
        9.07        11.70        50.56         1.15        12.23         1.84 
TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A9PA TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       16.54        78.25         3.91        97.45       125.49        97.12 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       17.88        64.80        66.41        23.64        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
       11.31        91.73        44.32        30.94        86.30        27.06 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 
        3.88         9.63         0.66        11.97        13.64        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RM 
       31.20        35.84        21.86        28.41        58.72        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA54 TCGA-ZF-AA5N 
        2.89        19.40         5.52 

  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       166.03                        163.30 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                        17.23                         17.16 
[1] "0.5 - 166.0 (17.2)" "0.1 - 163.3 (17.2)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(8P23.3) MUTATED         1       74        74       92
  DEL PEAK 14(8P23.3) WILD-TYPE       1       55        66       43
D47V3, multiclass
           clus
vv          DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           74                            55
  STAGE III                          74                            66
  STAGE IV                           92                            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                            T0+T1+T2  T3  T4
  DEL PEAK 14(8P23.3) MUTATED         71 112  37
  DEL PEAK 14(8P23.3) WILD-TYPE       52  83  21
D47V4, multiclass
          clus
vv         DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  T0+T1+T2                          71                            52
  T3                               112                            83
  T4                                37                            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                             N0  N1  N2  N3
  DEL PEAK 14(8P23.3) MUTATED   125  35  48   7
  DEL PEAK 14(8P23.3) WILD-TYPE 110  12  27   2
D47V5, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  N0                         125                           110
  N1                          35                            12
  N2                          48                            27
  N3                           7                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED   104   8
  DEL PEAK 14(8P23.3) WILD-TYPE  88   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED    104    8
  DEL PEAK 14(8P23.3) WILD-TYPE   88    3
   clus
vv  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  0                         104                            88
  1                           8                             3
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED    61 181
  DEL PEAK 14(8P23.3) WILD-TYPE  46 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     61  181
  DEL PEAK 14(8P23.3) WILD-TYPE   46  120
        clus
vv       DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  FEMALE                          61                            46
  MALE                           181                           120
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED   215   9
  DEL PEAK 14(8P23.3) WILD-TYPE 149  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED    215    9
  DEL PEAK 14(8P23.3) WILD-TYPE  149   10
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  NO                          215                           149
  YES                           9                            10
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, continuous
D47V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.3) MUTATED      17                        18   198
  DEL PEAK 14(8P23.3) WILD-TYPE    26                         4   129
D47V12, multiclass
                           clus
vv                          DEL PEAK 14(8P23.3) MUTATED
  ASIAN                                              17
  BLACK OR AFRICAN AMERICAN                          18
  WHITE                                             198
                           clus
vv                          DEL PEAK 14(8P23.3) WILD-TYPE
  ASIAN                                                26
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                               129
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     5 219
  DEL PEAK 14(8P23.3) WILD-TYPE   4 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      5  219
  DEL PEAK 14(8P23.3) WILD-TYPE    4  150
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         219
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           150
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 15(8P21.3) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P21.3) MUTATED   148 103
  DEL PEAK 15(8P21.3) WILD-TYPE  81  74
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          251                           155 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          103                            74 
$`DEL PEAK 15(8P21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.77        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BL-A0C8 
       15.12        10.22        47.80        29.65         2.50        40.08 
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD 
        2.66        19.04         5.06         8.35        16.18        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        28.70        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A8HX 
        1.94        12.56        13.97        12.16        10.95        11.34 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.87        12.92        18.48         5.19        29.79 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2HX 
       21.86         2.14        18.41       130.88       112.44        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95       142.78        87.32         4.80        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV 
        8.22        17.72        21.30        23.21         9.67        64.18 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R 
       15.68        50.70        38.24        52.01        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
      166.03        19.00        13.64        11.18        12.03        20.32 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       15.35        38.83        29.72        22.16        25.58         0.56 
TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H 
       26.96         4.24         0.92         1.22        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       14.37         8.09        16.77         8.94        33.04         4.01 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        19.79        12.85         7.56        27.35 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       15.58        26.73        19.33         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC 
       18.08         2.70         6.28        13.35        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.69        12.36         2.27         4.31        10.85        31.07 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EK 
       12.66        10.65        17.23        11.08        61.94        15.95 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       20.12        17.62        66.02         6.94        70.32        29.36 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW 
       19.13        15.91        14.07        17.75        24.92         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A76B TCGA-GU-A42P 
       13.91         7.73         2.10         3.12         7.36        10.92 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       18.97         7.63        20.05         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       32.98        21.34        19.10        19.82        20.28         8.48 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.58        19.07        22.72        19.40        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       12.16        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       27.68         9.07        17.72         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LC-A66R 
       11.80        52.73        35.97        46.98        44.38        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       15.58        21.07        13.48        12.23        16.67        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
        1.84        12.43        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD 
       76.01        69.34         3.02       112.83        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HG 
        6.21         3.85        51.32        45.04         6.58        15.35 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
        1.87        48.62        79.66         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 
       14.93         4.21        12.76        11.90        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT 
       66.64       110.60        54.90         7.63        71.57         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN5 
        8.32         6.77        98.99        56.48        61.45        75.39 
TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
       18.84        22.36        25.41        30.28        21.86        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T 
        3.48        64.08        88.87        20.22        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        63.02        56.35        35.41 
TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90         8.52        54.21        19.17        12.23 

$`DEL PEAK 15(8P21.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       94.88        44.94        16.83        34.98        50.04        66.54 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42         7.33         6.74        12.39         6.58        13.15 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       26.14        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F6 
       14.96         8.25        17.16         4.67        17.56        23.01 
TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47T TCGA-CF-A47V 
       12.79        12.59        12.13        13.08        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.10        12.62        12.26        13.12        12.00        12.10 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A5W6 TCGA-CU-A72E 
       18.58        13.08         4.90        15.12         1.84        13.58 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        19.00        16.70        16.14        17.62        15.62 
TCGA-DK-A2I2 TCGA-DK-A3IS TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
        7.79        50.27        20.81        10.55       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6Q 
       17.98        53.29        76.60        67.36        36.66        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3Y1 
       18.81        15.35        13.64        56.15        43.59         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
        2.24        16.70         0.66        26.24        24.03        24.66 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SQ 
       14.07        15.32        32.02        12.62        27.98        46.78 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
       14.96        20.91         3.62        53.88        11.01         5.36 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A871 
       58.92         7.10        18.81         3.06         9.67         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
        3.25        48.00        26.93        59.31        33.01         7.23 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 
       21.40        20.71        15.81         8.94        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-GV-A3QK 
       11.31        32.78         7.00        14.27        36.49        27.35 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A5RI TCGA-KQ-A41O TCGA-KQ-A41S TCGA-S5-AA26 
        1.51        38.60        11.70        50.56         1.15        16.54 
TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A9PA TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       86.83        78.25         3.91        97.45       125.49        97.12 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SY 
       17.88        64.80        66.41         5.98        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       28.24        18.90        16.27         2.10        13.74        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       10.82        11.31        91.73        44.32        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       27.06        18.15         3.88         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       13.64        21.11        31.20        35.84        28.41        94.29 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA54 TCGA-ZF-AA5N 
       58.72        47.84         2.89        19.40         5.52 

  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                       166.03                        163.30 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                        17.62                         16.83 
[1] "0.5 - 166.0 (17.6)" "0.1 - 163.3 (16.8)"
[1] "hr=" "1.1"
D48V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(8P21.3) MUTATED         1       79        76       95
  DEL PEAK 15(8P21.3) WILD-TYPE       1       50        64       40
D48V3, multiclass
           clus
vv          DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           79                            50
  STAGE III                          76                            64
  STAGE IV                           95                            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                            T0+T1+T2  T3  T4
  DEL PEAK 15(8P21.3) MUTATED         74 114  42
  DEL PEAK 15(8P21.3) WILD-TYPE       49  81  16
D48V4, multiclass
          clus
vv         DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  T0+T1+T2                          74                            49
  T3                               114                            81
  T4                                42                            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                             N0  N1  N2  N3
  DEL PEAK 15(8P21.3) MUTATED   132  33  51   8
  DEL PEAK 15(8P21.3) WILD-TYPE 103  14  24   1
D48V5, multiclass
    clus
vv   DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  N0                         132                           103
  N1                          33                            14
  N2                          51                            24
  N3                           8                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED   110   9
  DEL PEAK 15(8P21.3) WILD-TYPE  82   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED    110    9
  DEL PEAK 15(8P21.3) WILD-TYPE   82    2
   clus
vv  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  0                         110                            82
  1                           9                             2
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED    62 190
  DEL PEAK 15(8P21.3) WILD-TYPE  45 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED     62  190
  DEL PEAK 15(8P21.3) WILD-TYPE   45  111
        clus
vv       DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  FEMALE                          62                            45
  MALE                           190                           111
[1] 2 2
[1] FALSE
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED   224  10
  DEL PEAK 15(8P21.3) WILD-TYPE 140   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED    224   10
  DEL PEAK 15(8P21.3) WILD-TYPE  140    9
     clus
vv    DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  NO                          224                           140
  YES                          10                             9
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
D48V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P21.3) MUTATED      20                        17   206
  DEL PEAK 15(8P21.3) WILD-TYPE    23                         5   121
D48V12, multiclass
                           clus
vv                          DEL PEAK 15(8P21.3) MUTATED
  ASIAN                                              20
  BLACK OR AFRICAN AMERICAN                          17
  WHITE                                             206
                           clus
vv                          DEL PEAK 15(8P21.3) WILD-TYPE
  ASIAN                                                23
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED     6 227
  DEL PEAK 15(8P21.3) WILD-TYPE   3 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED      6  227
  DEL PEAK 15(8P21.3) WILD-TYPE    3  142
                        clus
vv                       DEL PEAK 15(8P21.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         227
                        clus
vv                       DEL PEAK 15(8P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           142
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 16(9P23) MUTATION ANALYSIS
D49V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(9P23) MUTATED   104  73
  DEL PEAK 16(9P23) WILD-TYPE 125 104
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        177                         229 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                         73                         104 
$`DEL PEAK 16(9P23) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       11.97        94.88       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-5N-A9KM TCGA-BL-A0C8 
       16.83        34.98        50.04         0.62        17.42        40.08 
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A20T 
        2.66        13.15        19.04        26.14        19.50        14.89 
TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E 
        8.35        17.16        16.18         9.96        28.70        36.43 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
        1.94        12.79        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF 
       12.16        12.62        13.12        12.00        11.34        11.87 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       18.58         4.90        18.48        29.79         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       21.86        19.00        16.70        17.62        15.62        17.95 
TCGA-DK-A3IK TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX 
        4.80         8.22        17.72        50.27        21.30        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P 
       66.05        17.98        64.18        15.68        50.70        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       166.03        19.00        13.64        15.35        13.64 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       11.18        12.03        20.32        43.59        38.83        29.72 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7DU TCGA-E7-A7PW 
       25.58         0.56         0.66         4.24         0.92        13.68 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        8.09        16.77         8.94        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BZ 
       19.79        12.85         7.56        26.73         5.36        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       18.08        58.92         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EJ 
       18.81         3.06        10.85        10.65        11.08        48.00 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F 
       59.31         7.23        17.62        66.02        70.32        29.36 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       14.07        24.92         8.94         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
        7.36        11.31         7.63         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-H4-A2HQ 
        7.00        21.34         8.48        27.35        22.72        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       38.60        64.01        25.02         3.45        21.24         2.76 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P 
        9.07        11.70        15.42        11.80        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       46.98        44.38         1.15        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A8OB TCGA-UY-A8OD 
       14.24         1.84        16.54        38.99        69.34       112.83 
TCGA-UY-A9PE TCGA-XF-A8HI TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
        6.21        17.88        15.98         4.21         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T4 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX 
       11.90        26.27        16.27        71.57        91.73         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R1 
       98.99        44.32        30.94        18.15        11.97        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4U 
       21.11        28.41        94.29         3.48        88.87         8.61 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       56.35        19.40         8.52 

$`DEL PEAK 16(9P23) WILD-TYPE`
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA81 
       24.13        44.94        16.77        17.16        27.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 
       51.16        66.54        15.12        10.22        47.80        29.65 
TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O 
        2.50         7.33         6.74        12.39         6.58        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD 
       17.88         5.06        14.96         5.06         8.25        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
        4.67        12.82        17.56        28.41         8.98        23.01 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.56        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU 
       12.10        11.34        13.08        12.92        15.12         5.19 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
        2.14        66.41        18.41       130.88       112.44        16.14 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM 
       46.68         7.79       142.78        87.32        13.58         8.15 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        20.81       163.30        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6T 
       67.36        36.66        38.24        52.01       165.73        18.81 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       56.15        15.35         0.10        22.16         2.24        16.70 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN 
       26.96        26.24        24.03        24.66         1.22        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 
       12.95        15.32        14.37        32.02        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X 
        5.52        25.74        27.35        14.96        20.91         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        53.88        11.01        19.33         5.69         8.25 
TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        2.70         6.15        12.69        12.36         2.27         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE 
        9.67        31.07        12.66        17.23         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3C 
       61.94        15.95        26.93        33.01        20.12         6.94 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC 
       21.40        20.71        15.81        19.13        15.91        17.75 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A42R 
        0.49        13.91         7.73         2.10        10.92        18.97 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ 
       32.78        20.05         5.62        14.27        19.10        19.82 
TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND 
       20.28        36.49         8.58        19.07         1.51         9.01 
TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       12.16         9.14        27.68        17.72         1.81        16.27 
TCGA-KQ-A41N TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G0 TCGA-UY-A78K 
       52.73        15.32        15.58        13.48        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       37.05        22.68        86.83        76.01        78.25         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
        3.91        29.56        17.82         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH 
        6.58        97.45       125.49        97.12        15.35         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM 
       48.62        64.80        79.66         3.22        66.41        34.45 
TCGA-XF-A9SP TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 
       14.93        23.64        21.04        28.24        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       11.31        54.90         7.63         2.96         8.32        56.48 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       61.45        86.30        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R4 
        9.63         0.66        13.64        22.36        31.20        30.28 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       35.84        21.86        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W 
       20.22         2.89        34.06        19.69        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       63.02        35.41        57.90        54.21        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                       0.56                        0.10 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                     166.03                      165.73 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                      16.54                       17.82 
[1] "0.6 - 166.0 (16.5)" "0.1 - 165.7 (17.8)"
[1] "hr=" "1"  
D49V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(9P23) MUTATED         1       56        65       55
  DEL PEAK 16(9P23) WILD-TYPE       1       73        75       80
D49V3, multiclass
           clus
vv          DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  STAGE I                           1                           1
  STAGE II                         56                          73
  STAGE III                        65                          75
  STAGE IV                         55                          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"
                             vv
clus                          T0+T1+T2  T3  T4
  DEL PEAK 16(9P23) MUTATED         52  86  26
  DEL PEAK 16(9P23) WILD-TYPE       71 109  32
D49V4, multiclass
          clus
vv         DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  T0+T1+T2                        52                          71
  T3                              86                         109
  T4                              26                          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                           N0  N1  N2  N3
  DEL PEAK 16(9P23) MUTATED   108  18  33   4
  DEL PEAK 16(9P23) WILD-TYPE 127  29  42   5
D49V5, multiclass
    clus
vv   DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  N0                       108                         127
  N1                        18                          29
  N2                        33                          42
  N3                         4                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    87   5
  DEL PEAK 16(9P23) WILD-TYPE 105   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     87    5
  DEL PEAK 16(9P23) WILD-TYPE  105    6
   clus
vv  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  0                        87                         105
  1                         5                           6
[1] 2 2
[1] FALSE
D49V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    48 130
  DEL PEAK 16(9P23) WILD-TYPE  59 171
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     48  130
  DEL PEAK 16(9P23) WILD-TYPE   59  171
        clus
vv       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  FEMALE                        48                          59
  MALE                         130                         171
[1] 2 2
[1] FALSE
D49V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED   160  10
  DEL PEAK 16(9P23) WILD-TYPE 204   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED    160   10
  DEL PEAK 16(9P23) WILD-TYPE  204    9
     clus
vv    DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  NO                        160                         204
  YES                        10                           9
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
D49V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P23) MUTATED      18                        10   141
  DEL PEAK 16(9P23) WILD-TYPE    25                        12   186
D49V12, multiclass
                           clus
vv                          DEL PEAK 16(9P23) MUTATED
  ASIAN                                            18
  BLACK OR AFRICAN AMERICAN                        10
  WHITE                                           141
                           clus
vv                          DEL PEAK 16(9P23) WILD-TYPE
  ASIAN                                              25
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             186
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED     4 162
  DEL PEAK 16(9P23) WILD-TYPE   5 207
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED      4  162
  DEL PEAK 16(9P23) WILD-TYPE    5  207
                        clus
vv                       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           5
  NOT HISPANIC OR LATINO                       162                         207
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 17(9P21.3) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9P21.3) MUTATED   133 105
  DEL PEAK 17(9P21.3) WILD-TYPE  96  72
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          238                           168 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          105                            72 
$`DEL PEAK 17(9P21.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.27        16.83        34.98        27.62        50.04         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       51.16        29.65        17.42        40.08         7.33         2.66 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        26.14        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X 
       19.50        14.89        14.96         5.06         8.35         8.25 
TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F0 
       16.18         9.96        17.56        28.70        36.43         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        12.79        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.16        12.66        12.62        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ 
       11.34        11.34        11.87        18.58         4.90        18.48 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA 
       29.79         1.84        13.58        21.86         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK 
       16.70        16.14        17.62        15.62        17.95         4.80 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX 
        8.22        17.72        50.27        21.30        20.81        10.55 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6P 
       66.05        17.98        64.18        15.68        50.70        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       166.03        19.00        13.64        15.35        13.64 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       11.18        12.03        20.32        43.59        38.83        29.72 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7DU 
       25.58         0.56         0.66        26.96         4.24         0.92 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 
       13.68        12.95        15.32        14.37         8.09         8.94 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       27.98        60.66        17.98        29.16        25.74        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y 
       19.79        12.85         7.56        20.91         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       26.73        19.33         5.36         5.69        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       58.92         7.10         6.28        13.35        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A871 
       12.69         3.06        10.85        31.07        10.65         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       11.08        61.94        59.31         7.23        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD 
       66.02         6.94        70.32        29.36        21.40        14.07 
TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       24.92         8.94        13.91         3.12        20.98         2.20 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A767 
        7.36        11.31        18.97         7.63        32.78         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QF TCGA-GV-A3QH 
       10.65        32.98         7.00        21.34        20.28         8.48 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       27.35         8.58        22.72        19.40        38.60        64.01 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01        25.02         3.45        21.24         2.76         9.14 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P 
        9.07        11.70        15.42        11.80        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       46.98        44.38         1.15        21.07        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78P 
       14.24         1.84        16.54        38.99        22.68        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH 
       69.34         3.02       112.83        17.82         6.21        51.32 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HI TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SU 
      125.49        97.12        17.88        15.98         4.21         5.98 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMQ 
       12.76        11.90        26.27        66.64        13.74        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       91.73         2.96         8.32         6.77        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3L 
       30.94        86.30        75.39        18.15         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        21.11        31.20        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W 
       94.29         3.48        88.87        20.22         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 
       56.35        57.90        19.40         8.52 

$`DEL PEAK 17(9P21.3) WILD-TYPE`
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 
       44.94        16.77        17.16        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A3JM TCGA-BT-A20O TCGA-BT-A20R 
       10.22        47.80         2.50         6.74        12.16         5.06 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42F TCGA-C4-A0EZ 
       17.16        20.48         4.67        12.82        28.41         8.98 
TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A9FM 
       12.56        10.95        12.46        12.10        12.26        13.08 
TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC 
       12.92        15.12         5.19        66.41        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL 
      112.44        46.68         7.79       142.78        87.32        13.58 
TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WY TCGA-DK-A6AW TCGA-DK-A6B0 
        8.15        23.21         9.67       163.30        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6T 
       67.36        36.66        38.24        52.01       165.73        18.81 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       56.15        15.35         0.10        22.16         2.24        16.70 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-FD-A3B3 
       26.24        24.03        24.66         1.22        14.07        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       16.77        33.04         4.01        12.62        22.52        24.30 
TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A5BS TCGA-FD-A5BT 
       23.41         5.52        27.35        14.96        53.88        11.01 
TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        8.25         2.70         6.15        12.36         2.27         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK 
        9.67        12.66        17.23         3.25        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2ES TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       26.93        33.01        20.71        15.81        19.13        15.91 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42P TCGA-GU-A764 
       17.75         0.49         7.73         2.10        10.92        20.05 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QI TCGA-GV-A40G 
        5.62        14.27        19.10        19.82        36.49        19.07 
TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
        1.51        12.16        27.68        17.72         1.81        16.27 
TCGA-KQ-A41N TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G0 TCGA-UY-A78K 
       52.73        15.32        15.58        13.48        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF 
       37.05        86.83        76.01         3.91        29.56         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG 
       45.04         6.58        97.45        15.35         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       64.80        79.66         3.22        66.41        34.45        14.93 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        28.24        18.90         2.24        16.27 
TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.10        92.98        10.82       110.60        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
        7.63        56.48        61.45        27.06         3.88        18.84 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF 
        9.63        13.64        30.28        35.84        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       58.72        47.84         2.89        34.06        19.69        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       63.02        35.41        54.21        19.17         5.52        12.23 

  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                         0.56                          0.10 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       166.03                        165.73 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                       16.765                        17.425 
[1] "0.6 - 166.0 (16.8)" "0.1 - 165.7 (17.4)"
[1] "hr=" "1.1"
D50V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(9P21.3) MUTATED         1       77        85       75
  DEL PEAK 17(9P21.3) WILD-TYPE       1       52        55       60
D50V3, multiclass
           clus
vv          DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           77                            52
  STAGE III                          85                            55
  STAGE IV                           75                            60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1+T2  T3  T4
  DEL PEAK 17(9P21.3) MUTATED         72 113  36
  DEL PEAK 17(9P21.3) WILD-TYPE       51  82  22
D50V4, multiclass
          clus
vv         DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  T0+T1+T2                          72                            51
  T3                               113                            82
  T4                                36                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 17(9P21.3) MUTATED   142  26  42   4
  DEL PEAK 17(9P21.3) WILD-TYPE  93  21  33   5
D50V5, multiclass
    clus
vv   DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  N0                         142                            93
  N1                          26                            21
  N2                          42                            33
  N3                           4                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED   116   6
  DEL PEAK 17(9P21.3) WILD-TYPE  76   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED    116    6
  DEL PEAK 17(9P21.3) WILD-TYPE   76    5
   clus
vv  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  0                         116                            76
  1                           6                             5
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED    66 173
  DEL PEAK 17(9P21.3) WILD-TYPE  41 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED     66  173
  DEL PEAK 17(9P21.3) WILD-TYPE   41  128
        clus
vv       DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  FEMALE                          66                            41
  MALE                           173                           128
[1] 2 2
[1] FALSE
D50V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED   215  13
  DEL PEAK 17(9P21.3) WILD-TYPE 149   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED    215   13
  DEL PEAK 17(9P21.3) WILD-TYPE  149    6
     clus
vv    DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  NO                          215                           149
  YES                          13                             6
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, continuous
D50V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9P21.3) MUTATED      26                        14   188
  DEL PEAK 17(9P21.3) WILD-TYPE    17                         8   139
D50V12, multiclass
                           clus
vv                          DEL PEAK 17(9P21.3) MUTATED
  ASIAN                                              26
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             188
                           clus
vv                          DEL PEAK 17(9P21.3) WILD-TYPE
  ASIAN                                                17
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED     4 218
  DEL PEAK 17(9P21.3) WILD-TYPE   5 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED      4  218
  DEL PEAK 17(9P21.3) WILD-TYPE    5  151
                        clus
vv                       DEL PEAK 17(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         218
                        clus
vv                       DEL PEAK 17(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           151
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 18(9Q22.33) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(9Q22.33) MUTATED   105  72
  DEL PEAK 18(9Q22.33) WILD-TYPE 124 105
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                           177                            229 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                            72                            105 
$`DEL PEAK 18(9Q22.33) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.27        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA83 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20P 
       66.54        29.65        17.42         6.58        26.14        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0F6 
       19.50        14.89        16.18        20.48        28.70        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       12.79        13.97        12.59        12.13        13.08        10.95 
TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.46        12.62        13.12        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       18.58        13.08         4.90        18.48         5.19         1.84 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AF 
       13.58         2.14        66.41        19.00       112.44        17.62 
TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3WX TCGA-DK-A3X2 
       15.62        17.72        50.27        21.30        10.55        17.98 
TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X 
       64.18        50.70        15.02        19.00        13.64        15.35 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       11.18        12.03        20.32        43.59        38.83        29.72 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7DU 
       16.70        25.58         0.56         0.66         4.24         0.92 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        1.22        13.68         8.09         8.94        33.04         4.01 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43X 
       17.98        46.78        19.79        12.85         7.56         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       15.58        26.73        19.33        27.45        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TF TCGA-FD-A6TG 
        7.10         6.28        62.86        18.81         2.27         3.06 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE 
       31.07        11.08        15.95        26.93        59.31        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3RD TCGA-GC-A4ZW 
       17.62        66.02        29.36        21.40        14.07         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A763 TCGA-GU-A767 
        8.94         7.73         2.10         2.20        32.78         4.73 
TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QK 
       10.65        32.98        14.27        21.34         8.48        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU TCGA-K4-A3WV 
       19.07        22.72        38.60        64.01         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RI TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76        27.68        11.70        11.80        50.56        35.97 
TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       46.98         1.15        21.07        16.67        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PD TCGA-UY-A9PF 
       16.54        12.43        38.99        76.01        17.82         3.85 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9ST 
       97.12        15.35        17.88        64.80        15.98         4.21 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
        5.98        12.76        26.27        71.57        91.73         8.32 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M 
       44.32        30.94        75.39        18.15        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        21.11        31.20        21.86        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4U 
       94.29         3.48        64.08        88.87        20.22         8.61 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA58 
       56.35        19.40        54.21 

$`DEL PEAK 18(9Q22.33) WILD-TYPE`
TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 
       44.94        16.77        27.62        41.75        51.16        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80         2.50        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R 
        6.74        12.39        13.15        19.04        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH 
       14.96         5.06         8.35         8.25        17.16         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ 
       12.82         9.96        17.56        36.43        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y 
        1.94        12.56        12.16        12.66        12.10        12.26 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-DK-A1A3 
       12.00        12.10        12.92        15.12        29.79        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 
       18.41        16.70       130.88        16.14        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       142.78        87.32         4.80        13.58         8.15 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
        8.22        23.21         9.67        20.81       163.30        66.05 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L 
       53.29        76.60        67.36        15.68        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA71 
       52.01        13.58       165.73       166.03        18.81        13.64 
TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A677 
       56.15        15.35         0.10        22.16         2.24        26.96 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       26.24        24.03        24.66        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37        32.02        16.77        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       60.66        24.30        23.41        29.16         5.52        25.74 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BV 
       27.35        14.96        20.91        53.88        11.01         5.36 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TD 
        5.69         8.25         2.70        13.35         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.36         4.31         9.67        10.85        12.66        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2ES 
       17.23         8.94         3.25        61.94        48.00        33.01 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.23         6.94        70.32        20.71        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91        17.75        24.92        13.91         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        7.36        10.92        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI 
        5.62         7.00        19.10        19.82        20.28        36.49 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS 
        8.58         1.51        19.40         9.01        12.16        25.02 
TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
        9.14         9.07        17.72         1.81        15.42        16.27 
TCGA-KQ-A41N TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       52.73        44.38        15.32        15.58        13.48        12.23 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        22.68        86.83        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH 
        3.02       112.83         3.91        29.56         6.21        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SG 
       45.04         6.58        97.45       125.49         1.87        48.62 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SW 
       79.66         3.22        66.41        34.45        14.93        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        28.24        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       66.64         2.10        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY 
       11.31        54.90         7.63         2.96         6.77        98.99 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN8 TCGA-YC-A89H 
       56.48        61.45        86.30        27.06         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RG 
        9.63         0.66        30.28        35.84        13.41        58.72 
TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4W 
       47.84         2.89        34.06        19.69        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       63.02        35.41        57.90         8.52        19.17         5.52 
TCGA-ZF-AA5P 
       12.23 

  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                        112.44                         166.03 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                         17.72                          16.70 
[1] "0.5 - 112.4 (17.7)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(9Q22.33) MUTATED         1       62        59       55
  DEL PEAK 18(9Q22.33) WILD-TYPE       1       67        81       80
D51V3, multiclass
           clus
vv          DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            62                             67
  STAGE III                           59                             81
  STAGE IV                            55                             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"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 18(9Q22.33) MUTATED         58  80  27
  DEL PEAK 18(9Q22.33) WILD-TYPE       65 115  31
D51V4, multiclass
          clus
vv         DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  T0+T1+T2                           58                             65
  T3                                 80                            115
  T4                                 27                             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                              N0  N1  N2  N3
  DEL PEAK 18(9Q22.33) MUTATED   106  17  32   4
  DEL PEAK 18(9Q22.33) WILD-TYPE 129  30  43   5
D51V5, multiclass
    clus
vv   DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  N0                          106                            129
  N1                           17                             30
  N2                           32                             43
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(9Q22.33) MUTATED   93  4
  DEL PEAK 18(9Q22.33) WILD-TYPE 99  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED     93    4
  DEL PEAK 18(9Q22.33) WILD-TYPE   99    7
   clus
vv  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  0                           93                             99
  1                            4                              7
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(9Q22.33) MUTATED    48 130
  DEL PEAK 18(9Q22.33) WILD-TYPE  59 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED     48  130
  DEL PEAK 18(9Q22.33) WILD-TYPE   59  171
        clus
vv       DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  FEMALE                           48                             59
  MALE                            130                            171
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(9Q22.33) MUTATED   160  10
  DEL PEAK 18(9Q22.33) WILD-TYPE 204   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED    160   10
  DEL PEAK 18(9Q22.33) WILD-TYPE  204    9
     clus
vv    DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  NO                           160                            204
  YES                           10                              9
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
D51V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(9Q22.33) MUTATED      21                         7   140
  DEL PEAK 18(9Q22.33) WILD-TYPE    22                        15   187
D51V12, multiclass
                           clus
vv                          DEL PEAK 18(9Q22.33) MUTATED
  ASIAN                                               21
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              140
                           clus
vv                          DEL PEAK 18(9Q22.33) WILD-TYPE
  ASIAN                                                 22
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                                cls
clus                               0   1
  DEL PEAK 18(9Q22.33) MUTATED     3 158
  DEL PEAK 18(9Q22.33) WILD-TYPE   6 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED      3  158
  DEL PEAK 18(9Q22.33) WILD-TYPE    6  211
                        clus
vv                       DEL PEAK 18(9Q22.33) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          158
                        clus
vv                       DEL PEAK 18(9Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            211
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 19(10P11.21) MUTATION ANALYSIS
D52V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 19(10P11.21) MUTATED    38  36
  DEL PEAK 19(10P11.21) WILD-TYPE 191 141
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             74                             332 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             36                             141 
$`DEL PEAK 19(10P11.21) MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA7Q TCGA-BT-A20J TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A42C 
      104.65        16.77        19.04        14.96        17.16        28.70 
TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A8HY TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 
        1.94        13.97        11.34        15.12        18.48         1.84 
TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-AA6L 
       46.68         7.79         4.80        50.27        21.30        38.24 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 
       52.01        15.02        19.00        13.64        15.35        11.18 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B4 
       12.03        43.59        15.35        25.58         1.22        16.77 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y 
        8.94         4.01        22.52        19.79        12.85        15.58 
TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EL 
        8.25        12.69        31.07        10.65        17.23        26.93 
TCGA-G2-A3IB TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A6I3 
        7.23        70.32        21.40        15.91        17.75        13.91 
TCGA-GV-A40G TCGA-H4-A2HQ TCGA-K4-A3WU TCGA-K4-A5RH TCGA-K4-A5RI TCGA-KQ-A41O 
       19.07        19.40         3.45         9.07        11.70        50.56 
TCGA-KQ-A41Q TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC 
       46.98        13.48        12.23        29.56         6.21         6.58 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SV TCGA-XF-AAMF 
      125.49         1.87        48.62        79.66        12.76        10.82 
TCGA-XF-AAMX TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-AA4N 
        6.77        25.41        13.41         3.48        47.84         2.89 
TCGA-ZF-AA4W TCGA-ZF-AA56 
       60.16         8.52 

$`DEL PEAK 19(10P11.21) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       47.80        29.65         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N 
        2.66         6.74        12.39         6.58        13.15        26.14 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.89         5.06 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
        8.35         8.25        16.18        20.48         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 
        9.96        17.56        36.43        28.41         8.98        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        12.56        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FL 
       13.12        12.00        12.10        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
       13.08        12.92         4.90         5.19        29.79        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
       21.86         2.14        66.41        18.41        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
      130.88       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      142.78        87.32        13.58         8.15         8.22        17.72 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       50.70        36.66        13.58       165.73       166.03        18.81 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.64        56.15        20.32        38.83        29.72         0.10 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       22.16         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
       26.24         4.24        24.03        24.66         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       14.07        12.95        15.32        14.37         8.09        32.02 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       33.04        12.62        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N 
       17.98        29.16         5.52        25.74        46.78         7.56 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.36         5.69        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA 
       58.92         2.70         7.10         6.28        13.35        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P 
        9.67        10.85        12.66         8.94         3.25        11.08 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE 
       61.94        48.00        15.95        59.31        33.01        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 
       19.13        14.07        24.92         0.49         8.94         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        2.10         3.12        20.98         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
       19.10        19.82        20.28         8.48        36.49        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.58        22.72         1.51        38.60        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       12.16        25.02        21.24         2.76         9.14        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       35.97        44.38         1.15        15.32        15.58        21.07 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-SY-A9G5 
       16.67        14.24         1.84        16.54        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P 
       17.62        37.05        22.68        86.83        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       69.34         3.02       112.83         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HI 
       51.32        45.04        97.45        97.12        15.35        17.88 
TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP 
       64.80         3.22        15.98        66.41        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        4.21         5.98        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       26.27        18.90         2.24        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       13.74        92.98       110.60        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ 
       71.57        91.73         2.96         8.32        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       56.48        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       13.64        22.36        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL 
       21.86        28.41        94.29        64.08        58.72        88.87 
TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       20.22        34.06        19.69         8.61        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        57.90        19.40        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                           1.22                            0.10 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                         125.49                          166.03 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                          15.35                           17.72 
[1] "1.2 - 125.5 (15.3)" "0.1 - 166.0 (17.7)"
[1] "hr=" "1.3"
D52V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(10P11.21) MUTATED         0       24        26       24
  DEL PEAK 19(10P11.21) WILD-TYPE       2      105       114      111
D52V3, multiclass
           clus
vv          DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  STAGE I                               0                               2
  STAGE II                             24                             105
  STAGE III                            26                             114
  STAGE IV                             24                             111
[1] 4 2
[1] 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(10P11.21) MUTATED         19  31  12
  DEL PEAK 19(10P11.21) WILD-TYPE      104 164  46
D52V4, multiclass
          clus
vv         DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  T0+T1+T2                            19                             104
  T3                                  31                             164
  T4                                  12                              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                               N0  N1  N2  N3
  DEL PEAK 19(10P11.21) MUTATED    46   6  13   4
  DEL PEAK 19(10P11.21) WILD-TYPE 189  41  62   5
D52V5, multiclass
    clus
vv   DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  N0                            46                             189
  N1                             6                              41
  N2                            13                              62
  N3                             4                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED    32   3
  DEL PEAK 19(10P11.21) WILD-TYPE 160   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED     32    3
  DEL PEAK 19(10P11.21) WILD-TYPE  160    8
   clus
vv  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  0                            32                             160
  1                             3                               8
[1] 2 2
[1] FALSE
D52V7, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED    20  54
  DEL PEAK 19(10P11.21) WILD-TYPE  87 247
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED     20   54
  DEL PEAK 19(10P11.21) WILD-TYPE   87  247
        clus
vv       DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  FEMALE                            20                              87
  MALE                              54                             247
[1] 2 2
[1] FALSE
D52V8, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED    67   4
  DEL PEAK 19(10P11.21) WILD-TYPE 297  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED     67    4
  DEL PEAK 19(10P11.21) WILD-TYPE  297   15
     clus
vv    DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  NO                             67                             297
  YES                             4                              15
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, continuous
D52V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10P11.21) MUTATED       4                         8    58
  DEL PEAK 19(10P11.21) WILD-TYPE    39                        14   269
D52V12, multiclass
                           clus
vv                          DEL PEAK 19(10P11.21) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                58
                           clus
vv                          DEL PEAK 19(10P11.21) WILD-TYPE
  ASIAN                                                  39
  BLACK OR AFRICAN AMERICAN                              14
  WHITE                                                 269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED     1  69
  DEL PEAK 19(10P11.21) WILD-TYPE   8 300
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED      1   69
  DEL PEAK 19(10P11.21) WILD-TYPE    8  300
                        clus
vv                       DEL PEAK 19(10P11.21) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            69
                        clus
vv                       DEL PEAK 19(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             300
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 20(10Q23.31) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(10Q23.31) MUTATED    86  80
  DEL PEAK 20(10Q23.31) WILD-TYPE 143  97
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            166                             240 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                             80                              97 
$`DEL PEAK 20(10Q23.31) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       24.13        11.97       104.65        16.27        16.77        17.16 
TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-5N-A9KI TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20U 
       51.16        15.12         2.50        26.14         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F6 
        5.06         8.35        20.48        17.56         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A5W6 
       13.97        11.34         4.90        18.48         5.19         1.84 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I6 
        2.14        18.41       112.44        46.68         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV 
        4.80        13.58         8.15         8.22        50.27         9.67 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R 
       67.36        36.66        38.24        52.01        15.02       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 TCGA-DK-AA76 
      166.03        19.00        13.64        15.35        11.18        12.03 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A6ME TCGA-E7-A7DV 
       43.59        29.72        22.16        25.58        24.03         1.22 
TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       13.68        15.32        33.04         4.01        22.52        24.30 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A5BY 
       19.79        12.85         7.56        27.35        20.91         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FJ-A3Z7 
       27.45        58.92        62.86        12.69         2.27        31.07 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
       10.65        17.23        11.08        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62        66.02         6.94        29.36        21.40 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75         0.49         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ 
        2.10         7.36        10.92        20.05         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       21.34        19.10        19.82        20.28         8.48        36.49 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
       19.07        22.72        19.40        64.01         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        3.45         9.14        27.68         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41S 
        1.81        11.80        50.56        35.97        46.98         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78O 
       15.32        15.58        13.48        12.23        38.99        76.01 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        3.91        17.82         6.21         6.58        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SP 
       97.12         1.87        48.62        79.66         3.22        14.93 
TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SX TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ 
        5.98        12.76        23.64        13.74        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN2 
        7.63         2.96         8.32         6.77        44.32        61.45 
TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       18.15        11.97        13.64        22.36        21.11        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T 
        3.48        47.84        20.22         2.89        34.06        19.69 
TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        63.02        56.35        35.41 

$`DEL PEAK 20(10Q23.31) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       108.95         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62        50.04         0.62        41.75        66.54        10.22 
TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80        29.65        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        6.74        12.39         6.58        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       17.88        19.50        14.89         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F 
        4.67        12.82         9.96        28.70        36.43        28.41 
TCGA-C4-A0EZ TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
        8.98        12.79        12.56        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.26        13.12        12.00        12.10        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E 
       18.58        13.08        12.92        15.12        29.79        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       21.86        66.41        19.00        16.70       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IT 
       17.62        15.62        17.95       142.78        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21        20.81        10.55       163.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6Q 
       64.18        53.29        76.60        15.68        50.70        13.58 
TCGA-DK-AA6T TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 
       18.81        13.64        56.15        20.32        15.35        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        0.10         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H 
       26.24         4.24        24.66         0.92        14.07        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       27.98        60.66        23.41        17.98        29.16         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       25.74        46.78        14.96         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5C0 
       53.88        11.01        19.33         5.36         5.69        18.08 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10         6.28        13.35        18.81         6.15 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
       12.36         3.06         4.31         9.67        10.85        12.66 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
        8.94         3.25        61.94        48.00        59.31        33.01 
TCGA-G2-AA3D TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GD-A2C5 
       70.32        20.71        15.81        19.13        24.92         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        3.12        20.98         2.20        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QK 
       32.78         5.62        10.65        32.98        14.27        27.35 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A4AB 
        8.58         1.51        38.60        12.16        21.24         2.76 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41R TCGA-LT-A8JT TCGA-PQ-A6FN 
       15.42        16.27        52.73        44.38        21.07        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        16.54        12.43        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       22.68        86.83        78.25        69.34         3.02       112.83 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HG TCGA-XF-A8HI 
       29.56         3.85        51.32        45.04        15.35        17.88 
TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW 
       64.80        15.98        66.41        34.45         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       21.04        28.24        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ 
       66.64         2.10        92.98       110.60        11.31        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
       91.73        98.99        56.48        30.94        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R1 
       75.39         3.88        18.84         9.63         0.66        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       31.20        30.28        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA53 
       64.08        58.72        88.87        59.38        60.16        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40         8.52        54.21        19.17         5.52        12.23 

  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                           0.49                            0.10 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                         166.03                          163.30 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                         16.965                          17.520 
[1] "0.5 - 166.0 (17.0)" "0.1 - 163.3 (17.5)"
[1] "hr=" "1.3"
D53V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(10Q23.31) MUTATED         0       55        52       59
  DEL PEAK 20(10Q23.31) WILD-TYPE       2       74        88       76
D53V3, multiclass
           clus
vv          DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  STAGE I                               0                               2
  STAGE II                             55                              74
  STAGE III                            52                              88
  STAGE IV                             59                              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"
                                 vv
clus                              T0+T1+T2  T3  T4
  DEL PEAK 20(10Q23.31) MUTATED         47  80  21
  DEL PEAK 20(10Q23.31) WILD-TYPE       76 115  37
D53V4, multiclass
          clus
vv         DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  T0+T1+T2                            47                              76
  T3                                  80                             115
  T4                                  21                              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                               N0  N1  N2  N3
  DEL PEAK 20(10Q23.31) MUTATED    85  20  30   6
  DEL PEAK 20(10Q23.31) WILD-TYPE 150  27  45   3
D53V5, multiclass
    clus
vv   DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  N0                            85                             150
  N1                            20                              27
  N2                            30                              45
  N3                             6                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED    69   6
  DEL PEAK 20(10Q23.31) WILD-TYPE 123   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED     69    6
  DEL PEAK 20(10Q23.31) WILD-TYPE  123    5
   clus
vv  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  0                            69                             123
  1                             6                               5
[1] 2 2
[1] FALSE
D53V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED    44 122
  DEL PEAK 20(10Q23.31) WILD-TYPE  63 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED     44  122
  DEL PEAK 20(10Q23.31) WILD-TYPE   63  179
        clus
vv       DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  FEMALE                            44                              63
  MALE                             122                             179
[1] 2 2
[1] FALSE
D53V8, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED   145   9
  DEL PEAK 20(10Q23.31) WILD-TYPE 219  10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED    145    9
  DEL PEAK 20(10Q23.31) WILD-TYPE  219   10
     clus
vv    DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  NO                            145                             219
  YES                             9                              10
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, continuous
D53V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q23.31) MUTATED      10                        10   136
  DEL PEAK 20(10Q23.31) WILD-TYPE    33                        12   191
D53V12, multiclass
                           clus
vv                          DEL PEAK 20(10Q23.31) MUTATED
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               136
                           clus
vv                          DEL PEAK 20(10Q23.31) WILD-TYPE
  ASIAN                                                  33
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED     3 149
  DEL PEAK 20(10Q23.31) WILD-TYPE   6 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED      3  149
  DEL PEAK 20(10Q23.31) WILD-TYPE    6  220
                        clus
vv                       DEL PEAK 20(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           149
                        clus
vv                       DEL PEAK 20(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             220
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(11P15.5) MUTATED   116  94
  DEL PEAK 21(11P15.5) WILD-TYPE 113  83
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           210                            196 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            94                             83 
$`DEL PEAK 21(11P15.5) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       24.13       104.65       108.95         8.35        16.83        16.77 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 
       34.98        27.62         0.62        15.12        47.80        29.65 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20N 
        2.50        17.42        40.08         2.66        19.04        26.14 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A3PK 
        5.06        14.89         5.06         8.35         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        28.70         8.98         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.56        13.97        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY 
       10.95        12.62        13.12        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 
       11.87        15.12        18.48         1.84        13.58         2.14 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 
       18.41        16.70       112.44        17.62        46.68        17.95 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         4.80        13.58         8.15         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6L 
       50.27        21.30        17.98        64.18        50.70        38.24 
TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA74 TCGA-DK-AA76 
       15.02       165.73       166.03        19.00        56.15        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A541 TCGA-E7-A5KE 
       20.32        15.35        38.83        29.72        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW 
        0.66         4.24        24.03         0.92         1.22        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ 
       12.95        14.37         8.09         8.94         4.01        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y 
       23.41        29.16        19.79        12.85         7.56        15.58 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28        62.86         6.15         2.27         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY 
       31.07        10.65        11.08        59.31        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD 
       66.02        70.32        29.36        21.40        20.71        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q 
       24.92         7.73         2.10         2.20         7.36        11.31 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       18.97         4.73        32.98         7.00        14.27        21.34 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
       20.28         8.58        19.07        22.72        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB 
       64.01         9.01        25.02        21.24        11.70        15.42 
TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       11.80        52.73        50.56        46.98        44.38         1.15 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 
       21.07        12.23        14.24         1.84        16.54        12.43 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       38.99        22.68        76.01        69.34         3.02       112.83 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG 
       17.82         6.21         3.85        51.32        97.12        15.35 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU 
       48.62        64.80         3.22        14.93         4.21         5.98 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       12.76        11.90        28.24         2.24        66.64         2.10 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW 
      110.60        54.90         7.63        71.57        91.73         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R0 
        6.77        44.32        56.48        18.15        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       25.41        21.11        30.28        21.86        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R 
        3.48        58.72        88.87        47.84        20.22        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       19.69         8.61        63.02        35.41        19.17        12.23 

$`DEL PEAK 21(11P15.5) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7Y 
       11.97        94.88        16.27        44.94        17.16        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A13I TCGA-BL-A3JM 
       41.75        51.16        66.54        10.22         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
       14.96         8.25        17.16        16.18        20.48        12.82 
TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       36.43        28.41        12.66        12.46        12.10        12.26 
TCGA-CF-A8HX TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3QU 
       11.34        18.58        13.08        12.92         4.90         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE 
       29.79        21.86        66.41        19.00       130.88        16.14 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       15.62         7.79       142.78        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       10.55       163.30        66.05        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W 
       15.68        36.66        52.01        13.58        18.81        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.35        13.64        11.18        43.59         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN 
        2.24        16.70        26.96        26.24        24.66        14.07 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.32        32.02        16.77        33.04        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       27.98        60.66        17.98         5.52        25.74        46.78 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62S TCGA-FD-A6TB 
       11.01        19.33         5.69         8.25        13.35        18.81 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
       12.69        12.36         9.67        10.85        12.66        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        61.94        48.00        15.95        26.93 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
       33.01         7.23         6.94        15.81        19.13        15.91 
TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         0.49         8.94        13.91         3.12        20.98 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
       10.92         7.63        32.78        20.05         5.62        10.65 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO 
       19.10        19.82         8.48        36.49        27.35         1.51 
TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       12.16         3.45         2.76         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41P TCGA-LC-A66R TCGA-LT-A5Z6 
       17.72         1.81        16.27        35.97        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78P 
       13.48        16.67        17.62        37.05        86.83        78.25 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE 
        3.91        29.56        45.04         6.58        97.45       125.49 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
        1.87        17.88        79.66        15.98        66.41        34.45 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T8 
       23.64        21.04        26.27        18.90        16.27        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMT TCGA-XF-AAMY TCGA-XF-AAN1 
       92.98        10.82        11.31         2.96        98.99        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H 
       61.45        86.30        27.06        75.39         3.88        18.84 
TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        9.63         0.66        13.64        31.20        35.84        28.41 
TCGA-ZF-A9RF TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 
       64.08         2.89        59.38        60.16        56.35        57.90 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       19.40         8.52        54.21         5.52 

  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                          0.56                           0.10 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        166.03                         163.30 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        17.125                         17.195 
[1] "0.6 - 166.0 (17.1)" "0.1 - 163.3 (17.2)"
[1] "hr=" "1.1"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(11P15.5) MUTATED         1       64        64       81
  DEL PEAK 21(11P15.5) WILD-TYPE       1       65        76       54
D54V3, multiclass
           clus
vv          DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            64                             65
  STAGE III                           64                             76
  STAGE IV                            81                             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 21(11P15.5) MUTATED         65 100  34
  DEL PEAK 21(11P15.5) WILD-TYPE       58  95  24
D54V4, multiclass
          clus
vv         DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  T0+T1+T2                           65                             58
  T3                                100                             95
  T4                                 34                             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                              N0  N1  N2  N3
  DEL PEAK 21(11P15.5) MUTATED   110  25  50   4
  DEL PEAK 21(11P15.5) WILD-TYPE 125  22  25   5
D54V5, multiclass
    clus
vv   DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  N0                          110                            125
  N1                           25                             22
  N2                           50                             25
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED   102   7
  DEL PEAK 21(11P15.5) WILD-TYPE  90   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED    102    7
  DEL PEAK 21(11P15.5) WILD-TYPE   90    4
   clus
vv  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  0                          102                             90
  1                            7                              4
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED    56 155
  DEL PEAK 21(11P15.5) WILD-TYPE  51 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     56  155
  DEL PEAK 21(11P15.5) WILD-TYPE   51  146
        clus
vv       DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  FEMALE                           56                             51
  MALE                            155                            146
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED   184  11
  DEL PEAK 21(11P15.5) WILD-TYPE 180   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED    184   11
  DEL PEAK 21(11P15.5) WILD-TYPE  180    8
     clus
vv    DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  NO                           184                            180
  YES                           11                              8
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
D54V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11P15.5) MUTATED      27                        11   161
  DEL PEAK 21(11P15.5) WILD-TYPE    16                        11   166
D54V12, multiclass
                           clus
vv                          DEL PEAK 21(11P15.5) MUTATED
  ASIAN                                               27
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              161
                           clus
vv                          DEL PEAK 21(11P15.5) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED     6 186
  DEL PEAK 21(11P15.5) WILD-TYPE   3 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      6  186
  DEL PEAK 21(11P15.5) WILD-TYPE    3  183
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          186
                        clus
vv                       DEL PEAK 21(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 22(11Q23.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(11Q23.3) MUTATED    86  69
  DEL PEAK 22(11Q23.3) WILD-TYPE 143 108
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           155                            251 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                            69                            108 
$`DEL PEAK 22(11Q23.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 
       24.13       104.65       108.95        16.83        34.98         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-BT-A20J TCGA-BT-A20N 
       41.75        51.16        29.65         2.50        19.04        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       14.89         8.35        17.16        16.18         4.67        17.56 
TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0EZ TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       28.70        28.41         8.98        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.13        12.62        13.12        12.10        11.34        11.34 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC 
       12.92        18.48         2.14        66.41        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV 
      112.44         8.15         8.22        17.72        50.27        64.18 
TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A2PC 
       36.66        15.02       165.73       166.03        11.18        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF 
       15.35        38.83        22.16        25.58         0.56         0.66 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        4.24        24.03         0.92        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43X 
        8.09         8.94         4.01        24.30         7.56         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       15.58        26.73         5.36         8.25        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH 
        2.70         7.10        13.35        62.86         6.15         4.31 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3YS 
       11.08        33.01         7.23        70.32        21.40        24.92 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q 
        0.49         8.94         7.73         2.10         7.36        11.31 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QK 
       18.97         4.73         7.00        14.27        21.34        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        8.58        19.07        22.72        19.40        38.60        64.01 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-KQ-A41O 
       21.24         2.76         9.14         9.07        11.70        50.56 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78N 
       46.98        44.38         1.15        12.23        38.99        86.83 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB 
       76.01        78.25        69.34         3.02       112.83        29.56 
TCGA-UY-A9PE TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SV 
        6.21        15.35        48.62        34.45         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMJ 
       11.90        66.64         2.10        10.82       110.60        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN1 
        7.63        71.57         2.96         8.32        56.48        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R7 
       61.45        18.15        22.36        21.11        30.28        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       94.29        13.41        20.22        19.69         8.61        63.02 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90        19.40        54.21        19.17        12.23 

$`DEL PEAK 22(11Q23.3) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       11.97        94.88         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
       17.16        27.62        50.04        66.54        15.12        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80        17.42        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
       12.39         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06        14.96         5.06         8.25        20.48        12.82 
TCGA-BT-A3PK TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MH 
        9.96        36.43         1.94        23.01        12.79        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.16        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5UA TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       12.00        11.87        18.58        13.08         4.90        15.12 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 
        5.19        29.79         1.84        13.58        21.86        18.41 
TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
       19.00        16.14        17.62        15.62        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IT 
        7.79       142.78        87.32         4.80        13.58        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       17.98        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       38.24        52.01        13.58        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E7-A3X6 
       15.35        13.64        56.15        12.03        20.32        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        0.10         2.24        16.70        26.96        26.24        24.66 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B6 
        1.22        14.07        15.32        32.02        16.77        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       29.16         5.52        25.74        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU 
       27.35        14.96        20.91        53.88        11.01        19.33 
TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        5.69        27.45         6.28        18.81        12.69        12.36 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        2.27         3.06         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       15.95        26.93        59.31        20.12        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        6.94        29.36        20.71        15.81        19.13        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       14.07        17.75        13.91         3.12        20.98         2.20 
TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO 
       10.92         7.63        32.78        20.05         5.62        10.65 
TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI 
       32.98        19.10        19.82        20.28         8.48        36.49 
TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R 
        1.51         9.01        12.16        25.02         3.45        27.68 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N 
       17.72         1.81        15.42        16.27        11.80        52.73 
TCGA-KQ-A41P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       35.97        15.32        15.58        21.07        13.48        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L 
       14.24         1.84        16.54        12.43        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HB 
       22.68         3.91        17.82         3.85        51.32        45.04 
TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A8HI 
        6.58        97.45       125.49        97.12         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP 
       64.80        79.66         3.22        15.98        66.41        14.93 
TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        23.64        21.04        28.24        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMR 
        2.24        16.27        13.74        92.98        11.31        91.73 
TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
        6.77        98.99        44.32        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF 
       25.41        31.20        35.84        28.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V 
       58.72        88.87        47.84         2.89        34.06        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        56.35        35.41         8.52         5.52 

  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                        166.03                         163.30 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                         17.16                          17.23 
[1] "0.5 - 166.0 (17.2)" "0.1 - 163.3 (17.2)"
[1] "hr=" "1"  
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(11Q23.3) MUTATED         0       52        51       51
  DEL PEAK 22(11Q23.3) WILD-TYPE       2       77        89       84
D55V3, multiclass
           clus
vv          DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            52                             77
  STAGE III                           51                             89
  STAGE IV                            51                             84
[1] 4 2
[1] 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(11Q23.3) MUTATED         55  67  26
  DEL PEAK 22(11Q23.3) WILD-TYPE       68 128  32
D55V4, multiclass
          clus
vv         DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  T0+T1+T2                           55                             68
  T3                                 67                            128
  T4                                 26                             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                              N0  N1  N2  N3
  DEL PEAK 22(11Q23.3) MUTATED    87  20  28   1
  DEL PEAK 22(11Q23.3) WILD-TYPE 148  27  47   8
D55V5, multiclass
    clus
vv   DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  N0                           87                            148
  N1                           20                             27
  N2                           28                             47
  N3                            1                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED    70   3
  DEL PEAK 22(11Q23.3) WILD-TYPE 122   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED     70    3
  DEL PEAK 22(11Q23.3) WILD-TYPE  122    8
   clus
vv  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  0                           70                            122
  1                            3                              8
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED    43 112
  DEL PEAK 22(11Q23.3) WILD-TYPE  64 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED     43  112
  DEL PEAK 22(11Q23.3) WILD-TYPE   64  189
        clus
vv       DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  FEMALE                           43                             64
  MALE                            112                            189
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED   136   9
  DEL PEAK 22(11Q23.3) WILD-TYPE 228  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED    136    9
  DEL PEAK 22(11Q23.3) WILD-TYPE  228   10
     clus
vv    DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  NO                           136                            228
  YES                            9                             10
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
D55V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11Q23.3) MUTATED      19                         9   118
  DEL PEAK 22(11Q23.3) WILD-TYPE    24                        13   209
D55V12, multiclass
                           clus
vv                          DEL PEAK 22(11Q23.3) MUTATED
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              118
                           clus
vv                          DEL PEAK 22(11Q23.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                209
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED     4 135
  DEL PEAK 22(11Q23.3) WILD-TYPE   5 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED      4  135
  DEL PEAK 22(11Q23.3) WILD-TYPE    5  234
                        clus
vv                       DEL PEAK 22(11Q23.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          135
                        clus
vv                       DEL PEAK 22(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            234
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 23(11Q25) MUTATION ANALYSIS
D56V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(11Q25) MUTATED    80  63
  DEL PEAK 23(11Q25) WILD-TYPE 149 114
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         143                          263 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                          63                          114 
$`DEL PEAK 23(11Q25) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 
       24.13       104.65       108.95        16.83        34.98         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BT-A20W TCGA-BT-A2LA 
       51.16        29.65         2.50        17.42         8.35        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ 
       16.18         4.67        17.56        28.70        36.43         8.98 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A5U8 
       12.56        13.97        12.59        12.13        12.62        13.12 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 
       12.10        11.34        11.34        12.92        18.48         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       66.41        16.70         8.15         8.22        17.72        50.27 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A2PC 
       64.18        36.66        15.02       166.03        11.18        43.59 
TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD 
       15.35        22.16        25.58         0.56         0.66         4.24 
TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q 
       24.03         0.92        13.68        12.95        14.37         8.09 
TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A43N TCGA-FD-A43Y TCGA-FD-A5BR 
        8.94         4.01        24.30         7.56        15.58        26.73 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        5.36         8.25        18.08        58.92         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3IB 
       13.35         6.15         4.31        11.08        33.01         7.23 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 
       17.62        21.40        24.92         0.49         8.94         7.73 
TCGA-GD-A3OP TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ 
        2.10         7.36        11.31        18.97         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       14.27        21.34        19.82        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WV 
       22.72        19.40        38.60        64.01         9.01        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-KQ-A41O TCGA-KQ-A41Q 
        2.76         9.14         9.07        11.70        50.56        46.98 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78N TCGA-UY-A78O 
       44.38         1.15        12.23        38.99        86.83        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HG 
       78.25        69.34       112.83        29.56         6.21        15.35 
TCGA-XF-A9SG TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 
       48.62        34.45        12.76        11.90        66.64         2.10 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMT TCGA-XF-AAMW 
      110.60        54.90         7.63        71.57         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       56.48        61.45        18.15        22.36        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4X 
       94.29        13.41        20.22        19.69         8.61        63.02 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5P 
       57.90        19.40        54.21        19.17        12.23 

$`DEL PEAK 23(11Q25) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       11.97        94.88         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 
       17.16        27.62        50.04        41.75        66.54        15.12 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       17.88        19.50         5.06        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F0 
        8.25        20.48        12.82         9.96        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       23.01        12.79        13.08        12.16        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A9FF TCGA-CF-A9FL 
       12.46        12.10        12.26        12.00        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       13.08         4.90        15.12         5.19        29.79         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AD 
       13.58        21.86        18.41        19.00       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62        46.68        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IT TCGA-DK-A3IU 
      142.78        87.32         4.80        13.58        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
        9.67        20.81        10.55       163.30        66.05        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       53.29        76.60        67.36        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W 
       52.01        13.58       165.73        18.81        19.00        13.64 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 
       15.35        13.64        56.15        12.03        20.32        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 
       29.72         0.10         2.24        16.70        26.96        26.24 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
       24.66         1.22        14.07        15.32        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL 
       33.04        12.62        22.52        27.98        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       17.98        29.16         5.52        25.74        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BS 
       12.85        27.35        14.96        20.91         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TA 
       11.01        19.33         5.69        27.45         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       18.81        12.69        12.36         2.27         3.06         9.67 
TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
       10.85        31.07        12.66        10.65        17.23         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        3.25        61.94        48.00        15.95        26.93        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3I6 
       20.12        66.02         6.94        70.32        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A6I3 
       15.81        19.13        15.91        14.07        17.75        13.91 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A763 
        3.12        20.98         2.20        10.92         7.63        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A3QF 
       20.05         5.62        10.65        32.98        19.10        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
        8.48        36.49         1.51        12.16        25.02         3.45 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       27.68        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       52.73        35.97        15.32        15.58        21.07        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78K 
       16.67        14.24         1.84        16.54        12.43        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF 
       37.05        22.68         3.02         3.91        17.82         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
       51.32        45.04         6.58        97.45       125.49        97.12 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.87        17.88        64.80        79.66         3.22        15.98 
TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SY 
       66.41        14.93         4.21         5.98        23.64        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 
       28.24        26.27        18.90         2.24        16.27        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY 
       92.98        10.82        11.31        91.73         6.77        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 
       44.32        30.94        86.30        27.06        75.39         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        13.64        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V 
       58.72        88.87        47.84         2.89        34.06        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        56.35        35.41         8.52         5.52 

  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                        0.49                         0.10 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                      166.03                       165.73 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                       16.70                        17.62 
[1] "0.5 - 166.0 (16.7)" "0.1 - 165.7 (17.6)"
[1] "hr=" "1.1"
D56V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(11Q25) MUTATED         0       48        50       44
  DEL PEAK 23(11Q25) WILD-TYPE       2       81        90       91
D56V3, multiclass
           clus
vv          DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  STAGE I                            0                            2
  STAGE II                          48                           81
  STAGE III                         50                           90
  STAGE IV                          44                           91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2  T3  T4
  DEL PEAK 23(11Q25) MUTATED         51  62  23
  DEL PEAK 23(11Q25) WILD-TYPE       72 133  35
D56V4, multiclass
          clus
vv         DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  T0+T1+T2                         51                           72
  T3                               62                          133
  T4                               23                           35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  DEL PEAK 23(11Q25) MUTATED    82  16  24   2
  DEL PEAK 23(11Q25) WILD-TYPE 153  31  51   7
D56V5, multiclass
    clus
vv   DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  N0                         82                          153
  N1                         16                           31
  N2                         24                           51
  N3                          2                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED    63   3
  DEL PEAK 23(11Q25) WILD-TYPE 129   8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     63    3
  DEL PEAK 23(11Q25) WILD-TYPE  129    8
   clus
vv  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  0                         63                          129
  1                          3                            8
[1] 2 2
[1] FALSE
D56V7, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED    41 102
  DEL PEAK 23(11Q25) WILD-TYPE  66 199
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     41  102
  DEL PEAK 23(11Q25) WILD-TYPE   66  199
        clus
vv       DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  FEMALE                         41                           66
  MALE                          102                          199
[1] 2 2
[1] FALSE
D56V8, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED   124   9
  DEL PEAK 23(11Q25) WILD-TYPE 240  10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED    124    9
  DEL PEAK 23(11Q25) WILD-TYPE  240   10
     clus
vv    DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  NO                         124                          240
  YES                          9                           10
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
D56V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q25) MUTATED      20                         9   107
  DEL PEAK 23(11Q25) WILD-TYPE    23                        13   220
D56V12, multiclass
                           clus
vv                          DEL PEAK 23(11Q25) MUTATED
  ASIAN                                             20
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            107
                           clus
vv                          DEL PEAK 23(11Q25) WILD-TYPE
  ASIAN                                               23
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              220
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED     4 126
  DEL PEAK 23(11Q25) WILD-TYPE   5 243
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED      4  126
  DEL PEAK 23(11Q25) WILD-TYPE    5  243
                        clus
vv                       DEL PEAK 23(11Q25) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        126
                        clus
vv                       DEL PEAK 23(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          243
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 24(12P13.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(12P13.1) MUTATED    36  32
  DEL PEAK 24(12P13.1) WILD-TYPE 193 145
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            68                            338 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            32                            145 
$`DEL PEAK 24(12P13.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BT-A20T TCGA-BT-A2LA 
       24.13         8.35        47.80         2.50        14.89        17.16 
TCGA-BT-A42C TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A9FL 
       28.70        13.97        12.16        12.62        12.10        18.58 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AC TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IV 
        5.19         1.84       130.88        13.58        17.72         9.67 
TCGA-DK-A6AV TCGA-E5-A2PC TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3SL TCGA-FD-A3SQ 
       64.18        43.59        12.95         8.09        23.41        46.78 
TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43X TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TC 
       19.79         7.56         3.62         5.69        18.08         6.15 
TCGA-FD-A6TE TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OS 
       12.36        70.32        29.36        24.92         7.73        20.98 
TCGA-GD-A76B TCGA-GU-A764 TCGA-GV-A3JW TCGA-K4-A6FZ TCGA-KQ-A41Q TCGA-KQ-A41R 
        7.36        20.05        21.34         1.81        46.98        44.38 
TCGA-KQ-A41S TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
        1.15        12.43        22.68        78.25       112.83        17.82 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SZ 
       97.12        15.35         1.87        14.93        12.76        28.24 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMX 
        2.24        10.82       110.60         7.63         8.32         6.77 
TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9RN TCGA-ZF-AA4T TCGA-ZF-AA4U 
       56.48        11.97        22.36        20.22        19.69         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA52 
       60.16        35.41 

$`DEL PEAK 24(12P13.1) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7N 
       11.97        94.88       104.65       108.95        16.27        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       16.83        16.77        17.16        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 
        0.62        41.75        51.16        66.54        15.12        10.22 
TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       29.65        17.42        40.08         7.33         2.66         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O 
       12.39         6.58        13.15        19.04        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W 
       17.88        19.50         5.06        14.96         5.06         8.35 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.25        16.18        20.48         4.67        12.82         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       17.56        36.43        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S 
       12.79        12.56        12.59        12.13        13.08        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO 
       11.34        11.34        11.87        13.08        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
       15.12        18.48        29.79        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00        16.70       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62        46.68        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT 
       87.32         4.80         8.15         8.22        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 
       23.21        20.81        10.55       163.30        66.05        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       53.29        76.60        67.36        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S 
       38.24        52.01        15.02        13.58       165.73       166.03 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 
       18.81        19.00        13.64        15.35        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       11.18        12.03        20.32        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE 
        0.10        22.16         2.24        16.70        25.58         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF 
        0.66        26.96        26.24         4.24        24.03        24.66 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
        0.92         1.22        13.68        14.07        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       32.02        16.77         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       22.52        27.98        60.66        24.30        17.98        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U 
        5.52        25.74        12.85        27.35        14.96        20.91 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV 
       15.58        26.73        53.88        11.01        19.33         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
        8.25        27.45        58.92         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
       13.35        62.86        18.81        12.69         2.27         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        4.31         9.67        10.85        31.07        12.66        10.65 
TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ 
       17.23         8.94         3.25        11.08        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
       17.62        66.02         6.94        21.40        20.71        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I1 
       19.13        15.91        14.07        17.75         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q 
       13.91         2.10         3.12         2.20        10.92        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       18.97         7.63        32.78         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       32.98         7.00        14.27        19.10        19.82        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
        8.48        36.49        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
        1.51        19.40        38.60        64.01         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       25.02         3.45        21.24         2.76         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
        9.07        11.70        17.72        15.42        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       52.73        50.56        35.97        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 
       13.48        12.23        16.67        14.24         1.84        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        86.83        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-UY-A9PH 
        3.02         3.91        29.56         6.21         3.85        51.32 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SG 
       45.04         6.58        97.45       125.49        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       64.80        79.66         3.22        15.98        66.41        34.45 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 
        4.21         5.98        11.90        23.64        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME 
       18.90        16.27        66.64         2.10        13.74        92.98 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMY 
       11.31        54.90        71.57        91.73         2.96        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       44.32        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M 
       18.15         3.88        18.84         9.63         0.66        13.64 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       25.41        21.11        31.20        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       28.41        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4V TCGA-ZF-AA4X 
       88.87        47.84         2.89        34.06        59.38        63.02 
TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        57.90        19.40         8.52        54.21        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                          1.15                           0.10 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                        130.88                         166.03 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                        16.255                         17.325 
[1] "1.1 - 130.9 (16.3)" "0.1 - 166.0 (17.3)"
[1] "hr=" "1.1"
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(12P13.1) MUTATED         0       16        26       26
  DEL PEAK 24(12P13.1) WILD-TYPE       2      113       114      109
D57V3, multiclass
           clus
vv          DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            16                            113
  STAGE III                           26                            114
  STAGE IV                            26                            109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 24(12P13.1) MUTATED         17  33  15
  DEL PEAK 24(12P13.1) WILD-TYPE      106 162  43
D57V4, multiclass
          clus
vv         DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  T0+T1+T2                           17                            106
  T3                                 33                            162
  T4                                 15                             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                              N0  N1  N2  N3
  DEL PEAK 24(12P13.1) MUTATED    34   8  16   1
  DEL PEAK 24(12P13.1) WILD-TYPE 201  39  59   8
D57V5, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  N0                           34                            201
  N1                            8                             39
  N2                           16                             59
  N3                            1                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    26   2
  DEL PEAK 24(12P13.1) WILD-TYPE 166   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     26    2
  DEL PEAK 24(12P13.1) WILD-TYPE  166    9
   clus
vv  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  0                           26                            166
  1                            2                              9
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    22  46
  DEL PEAK 24(12P13.1) WILD-TYPE  85 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     22   46
  DEL PEAK 24(12P13.1) WILD-TYPE   85  255
        clus
vv       DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  FEMALE                           22                             85
  MALE                             46                            255
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    60   3
  DEL PEAK 24(12P13.1) WILD-TYPE 304  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     60    3
  DEL PEAK 24(12P13.1) WILD-TYPE  304   16
     clus
vv    DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  NO                            60                            304
  YES                            3                             16
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
D57V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(12P13.1) MUTATED       8                         3    56
  DEL PEAK 24(12P13.1) WILD-TYPE    35                        19   271
D57V12, multiclass
                           clus
vv                          DEL PEAK 24(12P13.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               56
                           clus
vv                          DEL PEAK 24(12P13.1) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED     2  63
  DEL PEAK 24(12P13.1) WILD-TYPE   7 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED      2   63
  DEL PEAK 24(12P13.1) WILD-TYPE    7  306
                        clus
vv                       DEL PEAK 24(12P13.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 24(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            306
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 25(12Q24.33) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(12Q24.33) MUTATED    46  42
  DEL PEAK 25(12Q24.33) WILD-TYPE 183 135
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             88                             318 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             42                             135 
$`DEL PEAK 25(12Q24.33) MUTATED`
TCGA-2F-A9KR TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BT-A20W 
      104.65        15.12        10.22        47.80         2.50         8.35 
TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C 
       17.16        20.48        28.41         1.94        12.56        13.97 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FL TCGA-CU-A0YO 
       12.16        12.62        12.00        12.10        18.58         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 
       15.12         5.19       142.78        17.72         9.67        17.98 
TCGA-DK-AA6L TCGA-DK-AA6P TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV 
       38.24        15.02        43.59        15.35        25.58         1.22 
TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SS 
       13.68         8.09        23.41         5.52        46.78        12.85 
TCGA-FD-A43X TCGA-FD-A5BZ TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH 
        3.62        27.45         6.28        12.36         2.27         4.31 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD 
       11.08        17.62        70.32        29.36        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GD-A76B TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP 
       24.92         0.49         7.36         5.62         4.73        32.98 
TCGA-GV-A3JW TCGA-GV-A6ZA TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RJ 
       21.34        22.72        12.16         9.14         9.07        17.72 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-PQ-A6FI TCGA-SY-A9G0 TCGA-UY-A78M TCGA-UY-A8OB 
        1.15        15.32        12.23        12.43        22.68        69.34 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SH 
      112.83        17.82        51.32        97.12        15.35        64.80 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SX TCGA-XF-AAMF TCGA-XF-AAMJ 
       79.66         3.22        14.93        23.64        10.82        54.90 
TCGA-XF-AAML TCGA-XF-AAMW TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-ZF-A9R0 
        7.63         8.32        44.32        56.48        61.45        22.36 
TCGA-ZF-A9RM TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       47.84        63.02        35.41        19.17 

$`DEL PEAK 25(12Q24.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97        94.88       108.95         8.35        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       44.94        16.83        16.77        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 
       50.04         0.62        41.75        51.16        66.54        29.65 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       17.42        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        26.14        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       19.50         5.06        14.89        14.96         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       16.18         4.67        12.82         9.96        17.56        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG 
       36.43         8.98        23.01        12.79        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       13.08        10.95        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A0YN 
       13.12        11.34        11.34        11.87        13.08        12.92 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
       18.48        29.79         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00        16.70       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62        46.68        17.95         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS 
       87.32         4.80        13.58         8.15         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21        20.81        10.55       163.30        66.05 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 
       64.18        53.29        76.60        67.36        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T 
       36.66        52.01        13.58       165.73       166.03        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       19.00        13.64        15.35        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        20.32        38.83        29.72         0.10        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        2.24        16.70         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66         0.92        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.32        14.37        32.02        16.77         8.94        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
        4.01        12.62        22.52        27.98        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
       17.98        29.16        25.74        19.79         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91        15.58        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       19.33         5.36         5.69         8.25        18.08        58.92 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        2.70         7.10        13.35        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
       12.69         3.06         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       15.95        26.93        59.31        33.01         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       66.02         6.94        21.40        20.71        15.81        19.13 
TCGA-GC-A3WC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       17.75         8.94        13.91         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         2.20        10.92        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX 
       32.78        20.05        10.65         7.00        14.27        19.10 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
       19.82        20.28         8.48        36.49        27.35         8.58 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       19.07         1.51        19.40        38.60        64.01         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RI 
       25.02         3.45        21.24         2.76        27.68        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
        1.81        15.42        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V 
       35.97        46.98        44.38        15.58        21.07        13.48 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       16.67        14.24         1.84        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       37.05        86.83        76.01        78.25         3.02         3.91 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD 
       29.56         6.21         3.85        45.04         6.58        97.45 
TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SK TCGA-XF-A9SL 
      125.49         1.87        17.88        48.62        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       34.45         4.21         5.98        12.76        11.90        21.04 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       28.24        26.27        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ 
        2.10        13.74        92.98       110.60        11.31        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN3 
       91.73         2.96         6.77        98.99        30.94        86.30 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 
        0.66        11.97        13.64        25.41        21.11        31.20 
TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RD 
       30.28        35.84        21.86        28.41        94.29        13.41 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        64.08        58.72        88.87        20.22         2.89 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       34.06        19.69         8.61        59.38        60.16        56.35 
TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       57.90        19.40         8.52        54.21         5.52        12.23 

  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                           0.49                            0.10 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                         142.78                          166.03 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                         15.335                          17.620 
[1] "0.5 - 142.8 (15.3)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.2"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 25(12Q24.33) MUTATED         0       28        22       38
  DEL PEAK 25(12Q24.33) WILD-TYPE       2      101       118       97
D58V3, multiclass
           clus
vv          DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  STAGE I                               0                               2
  STAGE II                             28                             101
  STAGE III                            22                             118
  STAGE IV                             38                              97
[1] 4 2
[1] 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(12Q24.33) MUTATED         31  41  13
  DEL PEAK 25(12Q24.33) WILD-TYPE       92 154  45
D58V4, multiclass
          clus
vv         DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  T0+T1+T2                            31                              92
  T3                                  41                             154
  T4                                  13                              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                               N0  N1  N2  N3
  DEL PEAK 25(12Q24.33) MUTATED    42  12  22   3
  DEL PEAK 25(12Q24.33) WILD-TYPE 193  35  53   6
D58V5, multiclass
    clus
vv   DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  N0                            42                             193
  N1                            12                              35
  N2                            22                              53
  N3                             3                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED    36   3
  DEL PEAK 25(12Q24.33) WILD-TYPE 156   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED     36    3
  DEL PEAK 25(12Q24.33) WILD-TYPE  156    8
   clus
vv  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  0                            36                             156
  1                             3                               8
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED    20  68
  DEL PEAK 25(12Q24.33) WILD-TYPE  87 233
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED     20   68
  DEL PEAK 25(12Q24.33) WILD-TYPE   87  233
        clus
vv       DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  FEMALE                            20                              87
  MALE                              68                             233
[1] 2 2
[1] FALSE
D58V8, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED    78   6
  DEL PEAK 25(12Q24.33) WILD-TYPE 286  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED     78    6
  DEL PEAK 25(12Q24.33) WILD-TYPE  286   13
     clus
vv    DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  NO                             78                             286
  YES                             6                              13
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, continuous
D58V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(12Q24.33) MUTATED      13                         3    69
  DEL PEAK 25(12Q24.33) WILD-TYPE    30                        19   258
D58V12, multiclass
                           clus
vv                          DEL PEAK 25(12Q24.33) MUTATED
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                69
                           clus
vv                          DEL PEAK 25(12Q24.33) WILD-TYPE
  ASIAN                                                  30
  BLACK OR AFRICAN AMERICAN                              19
  WHITE                                                 258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED     1  80
  DEL PEAK 25(12Q24.33) WILD-TYPE   8 289
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED      1   80
  DEL PEAK 25(12Q24.33) WILD-TYPE    8  289
                        clus
vv                       DEL PEAK 25(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            80
                        clus
vv                       DEL PEAK 25(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             289
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 26(13Q14.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(13Q14.2) MUTATED    87  69
  DEL PEAK 26(13Q14.2) WILD-TYPE 142 108
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           156                            250 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            69                            108 
$`DEL PEAK 26(13Q14.2) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 
       16.27        16.77        34.98        27.62         0.62        51.16 
TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20N TCGA-BT-A20R 
       15.12        47.80         2.66         6.74        26.14         5.06 
TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89         5.06         8.25        17.16         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 
        9.96        17.56        28.70        36.43         8.98         1.94 
TCGA-CF-A1HS TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AC 
       12.56         5.19         1.84        21.86        18.41       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
      112.44        16.14        46.68         7.79       142.78        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 
        4.80         8.15         8.22        17.72         9.67        17.98 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W 
       67.36        36.66        52.01       165.73        18.81        13.64 
TCGA-DK-AA75 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE 
       11.18        43.59        29.72        22.16        25.58         0.56 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        4.24        24.03         1.22        13.68        12.95        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       32.02         8.94        33.04         4.01        22.52        24.30 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BU 
       29.16        46.78        19.79        12.85        27.35        19.33 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A6TC 
        5.36         8.25        27.45        58.92         2.70         6.15 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EO TCGA-G2-A2ES 
       12.36         4.31        17.23        11.08        59.31        33.01 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 
       29.36        21.40        15.81        19.13        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI 
       13.91         2.10         2.20        21.34        19.10        36.49 
TCGA-HQ-A2OE TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH 
       38.60         9.01        12.16         9.14        27.68         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R 
       17.72         1.81        52.73        46.98         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       15.58        13.48        12.23        16.67        16.54        17.62 
TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        86.83        69.34       112.83         3.91        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A9SG TCGA-XF-A9SJ 
       17.82         3.85         6.58        97.45        48.62         3.22 
TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 
       34.45        11.90        23.64        21.04         2.24        66.64 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMX TCGA-XF-AAMZ 
      110.60        54.90         7.63        71.57         6.77        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN7 TCGA-YF-AA3L TCGA-ZF-A9R9 TCGA-ZF-A9RE TCGA-ZF-A9RF 
       56.48        18.15        11.97        28.41         3.48        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4W 
       58.72        47.84        20.22         2.89        19.69        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       63.02        56.35        57.90        19.40        54.21        19.17 

$`DEL PEAK 26(13Q14.2) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 
       44.94        16.83        17.16        50.04        41.75        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        29.65         2.50        17.42        40.08         7.33 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42F 
       19.50        14.96         8.35        16.18        20.48        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       23.01        12.79        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       11.87        18.58        13.08        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA 
       18.48        29.79        13.58         2.14        66.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3IS 
       16.70        17.62        15.62        17.95        13.58        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        23.21        20.81        10.55       163.30        66.05 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       64.18        53.29        76.60        15.68        50.70        38.24 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 
       15.02        13.58       166.03        19.00        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA76 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 
       56.15        12.03        20.32        15.35        38.83         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF 
        2.24        16.70         0.66        26.96        26.24        24.66 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B8 
        0.92        14.07        15.32         8.09        16.77        12.62 
TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       27.98        60.66        23.41        17.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
        7.56        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62O TCGA-FD-A62P 
       53.88        11.01         5.69        18.08         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TF TCGA-FD-A6TG 
       13.35        62.86        18.81        12.69         2.27         3.06 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        9.67        10.85        31.07        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        3.25        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3I6 
       20.12        17.62        66.02         6.94        70.32        20.71 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OQ 
       15.91        14.07        17.75         0.49         7.73         3.12 
TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       20.98         7.36        10.92        11.31        18.97         7.63 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP 
       32.78        20.05         5.62         4.73        10.65        32.98 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        7.00        14.27        19.82        20.28         8.48        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        8.58        19.07        22.72         1.51        19.40        64.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A5RI TCGA-K4-A6MB 
       25.02         3.45        21.24         2.76        11.70        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-LT-A8JT 
       16.27        11.80        50.56        35.97        44.38        21.07 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78O 
       14.24         1.84        12.43        38.99        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HE 
       78.25         3.02         6.21        51.32        45.04       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.12        15.35         1.87        17.88        64.80        79.66 
TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV 
       15.98        66.41        14.93         4.21         5.98        12.76 
TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 
       28.24        26.27        18.90        16.27         2.10        13.74 
TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
       92.98        10.82        11.31        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        30.94        61.45        86.30        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 
        3.88        18.84         9.63         0.66        13.64        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       25.41        21.11        31.20        30.28        35.84        21.86 
TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V 
       94.29        13.41        88.87        34.06         8.61        59.38 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41         8.52         5.52        12.23 

  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                          0.56                           0.10 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                        165.73                         166.03 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                        18.065                         16.225 
[1] "0.6 - 165.7 (18.1)" "0.1 - 166.0 (16.2)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 26(13Q14.2) MUTATED         0       43        55       57
  DEL PEAK 26(13Q14.2) WILD-TYPE       2       86        85       78
D59V3, multiclass
           clus
vv          DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            43                             86
  STAGE III                           55                             85
  STAGE IV                            57                             78
[1] 4 2
[1] 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(13Q14.2) MUTATED         44  84  19
  DEL PEAK 26(13Q14.2) WILD-TYPE       79 111  39
D59V4, multiclass
          clus
vv         DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  T0+T1+T2                           44                             79
  T3                                 84                            111
  T4                                 19                             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                              N0  N1  N2  N3
  DEL PEAK 26(13Q14.2) MUTATED    78  20  35   4
  DEL PEAK 26(13Q14.2) WILD-TYPE 157  27  40   5
D59V5, multiclass
    clus
vv   DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  N0                           78                            157
  N1                           20                             27
  N2                           35                             40
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED    69   2
  DEL PEAK 26(13Q14.2) WILD-TYPE 123   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED     69    2
  DEL PEAK 26(13Q14.2) WILD-TYPE  123    9
   clus
vv  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  0                           69                            123
  1                            2                              9
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED    39 117
  DEL PEAK 26(13Q14.2) WILD-TYPE  68 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED     39  117
  DEL PEAK 26(13Q14.2) WILD-TYPE   68  184
        clus
vv       DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  FEMALE                           39                             68
  MALE                            117                            184
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED   135   7
  DEL PEAK 26(13Q14.2) WILD-TYPE 229  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED    135    7
  DEL PEAK 26(13Q14.2) WILD-TYPE  229   12
     clus
vv    DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  NO                           135                            229
  YES                            7                             12
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
D59V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(13Q14.2) MUTATED      11                        14   123
  DEL PEAK 26(13Q14.2) WILD-TYPE    32                         8   204
D59V12, multiclass
                           clus
vv                          DEL PEAK 26(13Q14.2) MUTATED
  ASIAN                                               11
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              123
                           clus
vv                          DEL PEAK 26(13Q14.2) WILD-TYPE
  ASIAN                                                 32
  BLACK OR AFRICAN AMERICAN                              8
  WHITE                                                204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED     5 134
  DEL PEAK 26(13Q14.2) WILD-TYPE   4 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED      5  134
  DEL PEAK 26(13Q14.2) WILD-TYPE    4  235
                        clus
vv                       DEL PEAK 26(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          134
                        clus
vv                       DEL PEAK 26(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            235
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 27(14Q24.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(14Q24.1) MUTATED    80  57
  DEL PEAK 27(14Q24.1) WILD-TYPE 149 120
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                           137                            269 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                            57                            120 
$`DEL PEAK 27(14Q24.1) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M 
       24.13        11.97       104.65       108.95         8.35        16.27 
TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 
       16.77         0.62        41.75        51.16        15.12        47.80 
TCGA-5N-A9KI TCGA-BT-A20J TCGA-BT-A20T TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB 
        2.50        19.04        14.89         5.06         8.35        16.18 
TCGA-BT-A3PK TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5U8 
        9.96        12.79        12.56        12.16        12.62        13.12 
TCGA-CF-A8HY TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34         4.90        15.12         5.19         1.84        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IQ 
        2.14        18.41       130.88       112.44        17.95        17.72 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6U 
       50.27        66.05        64.18        50.70       166.03        19.00 
TCGA-DK-AA76 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6MD TCGA-E7-A6ME 
       12.03        15.35        38.83        22.16         4.24        24.03 
TCGA-E7-A7DU TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP 
        0.92        12.95        15.32        24.30        29.16        25.74 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5C0 
       46.78        19.79         7.56        20.91        15.58        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH 
       58.92         6.28        62.86         6.15         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-A3VY 
       31.07        17.23        11.08        61.94        20.12        17.62 
TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A76B 
       66.02        70.32        14.07         0.49         7.73         7.36 
TCGA-GU-A42Q TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A40E 
       11.31        32.98        19.82        20.28        36.49         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WU 
       19.07        22.72        19.40        38.60        64.01         3.45 
TCGA-K4-A6MB TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       15.42        50.56        35.97        46.98        44.38         1.15 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 
       13.48        12.23        14.24         1.84        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A9PD TCGA-UY-A9PE 
       17.62        37.05        22.68        86.83        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SK 
        3.85        51.32        97.12         1.87        48.62        15.98 
TCGA-XF-A9ST TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-AAMJ TCGA-XF-AAML 
        4.21        23.64        28.24        26.27        54.90         7.63 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 
        8.32         6.77        98.99        44.32        56.48        61.45 
TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RM 
       86.30        13.64        25.41        28.41        94.29        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22         2.89        19.69        56.35        35.41 

$`DEL PEAK 27(14Q24.1) WILD-TYPE`
TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       94.88        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 
       50.04        66.54        10.22        29.65        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        13.15 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       26.14        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42B 
        8.25        17.16        20.48         4.67        12.82        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        36.43        28.41         8.98         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       13.97        12.59        12.13        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.46        12.10        12.26        12.00        12.10        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A3YL 
       11.87        18.58        13.08        12.92        18.48        29.79 
TCGA-CU-A72E TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AE TCGA-DK-A1AF 
       13.58        66.41        19.00        16.70        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
       15.62        46.68         7.79       142.78        87.32         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       13.58         8.15         8.22        21.30        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       20.81        10.55       163.30        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P 
       67.36        15.68        36.66        38.24        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 
       13.58       165.73        18.81        13.64        15.35        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       56.15        11.18        20.32        43.59        29.72         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
       26.24        24.66         1.22        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
        8.09        32.02        16.77         8.94        33.04         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM 
       12.62        22.52        27.98        60.66        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BR 
        5.52        12.85        27.35        14.96         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY 
       53.88        11.01        19.33         5.36         5.69         8.25 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD 
       27.45         2.70         7.10        13.35        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       12.36         2.27         9.67        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO 
        8.94         3.25        48.00        15.95        26.93        59.31 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 
       33.01         7.23         6.94        29.36        21.40        20.71 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 
       15.81        19.13        15.91        17.75        24.92         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P 
       13.91         2.10         3.12        20.98         2.20        10.92 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       18.97         7.63        32.78        20.05         5.62         4.73 
TCGA-GU-AATO TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       10.65         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WV 
       27.35         1.51         9.01        12.16        25.02        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        2.76         9.14        27.68         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        16.27        11.80        52.73        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       21.07        16.67        16.54        76.01        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC 
        3.02       112.83         3.91        29.56        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       97.45       125.49        15.35        17.88        64.80        79.66 
TCGA-XF-A9SJ TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SV 
        3.22        66.41        34.45        14.93         5.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 
       11.90        21.04        18.90         2.24        16.27        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
        2.10        13.74        92.98        10.82       110.60        11.31 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       71.57        91.73         2.96        30.94        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L 
       18.15         3.88        18.84         9.63         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        21.11        31.20        30.28        35.84        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.41         3.48        64.08        58.72        88.87        34.06 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA53 TCGA-ZF-AA54 
        8.61        59.38        60.16        63.02        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                        166.03                         165.73 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                         19.00                          16.27 
[1] "0.5 - 166.0 (19.0)" "0.1 - 165.7 (16.3)"
[1] "hr=" "1.2"
D60V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 27(14Q24.1) MUTATED         0       39        44       53
  DEL PEAK 27(14Q24.1) WILD-TYPE       2       90        96       82
D60V3, multiclass
           clus
vv          DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            39                             90
  STAGE III                           44                             96
  STAGE IV                            53                             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 27(14Q24.1) MUTATED         42  64  20
  DEL PEAK 27(14Q24.1) WILD-TYPE       81 131  38
D60V4, multiclass
          clus
vv         DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  T0+T1+T2                           42                             81
  T3                                 64                            131
  T4                                 20                             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                              N0  N1  N2  N3
  DEL PEAK 27(14Q24.1) MUTATED    71  12  38   2
  DEL PEAK 27(14Q24.1) WILD-TYPE 164  35  37   7
D60V5, multiclass
    clus
vv   DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  N0                           71                            164
  N1                           12                             35
  N2                           38                             37
  N3                            2                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED    63   3
  DEL PEAK 27(14Q24.1) WILD-TYPE 129   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED     63    3
  DEL PEAK 27(14Q24.1) WILD-TYPE  129    8
   clus
vv  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  0                           63                            129
  1                            3                              8
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED    29 108
  DEL PEAK 27(14Q24.1) WILD-TYPE  78 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED     29  108
  DEL PEAK 27(14Q24.1) WILD-TYPE   78  193
        clus
vv       DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  FEMALE                           29                             78
  MALE                            108                            193
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED   127   3
  DEL PEAK 27(14Q24.1) WILD-TYPE 237  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED    127    3
  DEL PEAK 27(14Q24.1) WILD-TYPE  237   16
     clus
vv    DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  NO                           127                            237
  YES                            3                             16
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
D60V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(14Q24.1) MUTATED      14                         5   111
  DEL PEAK 27(14Q24.1) WILD-TYPE    29                        17   216
D60V12, multiclass
                           clus
vv                          DEL PEAK 27(14Q24.1) MUTATED
  ASIAN                                               14
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                              111
                           clus
vv                          DEL PEAK 27(14Q24.1) WILD-TYPE
  ASIAN                                                 29
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                216
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED     3 120
  DEL PEAK 27(14Q24.1) WILD-TYPE   6 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED      3  120
  DEL PEAK 27(14Q24.1) WILD-TYPE    6  249
                        clus
vv                       DEL PEAK 27(14Q24.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       DEL PEAK 27(14Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            249
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 28(15Q13.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(15Q13.1) MUTATED    92  67
  DEL PEAK 28(15Q13.1) WILD-TYPE 137 110
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                           159                            247 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                            67                            110 
$`DEL PEAK 28(15Q13.1) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-5N-A9KI 
        8.35        27.62        51.16        15.12        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       17.42        40.08         2.66         6.58        19.04        26.14 
TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A42B TCGA-BT-A42C 
        8.35         8.25        16.18        20.48        17.56        28.70 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A47X TCGA-CU-A0YR TCGA-CU-A3QU 
       36.43         8.98         1.94        12.62        15.12         5.19 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
       66.41        18.41       112.44        46.68         7.79       142.78 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
        8.15         8.22        17.98        15.68        50.70        36.66 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 
       52.01        15.02       165.73        13.64        56.15        11.18 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME 
       12.03        43.59        22.16        25.58         0.56        24.03 
TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3N5 
        1.22        13.68        12.95         8.09        32.02        22.52 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV 
       60.66        24.30        29.16        25.74         7.56         5.36 
TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O 
        8.25        27.45        18.08        58.92         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       13.35        12.69         4.31        10.85        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B 
       11.08        61.94        26.93        20.12        17.62        66.02 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GD-A3OP 
       15.81        19.13        14.07        24.92         8.94         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 
        2.20         7.36        10.92         7.63         5.62         4.73 
TCGA-GU-AATO TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A40E 
       10.65        21.34        19.10        20.28         8.48         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WS 
       19.07        22.72        19.40        38.60        12.16        25.02 
TCGA-K4-A4AB TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76         9.07        11.70        17.72         1.81        15.42 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
       35.97        44.38        15.32        15.58        13.48        16.67 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       14.24        12.43        17.62        37.05        22.68        86.83 
TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB 
       76.01         3.91        29.56        17.82         6.21        45.04 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SJ 
       97.45        97.12        15.35         1.87        48.62         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T0 
       15.98        34.45        14.93         5.98        23.64        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAN2 
        2.24        66.64        54.90         7.63         2.96        61.45 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R9 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RG 
       11.97        13.64        28.41        94.29        64.08        58.72 
TCGA-ZF-A9RL TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V TCGA-ZF-AA4X 
       88.87         2.89        34.06        19.69        59.38        63.02 
TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        54.21        19.17 

$`DEL PEAK 28(15Q13.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       24.13        11.97        94.88       104.65       108.95        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A13I 
        0.62        41.75        66.54        10.22        29.65         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        12.39        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH 
        5.06        14.89        14.96         5.06        17.16         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       12.82         9.96        28.41        23.01        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       13.97        12.59        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA 
       12.66        12.46        12.10        12.26        13.12        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E 
       12.92         4.90        18.48        29.79         1.84        13.58 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       21.86         2.14        19.00        16.70       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       17.62        15.62        17.95        87.32         4.80        13.58 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
       17.72        50.27        21.30        23.21         9.67        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       163.30        66.05        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       67.36        38.24        13.58       166.03        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3X6 
       15.35        13.64        20.32        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        0.10         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
        4.24        24.66         0.92        14.07        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 
       16.77         8.94        33.04         4.01        12.62        27.98 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98         5.52        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       27.35        14.96        20.91         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TA 
       53.88        11.01        19.33         5.69         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TI 
       18.81         6.15        12.36         2.27         3.06         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66        10.65         8.94         3.25        48.00        15.95 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F 
       59.31        33.01         7.23         6.94        70.32        29.36 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 
       21.40        20.71        15.91        17.75         0.49        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 
        7.73         3.12        20.98        11.31        18.97        32.78 
TCGA-GU-A764 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JZ TCGA-GV-A3QI 
       20.05        32.98         7.00        14.27        19.82        36.49 
TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A3WV 
       27.35         1.51        64.01         9.01         3.45        21.24 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
        9.14        27.68        16.27        11.80        52.73        50.56 
TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 
       46.98         1.15        21.07        12.23         1.84        16.54 
TCGA-SY-A9G5 TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PF 
       38.99        78.25        69.34         3.02       112.83         3.85 
TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       51.32         6.58       125.49        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9SZ 
       66.41         4.21        12.76        11.90        21.04        28.24 
TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90        16.27         2.10        13.74        92.98        10.82 
TCGA-XF-AAMG TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMX 
      110.60        11.31        71.57        91.73         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN4 
       98.99        44.32        56.48        30.94        86.30        27.06 
TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       75.39        18.15         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       22.36        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U 
       21.86        13.41         3.48        47.84        20.22         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       60.16        56.35        57.90        19.40         8.52         5.52 
TCGA-ZF-AA5P 
       12.23 

  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                          0.56                           0.10 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                        165.73                         166.03 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                         17.62                          16.77 
[1] "0.6 - 165.7 (17.6)" "0.1 - 166.0 (16.8)"
[1] "hr=" "1.1"
D61V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 28(15Q13.1) MUTATED         1       45        54       59
  DEL PEAK 28(15Q13.1) WILD-TYPE       1       84        86       76
D61V3, multiclass
           clus
vv          DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            45                             84
  STAGE III                           54                             86
  STAGE IV                            59                             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"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 28(15Q13.1) MUTATED         43  81  19
  DEL PEAK 28(15Q13.1) WILD-TYPE       80 114  39
D61V4, multiclass
          clus
vv         DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  T0+T1+T2                           43                             80
  T3                                 81                            114
  T4                                 19                             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                              N0  N1  N2  N3
  DEL PEAK 28(15Q13.1) MUTATED    82  20  34   5
  DEL PEAK 28(15Q13.1) WILD-TYPE 153  27  41   4
D61V5, multiclass
    clus
vv   DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  N0                           82                            153
  N1                           20                             27
  N2                           34                             41
  N3                            5                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED    57   4
  DEL PEAK 28(15Q13.1) WILD-TYPE 135   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED     57    4
  DEL PEAK 28(15Q13.1) WILD-TYPE  135    7
   clus
vv  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  0                           57                            135
  1                            4                              7
[1] 2 2
[1] FALSE
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED    44 116
  DEL PEAK 28(15Q13.1) WILD-TYPE  63 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED     44  116
  DEL PEAK 28(15Q13.1) WILD-TYPE   63  185
        clus
vv       DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  FEMALE                           44                             63
  MALE                            116                            185
[1] 2 2
[1] FALSE
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED   145   5
  DEL PEAK 28(15Q13.1) WILD-TYPE 219  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED    145    5
  DEL PEAK 28(15Q13.1) WILD-TYPE  219   14
     clus
vv    DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  NO                           145                            219
  YES                            5                             14
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
D61V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(15Q13.1) MUTATED      10                         5   136
  DEL PEAK 28(15Q13.1) WILD-TYPE    33                        17   191
D61V12, multiclass
                           clus
vv                          DEL PEAK 28(15Q13.1) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                              136
                           clus
vv                          DEL PEAK 28(15Q13.1) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                191
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED     5 144
  DEL PEAK 28(15Q13.1) WILD-TYPE   4 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED      5  144
  DEL PEAK 28(15Q13.1) WILD-TYPE    4  225
                        clus
vv                       DEL PEAK 28(15Q13.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          144
                        clus
vv                       DEL PEAK 28(15Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 29(16P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16P13.3) MUTATED    98  76
  DEL PEAK 29(16P13.3) WILD-TYPE 131 101
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           174                            232 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                            76                            101 
$`DEL PEAK 29(16P13.3) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7W 
       24.13        11.97         8.35        16.27        16.77        27.62 
TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 
       41.75        15.12        10.22        47.80         2.50        40.08 
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20N TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA 
        2.66         6.58        26.14         5.06         8.35        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-BT-A42E TCGA-C4-A0F6 
       16.18         4.67        12.82        28.70        36.43        23.01 
TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A3KJ 
       12.56        12.66        11.34        11.87        12.92        18.48 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2HX TCGA-DK-A2I4 
        5.19         1.84        21.86        18.41        46.68       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV 
       87.32         4.80         8.15         8.22        21.30         9.67 
TCGA-DK-A3WX TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P 
       10.55        17.98        67.36        36.66        52.01        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A4TZ 
       13.58       165.73       166.03        11.18        12.03        15.35 
TCGA-E5-A4U1 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A3B3 TCGA-FD-A3B6 
       38.83        25.58         0.56        24.03        32.02        33.04 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BR 
       25.74        19.79         7.56        20.91        15.58        26.73 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
        5.36         8.25        27.45         2.70         7.10        13.35 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TK TCGA-FJ-A3Z7 
       12.69        12.36         2.27         4.31        10.85        31.07 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
       61.94        26.93        20.12        19.13        15.91        14.07 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       24.92         0.49         8.94         7.73         2.10         2.20 
TCGA-GU-A42P TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO 
       10.92        18.97         7.63         5.62         4.73        10.65 
TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A6ZA 
       32.98        21.34        19.10        19.82         8.48        22.72 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R 
       19.40        38.60        64.01        25.02         9.14        27.68 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41O 
        9.07        11.70        17.72         1.81        11.80        50.56 
TCGA-KQ-A41P TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN 
       35.97         1.15        15.32        15.58        13.48        16.67 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB 
        1.84        12.43        38.99        22.68        86.83        69.34 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
      112.83         3.91        29.56        17.82         6.21         3.85 
TCGA-XF-A8HC TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SI TCGA-XF-A9SM TCGA-XF-A9SP 
        6.58        97.12        15.35        79.66        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
        4.21         5.98        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMT TCGA-XF-AAMW 
       26.27         2.24         2.10         7.63         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
        6.77        44.32        56.48        61.45        86.30        18.15 
TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RF TCGA-ZF-A9RL 
       11.97        13.64        21.11        94.29        64.08        88.87 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        19.69         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       63.02        56.35        57.90        19.40        54.21        19.17 

$`DEL PEAK 29(16P13.3) WILD-TYPE`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65       108.95        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA89 
       34.98        50.04         0.62        51.16        66.54        29.65 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0YX TCGA-BT-A20J 
       17.42         7.33         6.74        12.39        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50        14.89        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0EZ 
        8.25        20.48         9.96        17.56        28.41         8.98 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
        1.94        12.79        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       12.16        10.95        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FL TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 
        4.90        15.12        29.79        13.58         2.14        66.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00        16.70       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS 
       15.62        17.95         7.79        13.58        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       23.21        20.81       163.30        66.05        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6T TCGA-DK-AA6U 
       76.60        15.68        50.70        38.24        18.81        19.00 
TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A2PC 
       13.64        15.35        13.64        56.15        20.32        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       29.72         0.10        22.16         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
       26.96        26.24         4.24        24.66         0.92         1.22 
TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       13.68        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       16.77         8.94         4.01        12.62        22.52        27.98 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       60.66        24.30        23.41        17.98        29.16         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A5BS 
       46.78        12.85        27.35        14.96         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       11.01        19.33         5.69        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z9 
       62.86        18.81         6.15         3.06         9.67        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ 
       10.65        17.23         8.94         3.25        11.08        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B 
       15.95        59.31        33.01         7.23        17.62        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        6.94        70.32        29.36        21.40        20.71        15.81 
TCGA-GC-A3WC TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42Q 
       17.75        13.91         3.12        20.98         7.36        11.31 
TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QI 
       32.78        20.05         7.00        14.27        20.28        36.49 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A5ND TCGA-HQ-A5NE 
       27.35         8.58        19.07         1.51         9.01        12.16 
TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41N 
        3.45        21.24         2.76        15.42        16.27        52.73 
TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-R3-A69X TCGA-S5-AA26 
       46.98        44.38        21.07        12.23        14.24        16.54 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PH 
       17.62        37.05        76.01        78.25         3.02        51.32 
TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       45.04        97.45       125.49         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SV TCGA-XF-A9T2 
       64.80         3.22        15.98        66.41        12.76        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG 
       16.27        66.64        13.74        92.98        10.82       110.60 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 
       11.31        54.90        71.57        91.73        98.99        30.94 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC 
       27.06        75.39         3.88        18.84         9.63         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       22.36        25.41        31.20        30.28        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-AA4R TCGA-ZF-AA4W 
       28.41        13.41         3.48        58.72        34.06        60.16 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       35.41         8.52         5.52        12.23 

  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                        166.03                         163.30 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                         16.72                          17.49 
[1] "0.5 - 166.0 (16.7)" "0.1 - 163.3 (17.5)"
[1] "hr=" "1.1"
D62V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 29(16P13.3) MUTATED         1       46        64       62
  DEL PEAK 29(16P13.3) WILD-TYPE       1       83        76       73
D62V3, multiclass
           clus
vv          DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            46                             83
  STAGE III                           64                             76
  STAGE IV                            62                             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"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 29(16P13.3) MUTATED         43  93  25
  DEL PEAK 29(16P13.3) WILD-TYPE       80 102  33
D62V4, multiclass
          clus
vv         DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  T0+T1+T2                           43                             80
  T3                                 93                            102
  T4                                 25                             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                              N0  N1  N2  N3
  DEL PEAK 29(16P13.3) MUTATED    90  16  43   3
  DEL PEAK 29(16P13.3) WILD-TYPE 145  31  32   6
D62V5, multiclass
    clus
vv   DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  N0                           90                            145
  N1                           16                             31
  N2                           43                             32
  N3                            3                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED    70   4
  DEL PEAK 29(16P13.3) WILD-TYPE 122   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED     70    4
  DEL PEAK 29(16P13.3) WILD-TYPE  122    7
   clus
vv  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  0                           70                            122
  1                            4                              7
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED    49 125
  DEL PEAK 29(16P13.3) WILD-TYPE  58 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED     49  125
  DEL PEAK 29(16P13.3) WILD-TYPE   58  176
        clus
vv       DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  FEMALE                           49                             58
  MALE                            125                            176
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED   153   5
  DEL PEAK 29(16P13.3) WILD-TYPE 211  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED    153    5
  DEL PEAK 29(16P13.3) WILD-TYPE  211   14
     clus
vv    DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  NO                           153                            211
  YES                            5                             14
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
D62V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16P13.3) MUTATED      10                         6   150
  DEL PEAK 29(16P13.3) WILD-TYPE    33                        16   177
D62V12, multiclass
                           clus
vv                          DEL PEAK 29(16P13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              150
                           clus
vv                          DEL PEAK 29(16P13.3) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                177
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED     3 158
  DEL PEAK 29(16P13.3) WILD-TYPE   6 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED      3  158
  DEL PEAK 29(16P13.3) WILD-TYPE    6  211
                        clus
vv                       DEL PEAK 29(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          158
                        clus
vv                       DEL PEAK 29(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            211
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 30(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q23.1) MUTATED    70  49
  DEL PEAK 30(16Q23.1) WILD-TYPE 159 128
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           119                            287 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                            49                            128 
$`DEL PEAK 30(16Q23.1) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA86 
       16.27        16.77         0.62        41.75        15.12        10.22 
TCGA-BL-A0C8 TCGA-CU-A0YN TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AC 
       40.08        12.92         5.19         1.84        21.86       130.88 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IN 
       46.68        17.95         7.79       142.78        87.32         8.22 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M 
        9.67        20.81        17.98        67.36        36.66        52.01 
TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA76 TCGA-E5-A4TZ 
       15.02       165.73        19.00        13.64        12.03        15.35 
TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       22.16        25.58        26.96        24.03        13.68        12.95 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43U 
        8.94        22.52         5.52        12.85         7.56        20.91 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 
        2.70         7.10         6.15        12.69        12.36        31.07 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD 
       11.08        61.94        48.00        20.12        15.91        14.07 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A766 
        2.10         2.20        10.92        11.31         7.63         5.62 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        19.10        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A4AC TCGA-K4-A5RI 
       36.49        19.40        38.60        21.24         9.14        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41R TCGA-KQ-A41S 
       17.72         1.81        50.56        35.97        44.38         1.15 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A8OB 
       15.58        13.48        12.23        12.43        86.83        69.34 
TCGA-UY-A9PA TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.91         3.85         6.58       125.49        97.12        15.35 
TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
       79.66         3.22        14.93        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML TCGA-XF-AAN0 
       26.27         2.10        10.82       110.60         7.63        56.48 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R4 
       86.30        18.15         0.66        11.97        13.64        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U 
       94.29         3.48        64.08         2.89        19.69         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA53 
       59.38        60.16        63.02        56.35        57.90 

$`DEL PEAK 30(16Q23.1) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-2F-A9KW 
       24.13        11.97        94.88       104.65       108.95         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       44.94        16.83        17.16        34.98        27.62        50.04 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        47.80        29.65         2.50        17.42 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX 
        7.33         2.66         6.74        12.39         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        26.14        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A20X TCGA-BT-A2LA 
       14.89        14.96         5.06         8.35         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
       16.18        20.48         4.67        12.82         9.96        17.56 
TCGA-BT-A42C TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 
       28.70        36.43        28.41         8.98         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH 
       12.79        12.56        13.97        12.59        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       12.16        10.95        12.66        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY 
       12.26        13.12        12.00        12.10        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       11.87        18.58        13.08         4.90        15.12        18.48 
TCGA-CU-A3YL TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       29.79        13.58         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK 
       16.70       112.44        16.14        17.62        15.62         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       13.58         8.15        17.72        50.27        21.30        23.21 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       10.55       163.30        66.05        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6S TCGA-DK-AA6T 
       15.68        50.70        38.24        13.58       166.03        18.81 
TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A2PC 
       15.35        13.64        56.15        11.18        20.32        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       38.83        29.72         0.10         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7DV 
        0.66        26.24         4.24        24.66         0.92         1.22 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       14.07        15.32        14.37         8.09        32.02        16.77 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       33.04         4.01        12.62        27.98        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       23.41        17.98        29.16        25.74        46.78        19.79 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TB 
       18.08        58.92         6.28        13.35        62.86        18.81 
TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.27         3.06         4.31         9.67        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL 
       10.65        17.23         8.94         3.25        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3C 
       59.31        33.01         7.23        17.62        66.02         6.94 
TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       70.32        29.36        21.40        20.71        15.81        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       17.75        24.92         0.49         8.94        13.91         7.73 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A76B TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-A764 
        3.12        20.98         7.36        18.97        32.78        20.05 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW TCGA-GV-A3QK TCGA-GV-A40E 
        4.73        10.65        32.98        21.34        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE 
       19.07        22.72         1.51        64.01         9.01        12.16 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6MB 
       25.02         3.45         2.76        27.68         9.07        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-LC-A66R TCGA-LT-A8JT 
       16.27        11.80        52.73        46.98        15.32        21.07 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       16.67        14.24         1.84        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        76.01        78.25         3.02       112.83 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD 
       29.56        17.82         6.21        51.32        45.04        97.45 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SK TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        15.98        66.41 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SZ TCGA-XF-A9T2 
       34.45         4.21         5.98        12.76        28.24        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH 
        2.24        16.27        66.64        13.74        92.98        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       54.90        71.57        91.73         2.96         8.32         6.77 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 
       98.99        44.32        30.94        61.45        27.06        75.39 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 
        3.88        18.84         9.63        22.36        25.41        21.11 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG 
       31.20        35.84        21.86        28.41        13.41        58.72 
TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA52 TCGA-ZF-AA54 
       88.87        47.84        20.22        34.06        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21        19.17         5.52        12.23 

  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                          0.62                           0.10 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                        165.73                         166.03 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                         15.91                          17.56 
[1] "0.6 - 165.7 (15.9)" "0.1 - 166.0 (17.6)"
[1] "hr=" "1.1"
D63V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 30(16Q23.1) MUTATED         1       39        36       42
  DEL PEAK 30(16Q23.1) WILD-TYPE       1       90       104       93
D63V3, multiclass
           clus
vv          DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            39                             90
  STAGE III                           36                            104
  STAGE IV                            42                             93
[1] 4 2
[1] 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(16Q23.1) MUTATED         33  54  18
  DEL PEAK 30(16Q23.1) WILD-TYPE       90 141  40
D63V4, multiclass
          clus
vv         DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  T0+T1+T2                           33                             90
  T3                                 54                            141
  T4                                 18                             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                              N0  N1  N2  N3
  DEL PEAK 30(16Q23.1) MUTATED    56  13  24   4
  DEL PEAK 30(16Q23.1) WILD-TYPE 179  34  51   5
D63V5, multiclass
    clus
vv   DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  N0                           56                            179
  N1                           13                             34
  N2                           24                             51
  N3                            4                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED    49   4
  DEL PEAK 30(16Q23.1) WILD-TYPE 143   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     49    4
  DEL PEAK 30(16Q23.1) WILD-TYPE  143    7
   clus
vv  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  0                           49                            143
  1                            4                              7
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED    23  96
  DEL PEAK 30(16Q23.1) WILD-TYPE  84 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED     23   96
  DEL PEAK 30(16Q23.1) WILD-TYPE   84  205
        clus
vv       DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  FEMALE                           23                             84
  MALE                             96                            205
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED   107   5
  DEL PEAK 30(16Q23.1) WILD-TYPE 257  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED    107    5
  DEL PEAK 30(16Q23.1) WILD-TYPE  257   14
     clus
vv    DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  NO                           107                            257
  YES                            5                             14
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
D63V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(16Q23.1) MUTATED       8                         4   103
  DEL PEAK 30(16Q23.1) WILD-TYPE    35                        18   224
D63V12, multiclass
                           clus
vv                          DEL PEAK 30(16Q23.1) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                              103
                           clus
vv                          DEL PEAK 30(16Q23.1) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED     5 104
  DEL PEAK 30(16Q23.1) WILD-TYPE   4 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED      5  104
  DEL PEAK 30(16Q23.1) WILD-TYPE    4  265
                        clus
vv                       DEL PEAK 30(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 30(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            265
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 31(17P12) MUTATION ANALYSIS
D64V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(17P12) MUTATED   117  92
  DEL PEAK 31(17P12) WILD-TYPE 112  85
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         209                          197 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                          92                           85 
$`DEL PEAK 31(17P12) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7R TCGA-4Z-AA7S 
       24.13       104.65       108.95        16.27        17.16        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 
        0.62        51.16        15.12        47.80        17.42        40.08 
TCGA-BL-A13J TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q 
        2.66        12.39        19.04        26.14        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A3PK 
       14.89         8.25        17.16        16.18         4.67         9.96 
TCGA-BT-A42E TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       36.43         8.98         1.94        12.79        12.56        13.97 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5UA TCGA-CU-A3KJ TCGA-CU-A5W6 
       12.13        12.16        12.62        12.00        18.48         1.84 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
        2.14        66.41        18.41        16.70       130.88       112.44 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN 
       46.68        17.95        87.32         4.80        13.58         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       17.72        50.27        21.30         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6R 
       64.18        50.70        36.66        15.02        13.58       165.73 
TCGA-DK-AA6S TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC 
      166.03        19.00        15.35        11.18        12.03        43.59 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 
       15.35        38.83        22.16        25.58         0.56        26.96 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7DU TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
        4.24        24.03         0.92        13.68        12.95         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO 
       16.77         8.94        60.66        24.30        29.16         5.52 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43X 
       46.78        12.85         7.56        27.35        20.91         3.62 
TCGA-FD-A5BR TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S 
       26.73         5.36         8.25         7.10         6.28        13.35 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TK 
       62.86        18.81         6.15        12.69         3.06        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
       31.07        10.65        61.94        48.00        26.93        59.31 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3B TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       20.12        17.62        66.02        70.32        21.40        19.13 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       14.07        24.92         0.49        13.91         7.73         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.20         7.36        10.92        11.31        18.97         7.63 
TCGA-GU-A767 TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.73        32.98         7.00        19.82        20.28         8.48 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
        8.58        19.07        19.40        38.60        64.01         9.01 
TCGA-HQ-A5NE TCGA-K4-A4AC TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO 
       12.16         9.14        11.70        17.72        15.42        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-PQ-A6FN 
       52.73        50.56        46.98         1.15        12.23        16.67 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O 
       14.24         1.84        12.43        38.99        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE 
       78.25        69.34         3.02       112.83        17.82         6.21 
TCGA-UY-A9PF TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG 
        3.85        51.32        97.45       125.49        97.12        15.35 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP 
        1.87        48.62        79.66         3.22        15.98        14.93 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T3 TCGA-XF-AAMF 
        4.21         5.98        23.64        28.24         2.24        10.82 
TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMW 
      110.60        54.90        71.57        91.73         2.96         8.32 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-YF-AA3L 
       98.99        44.32        56.48        30.94        86.30        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       13.64        22.36        25.41        31.20        21.86        28.41 
TCGA-ZF-A9RE TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
        3.48        58.72        88.87        47.84        20.22         2.89 
TCGA-ZF-AA4T TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA56 
       19.69        60.16        56.35        57.90         8.52 

$`DEL PEAK 31(17P12) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q 
       11.97        94.88         8.35        44.94        16.83        16.77 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA89 
       27.62        50.04        41.75        66.54        10.22        29.65 
TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        2.50         7.33         6.74         6.58        13.15        12.16 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ 
        5.06        14.96         5.06         8.35        20.48        12.82 
TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A3MF TCGA-CF-A3MH 
       17.56        28.70        28.41        23.01        12.59        13.08 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM 
       12.10        11.34        11.34        11.87        18.58        13.08 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A72E 
       12.92         4.90        15.12         5.19        29.79        13.58 
TCGA-DK-A1A3 TCGA-DK-A1AA TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       21.86        19.00        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
      142.78         8.15        23.21        20.81        10.55       163.30 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        76.60        67.36        15.68        38.24        52.01 
TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A3X6 
       18.81        13.64        13.64        56.15        20.32        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MF 
        0.10         2.24        16.70         0.66        26.24        24.66 
TCGA-E7-A7DV TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B6 
        1.22        14.07        15.32        14.37        32.02        33.04 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM 
        4.01        12.62        22.52        27.98        23.41        17.98 
TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A43S TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       25.74        19.79        14.96        15.58        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62N 
       19.33         5.69        27.45        18.08        58.92         2.70 
TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z9 TCGA-FJ-A3ZF 
       12.36         2.27         4.31         9.67        12.66        17.23 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB 
        8.94         3.25        11.08        15.95        33.01         7.23 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3WC 
        6.94        29.36        20.71        15.81        15.91        17.75 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
        8.94         3.12        20.98        32.78        20.05         5.62 
TCGA-GU-AATO TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-GV-A3QK 
       10.65        14.27        21.34        19.10        36.49        27.35 
TCGA-GV-A6ZA TCGA-H4-A2HO TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB 
       22.72         1.51        25.02         3.45        21.24         2.76 
TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41P TCGA-KQ-A41R 
       27.68         9.07         1.81        16.27        35.97        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K 
       15.32        15.58        21.07        13.48        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78N TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC 
       37.05        86.83         3.91        29.56        45.04         6.58 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SW 
       17.88        64.80        66.41        34.45        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90        16.27        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMX TCGA-XF-AAN2 
       13.74        92.98        11.31         7.63         6.77        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC TCGA-ZF-A9RD 
        0.66        21.11        30.28        35.84        94.29        13.41 
TCGA-ZF-A9RF TCGA-ZF-AA4R TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 
       64.08        34.06         8.61        59.38        63.02        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-ZF-AA5P 
       19.40        54.21        19.17         5.52        12.23 

  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                        0.49                         0.10 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                      166.03                       163.30 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                       17.72                        16.54 
[1] "0.5 - 166.0 (17.7)" "0.1 - 163.3 (16.5)"
[1] "hr=" "1.1"
D64V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 31(17P12) MUTATED         1       61        70       76
  DEL PEAK 31(17P12) WILD-TYPE       1       68        70       59
D64V3, multiclass
           clus
vv          DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  STAGE I                            1                            1
  STAGE II                          61                           68
  STAGE III                         70                           70
  STAGE IV                          76                           59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1+T2 T3 T4
  DEL PEAK 31(17P12) MUTATED         56 99 35
  DEL PEAK 31(17P12) WILD-TYPE       67 96 23
D64V4, multiclass
          clus
vv         DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  T0+T1+T2                         56                           67
  T3                               99                           96
  T4                               35                           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                            N0  N1  N2  N3
  DEL PEAK 31(17P12) MUTATED   113  24  46   4
  DEL PEAK 31(17P12) WILD-TYPE 122  23  29   5
D64V5, multiclass
    clus
vv   DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  N0                        113                          122
  N1                         24                           23
  N2                         46                           29
  N3                          4                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                              cls
clus                            0  1
  DEL PEAK 31(17P12) MUTATED   97  4
  DEL PEAK 31(17P12) WILD-TYPE 95  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED     97    4
  DEL PEAK 31(17P12) WILD-TYPE   95    7
   clus
vv  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  0                         97                           95
  1                          4                            7
[1] 2 2
[1] FALSE
D64V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(17P12) MUTATED    59 150
  DEL PEAK 31(17P12) WILD-TYPE  48 151
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED     59  150
  DEL PEAK 31(17P12) WILD-TYPE   48  151
        clus
vv       DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  FEMALE                         59                           48
  MALE                          150                          151
[1] 2 2
[1] FALSE
D64V8, binary
                              cls
clus                             0   1
  DEL PEAK 31(17P12) MUTATED   189   7
  DEL PEAK 31(17P12) WILD-TYPE 175  12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED    189    7
  DEL PEAK 31(17P12) WILD-TYPE  175   12
     clus
vv    DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  NO                         189                          175
  YES                          7                           12
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
D64V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(17P12) MUTATED      18                        12   165
  DEL PEAK 31(17P12) WILD-TYPE    25                        10   162
D64V12, multiclass
                           clus
vv                          DEL PEAK 31(17P12) MUTATED
  ASIAN                                             18
  BLACK OR AFRICAN AMERICAN                         12
  WHITE                                            165
                           clus
vv                          DEL PEAK 31(17P12) WILD-TYPE
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                              cls
clus                             0   1
  DEL PEAK 31(17P12) MUTATED     6 183
  DEL PEAK 31(17P12) WILD-TYPE   3 186
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED      6  183
  DEL PEAK 31(17P12) WILD-TYPE    3  186
                        clus
vv                       DEL PEAK 31(17P12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        183
                        clus
vv                       DEL PEAK 31(17P12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          186
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 32(18Q23) MUTATION ANALYSIS
D65V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(18Q23) MUTATED   109  71
  DEL PEAK 32(18Q23) WILD-TYPE 120 106
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         180                          226 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                          71                          106 
$`DEL PEAK 32(18Q23) MUTATED`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7R 
       24.13        94.88       104.65         8.35        16.27        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI 
       34.98        27.62        51.16        66.54        10.22         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
       17.42        40.08         2.66        13.15        19.04        26.14 
TCGA-BT-A20R TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        5.06         8.35        17.16        17.56        28.70        36.43 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
       12.79        12.56        12.13        13.08        12.16        10.95 
TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A0YN TCGA-CU-A0YR 
       12.66        11.34        11.34        11.87        12.92        15.12 
TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC 
        1.84        13.58         2.14        18.41        16.70       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I6 
      112.44        16.14        17.62        46.68        17.95        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT 
        4.80        13.58         8.15         8.22        50.27        21.30 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6P 
       66.05        64.18        15.68        50.70        52.01        15.02 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6X TCGA-DK-AA74 TCGA-E5-A2PC TCGA-E7-A3X6 
      165.73       166.03        15.35        56.15        43.59        29.72 
TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7DV TCGA-E7-A85H 
       25.58         0.56        26.96         4.24         1.22        12.95 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN 
        8.09        16.77         4.01        60.66        24.30        29.16 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y 
        5.52        25.74        46.78        12.85         7.56        15.58 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG 
        2.70         7.10        13.35        62.86        12.69         3.06 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F 
        4.31        17.23        61.94        20.12        66.02        29.36 
TCGA-GC-A3BM TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 
       21.40        15.91        14.07        24.92         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GU-A762 
       13.91         2.10        20.98         2.20        10.92         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JW 
       20.05         5.62         4.73        10.65        32.98        21.34 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40G TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10        19.82        19.07        22.72        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WS TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-AAQO 
       64.01        25.02         9.07        11.70        17.72        11.80 
TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
       52.73        46.98         1.15        15.32        13.48        12.23 
TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB 
       16.67        14.24        12.43        38.99        76.01        69.34 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HF 
       29.56        17.82         6.21         3.85         6.58        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX 
        3.22        15.98        14.93         4.21        11.90        23.64 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       66.64         2.10       110.60        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3L 
       91.73         2.96         6.77        44.32        86.30        11.97 
TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R2 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       13.64        22.36        21.11        21.86        28.41        13.41 
TCGA-ZF-A9RG TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       58.72        88.87        47.84         2.89         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        57.90        19.40        54.21        19.17 

$`DEL PEAK 32(18Q23) WILD-TYPE`
TCGA-2F-A9KP TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7Y 
       11.97       108.95        44.94        16.83        16.77        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA84 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-BL-A13I 
        0.62        41.75        15.12        47.80        29.65         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        12.39         6.58        12.16        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A2LD 
       14.89        14.96         5.06         8.25        16.18        20.48 
TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
        4.67        12.82         9.96        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       23.01        13.97        12.59        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FL TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        18.58        13.08 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
        4.90        18.48         5.19        29.79        21.86        66.41 
TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IQ TCGA-DK-A3IU 
       19.00        15.62         7.79       142.78        17.72        23.21 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X2 TCGA-DK-A6AW 
        9.67        20.81        10.55       163.30        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6T 
       76.60        67.36        36.66        38.24        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA76 TCGA-DK-AA77 
       19.00        13.64        13.64        11.18        12.03        20.32 
TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83         0.10        22.16         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
        0.66        26.24        24.03        24.66         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       14.07        15.32        14.37        32.02         8.94        33.04 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR 
       12.62        22.52        27.98        23.41        17.98        19.79 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5BZ 
       11.01        19.33         5.36         5.69         8.25        27.45 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
       18.08        58.92         6.28        18.81         6.15        12.36 
TCGA-FD-A6TF TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        2.27         9.67        10.85        31.07        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
        8.94         3.25        11.08        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D 
       59.31        33.01         7.23        17.62         6.94        70.32 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GD-A2C5 TCGA-GD-A3OQ 
       20.71        15.81        19.13        17.75         7.73         3.12 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A763 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.36        11.31        18.97        32.78         7.00        14.27 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO 
       20.28         8.48        36.49        27.35         8.58         1.51 
TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
        9.01        12.16         3.45        21.24         2.76         9.14 
TCGA-K4-A54R TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41O TCGA-KQ-A41P 
       27.68         1.81        15.42        16.27        50.56        35.97 
TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78K 
       44.38        15.58        21.07         1.84        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        86.83        78.25         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        3.91        51.32        45.04        97.45       125.49        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        1.87        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SM TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 
       34.45         5.98        12.76        21.04        28.24        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF 
       18.90         2.24        16.27        13.74        92.98        10.82 
TCGA-XF-AAMH TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
       11.31         8.32        98.99        56.48        30.94        61.45 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       27.06        75.39        18.15         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RC 
        0.66        25.41        31.20        30.28        35.84        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
        3.48        64.08        20.22        34.06        19.69        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-ZF-AA5P 
       63.02         8.52         5.52        12.23 

  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                        0.49                         0.10 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                      166.03                       163.30 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                      17.195                       17.225 
[1] "0.5 - 166.0 (17.2)" "0.1 - 163.3 (17.2)"
[1] "hr=" "1.3"
D65V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 32(18Q23) MUTATED         1       51        66       61
  DEL PEAK 32(18Q23) WILD-TYPE       1       78        74       74
D65V3, multiclass
           clus
vv          DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  STAGE I                            1                            1
  STAGE II                          51                           78
  STAGE III                         66                           74
  STAGE IV                          61                           74
[1] 4 2
[1] 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(18Q23) MUTATED         51  92  26
  DEL PEAK 32(18Q23) WILD-TYPE       72 103  32
D65V4, multiclass
          clus
vv         DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  T0+T1+T2                         51                           72
  T3                               92                          103
  T4                               26                           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                            N0  N1  N2  N3
  DEL PEAK 32(18Q23) MUTATED   102  19  37   4
  DEL PEAK 32(18Q23) WILD-TYPE 133  28  38   5
D65V5, multiclass
    clus
vv   DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  N0                        102                          133
  N1                         19                           28
  N2                         37                           38
  N3                          4                            5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED    86   1
  DEL PEAK 32(18Q23) WILD-TYPE 106  10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED     86    1
  DEL PEAK 32(18Q23) WILD-TYPE  106   10
   clus
vv  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  0                         86                          106
  1                          1                           10
[1] 2 2
[1] FALSE
D65V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED    50 130
  DEL PEAK 32(18Q23) WILD-TYPE  57 171
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED     50  130
  DEL PEAK 32(18Q23) WILD-TYPE   57  171
        clus
vv       DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  FEMALE                         50                           57
  MALE                          130                          171
[1] 2 2
[1] FALSE
D65V8, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED   162   6
  DEL PEAK 32(18Q23) WILD-TYPE 202  13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED    162    6
  DEL PEAK 32(18Q23) WILD-TYPE  202   13
     clus
vv    DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  NO                         162                          202
  YES                          6                           13
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
D65V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(18Q23) MUTATED      17                        11   146
  DEL PEAK 32(18Q23) WILD-TYPE    26                        11   181
D65V12, multiclass
                           clus
vv                          DEL PEAK 32(18Q23) MUTATED
  ASIAN                                             17
  BLACK OR AFRICAN AMERICAN                         11
  WHITE                                            146
                           clus
vv                          DEL PEAK 32(18Q23) WILD-TYPE
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED     5 161
  DEL PEAK 32(18Q23) WILD-TYPE   4 208
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED      5  161
  DEL PEAK 32(18Q23) WILD-TYPE    4  208
                        clus
vv                       DEL PEAK 32(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        161
                        clus
vv                       DEL PEAK 32(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          208
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 33(19P13.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(19P13.3) MUTATED    76  70
  DEL PEAK 33(19P13.3) WILD-TYPE 153 107
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           146                            260 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            70                            107 
$`DEL PEAK 33(19P13.3) MUTATED`
TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-5N-A9KI 
        8.35        27.62         0.62        51.16        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A5ZZ TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20T 
       17.42        40.08        12.39        19.04         5.06        14.89 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
        5.06         8.35        16.18        20.48         4.67         9.96 
TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.56        36.43        28.41         8.98        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-DK-A1A5 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AD 
       12.56        12.13         2.14        18.41        16.70       112.44 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 
       87.32        13.58        17.72        21.30        66.05        17.98 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q TCGA-DK-AA6W TCGA-DK-AA6X TCGA-DK-AA75 
       50.70        38.24        13.58        13.64        15.35        11.18 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A7DV TCGA-E7-A85H 
       12.03        43.59        15.35        22.16         1.22        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL 
       14.37         8.09        16.77        33.04        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SS TCGA-FD-A43N TCGA-FD-A43Y 
       17.98        29.16         5.52        12.85         7.56        15.58 
TCGA-FD-A5BV TCGA-FD-A5BY TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TB 
        5.36         8.25        27.45        18.08        58.92        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TH TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
        6.15        12.36         2.27         4.31        10.65        17.23 
TCGA-FJ-A871 TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
        8.94        11.08        61.94        33.01         7.23        20.12 
TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GC-A6I1 
       17.62        29.36        20.71        19.13        24.92         8.94 
TCGA-GU-A42P TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-AATO TCGA-GU-AATQ 
       10.92        11.31        18.97         7.63        10.65         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10        19.82        19.07         1.51        19.40 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
        9.01        25.02        27.68         9.07        17.72        15.42 
TCGA-KQ-A41Q TCGA-KQ-A41S TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-R3-A69X 
       46.98         1.15        13.48        12.23        16.67        14.24 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A78P 
       16.54        38.99        37.05        22.68        86.83        78.25 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB 
       69.34       112.83         3.91        29.56         3.85        45.04 
TCGA-XF-A8HF TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9ST 
       97.12        48.62        64.80         3.22        34.45         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMG TCGA-XF-AAMJ 
       12.76        11.90        66.64         2.10       110.60        54.90 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9R9 
        2.96         6.77        86.30        13.64        30.28        28.41 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4V 
       94.29        88.87        47.84        34.06        19.69        59.38 
TCGA-ZF-AA53 TCGA-ZF-AA5H 
       57.90        19.17 

$`DEL PEAK 33(19P13.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7M 
       24.13        11.97        94.88       104.65       108.95        16.27 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Q TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       44.94        16.83        16.77        17.16        34.98        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA89 TCGA-BL-A13I 
       41.75        66.54        15.12        10.22        29.65         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O 
        2.66         6.74         6.58        13.15        26.14        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PJ 
       17.88        19.50        14.96         8.25        17.16        12.82 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI 
       28.70         1.94        13.97        12.59        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       10.95        12.66        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       13.12        12.00        12.10        11.34        11.34        11.87 
TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       18.58        13.08        12.92         4.90        15.12        18.48 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 
        5.19        29.79         1.84        13.58        21.86        66.41 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
       19.00       130.88        16.14        17.62        15.62        46.68 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN 
       17.95         7.79       142.78         4.80         8.15         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       50.27        23.21         9.67        20.81        10.55       163.30 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 
       64.18        53.29        76.60        67.36        15.68        36.66 
TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6T TCGA-DK-AA6U 
       52.01        15.02       165.73       166.03        18.81        19.00 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.64        56.15        20.32        38.83        29.72         0.10 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        2.24        16.70        25.58         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7DU TCGA-E7-A7PW 
       26.24         4.24        24.03        24.66         0.92        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
       14.07        15.32        32.02         8.94         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.52        27.98        60.66        25.74        46.78        19.79 
TCGA-FD-A43P TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       27.35        14.96        20.91         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P 
       11.01        19.33         5.69         2.70         7.10         6.28 
TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FD-A6TK 
       13.35        62.86        12.69         3.06         9.67        10.85 
TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       31.07        12.66         3.25        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3OO 
       59.31        66.02         6.94        70.32        21.40        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        14.07        17.75         0.49        13.91         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A763 
        2.10         3.12        20.98         2.20         7.36        32.78 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATP TCGA-GV-A3JV TCGA-GV-A3QF 
       20.05         5.62         4.73        32.98        14.27        20.28 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A2OE 
        8.48        36.49        27.35         8.58        22.72        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC 
       64.01        12.16         3.45        21.24         2.76         9.14 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41N TCGA-KQ-A41O 
       11.70         1.81        16.27        11.80        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-A6DX 
       35.97        44.38        15.32        15.58        21.07         1.84 
TCGA-SY-A9G0 TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE 
       12.43        17.62        76.01         3.02        17.82         6.21 
TCGA-UY-A9PH TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A8HH 
       51.32         6.58        97.45       125.49        15.35         1.87 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SP TCGA-XF-A9SU 
       17.88        79.66        15.98        66.41        14.93         5.98 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       23.64        21.04        28.24        26.27        18.90         2.24 
TCGA-XF-A9T4 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML 
       16.27        13.74        92.98        10.82        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 
       71.57        91.73         8.32        98.99        44.32        56.48 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 TCGA-XF-AAN8 
       30.94        61.45        27.06        75.39        18.15         3.88 
TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       18.84         9.63         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RE 
       21.11        31.20        35.84        21.86        13.41         3.48 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       64.08        58.72        20.22         2.89         8.61        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       63.02        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                          0.62                           0.10 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        112.83                         166.03 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        17.670                         16.735 
[1] "0.6 - 112.8 (17.7)" "0.1 - 166.0 (16.7)"
[1] "hr=" "1.2"
D66V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 33(19P13.3) MUTATED         1       34        52       59
  DEL PEAK 33(19P13.3) WILD-TYPE       1       95        88       76
D66V3, multiclass
           clus
vv          DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            34                             95
  STAGE III                           52                             88
  STAGE IV                            59                             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"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 33(19P13.3) MUTATED         33  76  26
  DEL PEAK 33(19P13.3) WILD-TYPE       90 119  32
D66V4, multiclass
          clus
vv         DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  T0+T1+T2                           33                             90
  T3                                 76                            119
  T4                                 26                             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                              N0  N1  N2  N3
  DEL PEAK 33(19P13.3) MUTATED    73  23  30   5
  DEL PEAK 33(19P13.3) WILD-TYPE 162  24  45   4
D66V5, multiclass
    clus
vv   DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  N0                           73                            162
  N1                           23                             24
  N2                           30                             45
  N3                            5                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    54   7
  DEL PEAK 33(19P13.3) WILD-TYPE 138   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     54    7
  DEL PEAK 33(19P13.3) WILD-TYPE  138    4
   clus
vv  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  0                           54                            138
  1                            7                              4
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    40 106
  DEL PEAK 33(19P13.3) WILD-TYPE  67 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     40  106
  DEL PEAK 33(19P13.3) WILD-TYPE   67  195
        clus
vv       DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  FEMALE                           40                             67
  MALE                            106                            195
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED   136   4
  DEL PEAK 33(19P13.3) WILD-TYPE 228  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED    136    4
  DEL PEAK 33(19P13.3) WILD-TYPE  228   15
     clus
vv    DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  NO                           136                            228
  YES                            4                             15
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, continuous
D66V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(19P13.3) MUTATED      10                         9   121
  DEL PEAK 33(19P13.3) WILD-TYPE    33                        13   206
D66V12, multiclass
                           clus
vv                          DEL PEAK 33(19P13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              121
                           clus
vv                          DEL PEAK 33(19P13.3) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                206
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED     6 131
  DEL PEAK 33(19P13.3) WILD-TYPE   3 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED      6  131
  DEL PEAK 33(19P13.3) WILD-TYPE    3  238
                        clus
vv                       DEL PEAK 33(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          131
                        clus
vv                       DEL PEAK 33(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 34(22Q13.32) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 34(22Q13.32) MUTATED   104  83
  DEL PEAK 34(22Q13.32) WILD-TYPE 125  94
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            187                             219 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                             83                              94 
$`DEL PEAK 34(22Q13.32) MUTATED`
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA7W TCGA-4Z-AA80 
       11.97         8.35        16.27        16.77        27.62         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R 
       41.75        10.22        47.80         2.66        19.04         5.06 
TCGA-BT-A20V TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42B TCGA-BT-A42C TCGA-BT-A42E 
        5.06         8.35        12.82        17.56        28.70        36.43 
TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A9FF 
        8.98         1.94        23.01        12.16        12.62        11.87 
TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I1 
       12.92         5.19        18.41       130.88        46.68        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        7.79       142.78        13.58         8.15         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       21.30        17.98        67.36        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6Q TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA6X 
       52.01        13.58       165.73       166.03        13.64        15.35 
TCGA-DK-AA75 TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4TZ TCGA-E7-A4IJ TCGA-E7-A541 
       11.18        12.03        43.59        15.35        22.16        25.58 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B3 
        0.56        24.03         1.22        13.68        12.95        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
       16.77         8.94        33.04        22.52        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43N 
       23.41        29.16         5.52        19.79        12.85         7.56 
TCGA-FD-A43P TCGA-FD-A43U TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BV TCGA-FD-A5BY 
       27.35        20.91        15.58        11.01         5.36         8.25 
TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A62N TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC 
       27.45        18.08         2.70         6.28        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.69        12.36         2.27        10.85        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3RC 
       11.08        61.94         7.23        20.12        17.62        15.91 
TCGA-GC-A3YS TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       24.92         0.49         8.94        13.91         7.73         2.10 
TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
        2.20         7.36        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-AATO TCGA-GU-AATP TCGA-GV-A3JX TCGA-GV-A40E TCGA-GV-A40G 
        5.62        10.65        32.98        19.10         8.58        19.07 
TCGA-GV-A6ZA TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A5RH 
       22.72        19.40        12.16        25.02         3.45         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41Q TCGA-KQ-A41R 
       11.70        17.72         1.81        15.42        46.98        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
        1.15        15.32        15.58        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        86.83        69.34 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
      112.83         3.91        29.56         6.21         3.85         6.58 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       97.12        15.35        48.62         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9SZ 
       14.93         4.21        11.90        23.64        21.04        28.24 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAML 
       26.27         2.24         2.10        10.82       110.60         7.63 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN2 
        2.96         6.77        98.99        44.32        56.48        61.45 
TCGA-XF-AAN3 TCGA-YF-AA3L TCGA-YF-AA3M TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RC 
       86.30        11.97        13.64        21.86        28.41        94.29 
TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4R 
       13.41         3.48        64.08        58.72        47.84        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       19.69         8.61        60.16        63.02        35.41        19.17 
TCGA-ZF-AA5P 
       12.23 

$`DEL PEAK 34(22Q13.32) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        94.88       104.65       108.95        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA84 
       17.16        34.98        50.04        51.16        66.54        15.12 
TCGA-4Z-AA89 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       29.65         2.50        17.42        40.08         7.33         6.74 
TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
       12.39         6.58        13.15        26.14        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       19.50        14.89        14.96         8.25        17.16        16.18 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS 
       20.48         4.67         9.96        28.41        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       13.97        12.59        12.13        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.26        13.12        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR 
       11.34        11.34        18.58        13.08         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A5 
       18.48        29.79         1.84        13.58        21.86         2.14 
TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       66.41        19.00        16.70       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
       15.62        87.32         4.80        50.27        23.21         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW 
       20.81        10.55       163.30        66.05        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B6 TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA71 
       76.60        36.66        15.02        18.81        19.00        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       56.15        20.32        38.83        29.72         0.10         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
       16.70         0.66        26.96        26.24         4.24        24.66 
TCGA-E7-A7DU TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B7 
        0.92        14.07        15.32        14.37         8.09         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43S 
       12.62        27.98        17.98        25.74        46.78        14.96 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BU TCGA-FD-A5BX TCGA-FD-A5C1 
        3.62        26.73        53.88        19.33         5.69        58.92 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        7.10        13.35        62.86         3.06         4.31         9.67 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66        10.65         8.94         3.25        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3D 
       26.93        59.31        33.01        66.02         6.94        70.32 
TCGA-G2-AA3F TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD 
       29.36        21.40        20.71        15.81        19.13        14.07 
TCGA-GC-A3WC TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-A767 
       17.75         3.12        20.98        10.92        32.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        7.00        14.27        21.34        19.82        20.28         8.48 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5ND 
       36.49        27.35         1.51        38.60        64.01         9.01 
TCGA-K4-A3WV TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A83P TCGA-K4-AAQO 
       21.24         2.76         9.14        27.68        16.27        11.80 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-LT-A8JT TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        21.07        14.24         1.84 
TCGA-S5-AA26 TCGA-SY-A9G0 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PD 
       16.54        12.43        76.01        78.25         3.02        17.82 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HH TCGA-XF-A8HI 
       51.32        45.04        97.45       125.49         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9T2 
       64.80        79.66        66.41         5.98        12.76        18.90 
TCGA-XF-A9T4 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAME TCGA-XF-AAMH TCGA-XF-AAMJ 
       16.27        66.64        13.74        92.98        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-XF-AAN4 TCGA-XF-AAN5 
       71.57        91.73         8.32        30.94        27.06        75.39 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-ZF-A9R0 
       18.15         3.88        18.84         9.63         0.66        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 TCGA-ZF-A9RL 
       25.41        21.11        31.20        30.28        35.84        88.87 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA53 TCGA-ZF-AA54 
       20.22         2.89        59.38        56.35        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
        8.52        54.21         5.52 

  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                           0.49                            0.10 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                         166.03                          163.30 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                          15.98                           17.88 
[1] "0.5 - 166.0 (16.0)" "0.1 - 163.3 (17.9)"
[1] "hr=" "1.1"
D67V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 34(22Q13.32) MUTATED         0       52        64       71
  DEL PEAK 34(22Q13.32) WILD-TYPE       2       77        76       64
D67V3, multiclass
           clus
vv          DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  STAGE I                               0                               2
  STAGE II                             52                              77
  STAGE III                            64                              76
  STAGE IV                             71                              64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1+T2  T3  T4
  DEL PEAK 34(22Q13.32) MUTATED         50  93  29
  DEL PEAK 34(22Q13.32) WILD-TYPE       73 102  29
D67V4, multiclass
          clus
vv         DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  T0+T1+T2                            50                              73
  T3                                  93                             102
  T4                                  29                              29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 34(22Q13.32) MUTATED    98  21  46   4
  DEL PEAK 34(22Q13.32) WILD-TYPE 137  26  29   5
D67V5, multiclass
    clus
vv   DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  N0                            98                             137
  N1                            21                              26
  N2                            46                              29
  N3                             4                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED    64   4
  DEL PEAK 34(22Q13.32) WILD-TYPE 128   7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED     64    4
  DEL PEAK 34(22Q13.32) WILD-TYPE  128    7
   clus
vv  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  0                            64                             128
  1                             4                               7
[1] 2 2
[1] FALSE
D67V7, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED    48 139
  DEL PEAK 34(22Q13.32) WILD-TYPE  59 162
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED     48  139
  DEL PEAK 34(22Q13.32) WILD-TYPE   59  162
        clus
vv       DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  FEMALE                            48                              59
  MALE                             139                             162
[1] 2 2
[1] FALSE
D67V8, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED   167   5
  DEL PEAK 34(22Q13.32) WILD-TYPE 197  14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED    167    5
  DEL PEAK 34(22Q13.32) WILD-TYPE  197   14
     clus
vv    DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  NO                            167                             197
  YES                             5                              14
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, continuous
D67V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(22Q13.32) MUTATED      12                        12   156
  DEL PEAK 34(22Q13.32) WILD-TYPE    31                        10   171
D67V12, multiclass
                           clus
vv                          DEL PEAK 34(22Q13.32) MUTATED
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               156
                           clus
vv                          DEL PEAK 34(22Q13.32) WILD-TYPE
  ASIAN                                                  31
  BLACK OR AFRICAN AMERICAN                              10
  WHITE                                                 171
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED     6 168
  DEL PEAK 34(22Q13.32) WILD-TYPE   3 201
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED      6  168
  DEL PEAK 34(22Q13.32) WILD-TYPE    3  201
                        clus
vv                       DEL PEAK 34(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           168
                        clus
vv                       DEL PEAK 34(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             201
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 35(XP11.3) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 35(XP11.3) MUTATED    53  39
  DEL PEAK 35(XP11.3) WILD-TYPE 176 138
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           92                           314 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           39                           138 
$`DEL PEAK 35(XP11.3) MUTATED`
TCGA-2F-A9KQ TCGA-2F-A9KT TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       108.95         8.35        16.27        16.83        34.98 
TCGA-4Z-AA84 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20T TCGA-BT-A20V 
       15.12         2.50         2.66        17.88        14.89         5.06 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH 
        4.67        17.56        36.43        13.97        12.13        13.08 
TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CU-A0YN TCGA-CU-A3QU TCGA-DK-A1A5 
       12.62        12.10        11.34        12.92         5.19         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I6 TCGA-DK-A3IS 
       19.00        16.70       112.44        15.62        87.32        50.27 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6Q 
       21.30         9.67        15.68        50.70        38.24        13.58 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A7DU 
      165.73       166.03        13.64        43.59        29.72         0.92 
TCGA-E7-A7DV TCGA-FD-A3B4 TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS 
        1.22        16.77        33.04        29.16        19.79        12.85 
TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A62N TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TF 
       15.58         8.25         2.70        62.86         6.15         2.27 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3VY TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A3OS 
       26.93         7.23        17.62        29.36         0.49        20.98 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-K4-A3WS 
       19.10         8.48        36.49        64.01         9.01        25.02 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41O TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       17.72         1.81        11.80        50.56        15.58        12.23 
TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HF 
       16.54        76.01        78.25         3.02       112.83        97.12 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SZ TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMT 
       34.45        14.93        28.24        13.74         7.63         2.96 
TCGA-XF-AAMW TCGA-XF-AAN1 TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA51 
        8.32        30.94        28.41        88.87        34.06        56.35 
TCGA-ZF-AA56 TCGA-ZF-AA58 
        8.52        54.21 

$`DEL PEAK 35(XP11.3) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7Q TCGA-4Z-AA7R 
       24.13        11.97       104.65        44.94        16.77        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       27.62        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80        29.65        17.42        40.08         7.33 
TCGA-BL-A3JM TCGA-BL-A5ZZ TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N 
        6.74        12.39         6.58        13.15        19.04        26.14 
TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A20X 
       12.16        19.50         5.06        14.96         8.35         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       17.16        16.18        20.48        12.82         9.96        28.70 
TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.41         8.98         1.94        23.01        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.59        12.16        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL 
       12.26        13.12        12.00        11.34        11.87        18.58 
TCGA-CF-A9FM TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL TCGA-CU-A5W6 
       13.08         4.90        15.12        18.48        29.79         1.84 
TCGA-CU-A72E TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AC TCGA-DK-A1AE 
       13.58        21.86        66.41        18.41       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        46.68        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3WW 
       13.58         8.15         8.22        17.72        23.21        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       10.55       163.30        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6T 
       76.60        67.36        36.66        52.01        15.02        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA76 
       19.00        15.35        13.64        56.15        11.18        12.03 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       20.32        15.35        38.83         0.10        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A541 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       16.70        25.58         0.56         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
        4.24        24.03        24.66        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 
       15.32        14.37         8.09        32.02         8.94         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
       12.62        22.52        27.98        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A43N TCGA-FD-A43P 
       17.98         5.52        25.74        46.78         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       14.96        20.91         3.62        26.73        53.88        11.01 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 TCGA-FD-A5C1 
       19.33         5.36         5.69        27.45        18.08        58.92 
TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        7.10         6.28        13.35        18.81        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z7 TCGA-FJ-A3Z9 
        3.06         4.31         9.67        10.85        31.07        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 TCGA-FT-A3EE TCGA-FT-A61P TCGA-G2-A2EF 
       10.65        17.23         8.94         3.25        11.08        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-AA3B 
       48.00        15.95        59.31        33.01        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        6.94        70.32        21.40        20.71        15.81        19.13 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.91        14.07        17.75        24.92         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GD-A76B TCGA-GU-A42P 
        7.73         2.10         3.12         2.20         7.36        10.92 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 TCGA-GU-A766 
       11.31        18.97         7.63        32.78        20.05         5.62 
TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
        4.73        10.65        32.98         7.00        14.27        21.34 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       19.82        20.28        27.35         8.58        19.07        22.72 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51        19.40        38.60        12.16         3.45        21.24 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB 
        2.76         9.14        27.68         9.07        11.70        15.42 
TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       16.27        52.73        35.97        46.98        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-R3-A69X TCGA-S5-A6DX 
       15.32        21.07        13.48        16.67        14.24         1.84 
TCGA-SY-A9G0 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N 
       12.43        38.99        17.62        37.05        22.68        86.83 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.91        29.56        17.82         6.21         3.85 
TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
       51.32        45.04         6.58        97.45       125.49        15.35 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ 
        1.87        17.88        48.62        64.80        79.66         3.22 
TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        66.41         4.21         5.98        12.76        11.90 
TCGA-XF-A9SX TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 
       23.64        21.04        26.27        18.90         2.24        16.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAME TCGA-XF-AAMF TCGA-XF-AAMG TCGA-XF-AAMH 
       66.64         2.10        92.98        10.82       110.60        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMX TCGA-XF-AAMY TCGA-XF-AAMZ 
       54.90        71.57        91.73         6.77        98.99        44.32 
TCGA-XF-AAN0 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN7 
       56.48        61.45        86.30        27.06        75.39        18.15 
TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-YF-AA3M 
        3.88        18.84         9.63         0.66        11.97        13.64 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
       22.36        25.41        21.11        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       47.84        20.22         2.89        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       60.16        63.02        35.41        57.90        19.40        19.17 
TCGA-ZF-AA5N TCGA-ZF-AA5P 
        5.52        12.23 

  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                         0.49                          0.10 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                       166.03                        163.30 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                        16.62                         17.62 
[1] "0.5 - 166.0 (16.6)" "0.1 - 163.3 (17.6)"
[1] "hr=" "1.1"
D68V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 35(XP11.3) MUTATED         0       27        34       31
  DEL PEAK 35(XP11.3) WILD-TYPE       2      102       106      104
D68V3, multiclass
           clus
vv          DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           27                           102
  STAGE III                          34                           106
  STAGE IV                           31                           104
[1] 4 2
[1] 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(XP11.3) MUTATED         23  45  16
  DEL PEAK 35(XP11.3) WILD-TYPE      100 150  42
D68V4, multiclass
          clus
vv         DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  T0+T1+T2                          23                           100
  T3                                45                           150
  T4                                16                            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                             N0  N1  N2  N3
  DEL PEAK 35(XP11.3) MUTATED    52  14  14   2
  DEL PEAK 35(XP11.3) WILD-TYPE 183  33  61   7
D68V5, multiclass
    clus
vv   DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  N0                          52                           183
  N1                          14                            33
  N2                          14                            61
  N3                           2                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    44   2
  DEL PEAK 35(XP11.3) WILD-TYPE 148   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     44    2
  DEL PEAK 35(XP11.3) WILD-TYPE  148    9
   clus
vv  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  0                          44                           148
  1                           2                             9
[1] 2 2
[1] FALSE
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    24  68
  DEL PEAK 35(XP11.3) WILD-TYPE  83 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     24   68
  DEL PEAK 35(XP11.3) WILD-TYPE   83  233
        clus
vv       DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  FEMALE                          24                            83
  MALE                            68                           233
[1] 2 2
[1] FALSE
D68V8, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    82   5
  DEL PEAK 35(XP11.3) WILD-TYPE 282  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     82    5
  DEL PEAK 35(XP11.3) WILD-TYPE  282   14
     clus
vv    DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  NO                           82                           282
  YES                           5                            14
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
D68V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(XP11.3) MUTATED       8                         7    73
  DEL PEAK 35(XP11.3) WILD-TYPE    35                        15   254
D68V12, multiclass
                           clus
vv                          DEL PEAK 35(XP11.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              73
                           clus
vv                          DEL PEAK 35(XP11.3) WILD-TYPE
  ASIAN                                                35
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED     1  83
  DEL PEAK 35(XP11.3) WILD-TYPE   8 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED      1   83
  DEL PEAK 35(XP11.3) WILD-TYPE    8  286
                        clus
vv                       DEL PEAK 35(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK 35(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           286
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 36(XQ21.33) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(XQ21.33) MUTATED    55  29
  DEL PEAK 36(XQ21.33) WILD-TYPE 174 148
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            84                            322 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            29                            148 
$`DEL PEAK 36(XQ21.33) MUTATED`
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KT TCGA-4Z-AA7O TCGA-4Z-AA80 TCGA-BT-A20T 
       94.88       104.65       108.95        16.83         0.62        14.89 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42C 
        5.06         8.25        16.18         4.67        17.56        28.70 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CU-A3KJ 
       12.56        13.97        12.62        12.10        11.34        18.48 
TCGA-CU-A3QU TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A6B5 
        5.19        16.70       130.88        50.27        21.30        50.70 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        13.64        13.64        12.03        43.59 
TCGA-E7-A3X6 TCGA-E7-A7DU TCGA-E7-A85H TCGA-FD-A3B4 TCGA-FD-A3SN TCGA-FD-A3SS 
       29.72         0.92        12.95        16.77        29.16        12.85 
TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IB 
        8.25        62.86        31.07         3.25        26.93         7.23 
TCGA-G2-AA3B TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GU-A42P TCGA-GV-A3JW 
       66.02         0.49         8.94         2.20        10.92        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40G TCGA-HQ-A2OE TCGA-K4-A3WV 
       19.10         8.48        36.49        19.07        38.60        21.24 
TCGA-K4-A54R TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41O TCGA-LT-A5Z6 TCGA-MV-A51V 
       27.68        17.72        11.80        50.56        15.58        13.48 
TCGA-PQ-A6FI TCGA-S5-A6DX TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD 
       12.23         1.84        16.54        76.01        78.25       112.83 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SP TCGA-XF-A9SZ TCGA-XF-A9T5 
       17.82         3.85        17.88        14.93        28.24        66.64 
TCGA-XF-A9T8 TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN7 TCGA-YF-AA3L 
       13.74       110.60         2.96         6.77        18.15        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R2 TCGA-ZF-A9R9 TCGA-ZF-A9RL TCGA-ZF-A9RM TCGA-ZF-AA5H 
       25.41        21.11        28.41        88.87        47.84        19.17 

$`DEL PEAK 36(XQ21.33) WILD-TYPE`
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7M TCGA-4Z-AA7N TCGA-4Z-AA7Q 
       24.13        11.97         8.35        16.27        44.94        16.77 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 
       17.16        34.98        27.62        50.04        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA84 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-4Z-AA89 TCGA-5N-A9KI 
       66.54        15.12        10.22        47.80        29.65         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BL-A5ZZ 
       17.42        40.08         7.33         2.66         6.74        12.39 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        6.58        13.15        19.04        26.14        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LA TCGA-BT-A2LD 
       19.50         5.06        14.96         8.35        17.16        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0EZ TCGA-C4-A0F0 
       12.82         9.96        36.43        28.41         8.98         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       23.01        12.79        12.59        12.13        13.08        12.16 
TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       10.95        12.66        12.46        12.10        12.26        13.12 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FL TCGA-CF-A9FM TCGA-CU-A0YN 
       12.00        11.34        11.87        18.58        13.08        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-CU-A72E TCGA-DK-A1A3 
        4.90        15.12        29.79         1.84        13.58        21.86 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AD TCGA-DK-A1AE 
        2.14        66.41        18.41        19.00       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62        46.68        17.95         7.79       142.78 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         4.80        13.58         8.15         8.22        17.72 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       23.21         9.67        20.81        10.55       163.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       17.98        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6P TCGA-DK-AA6R TCGA-DK-AA6S 
       36.66        38.24        52.01        15.02       165.73       166.03 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       19.00        15.35        56.15        11.18        20.32        15.35 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A541 
       38.83         0.10        22.16         2.24        16.70        25.58 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        0.56         0.66        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7DV TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66         1.22        13.68        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        8.09        32.02         8.94        33.04         4.01        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       22.52        27.98        60.66        24.30        23.41        17.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43N TCGA-FD-A43P 
        5.52        25.74        46.78        19.79         7.56        27.35 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       14.96        20.91         3.62        15.58        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BX TCGA-FD-A5BZ TCGA-FD-A5C0 
       11.01        19.33         5.36         5.69        27.45        18.08 
TCGA-FD-A5C1 TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62P TCGA-FD-A62S TCGA-FD-A6TB 
       58.92         2.70         7.10         6.28        13.35        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TF TCGA-FD-A6TG TCGA-FD-A6TH 
        6.15        12.69        12.36         2.27         3.06         4.31 
TCGA-FD-A6TI TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FJ-A871 
        9.67        10.85        12.66        10.65        17.23         8.94 
TCGA-FT-A61P TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
       11.08        61.94        48.00        15.95        59.31        33.01 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-G2-AA3C TCGA-G2-AA3D TCGA-G2-AA3F TCGA-GC-A3BM 
       20.12        17.62         6.94        70.32        29.36        21.40 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
       20.71        15.81        19.13        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       24.92        13.91         7.73         2.10         3.12        20.98 
TCGA-GD-A76B TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A763 TCGA-GU-A764 
        7.36        11.31        18.97         7.63        32.78        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATO TCGA-GU-AATP TCGA-GU-AATQ TCGA-GV-A3JV 
        5.62         4.73        10.65        32.98         7.00        14.27 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-H4-A2HO 
       19.82        20.28        27.35         8.58        22.72         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5ND TCGA-HQ-A5NE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.40        64.01         9.01        12.16        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
        2.76         9.14         9.07        11.70         1.81        15.42 
TCGA-K4-A83P TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-KQ-A41R TCGA-KQ-A41S 
       16.27        52.73        35.97        46.98        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-R3-A69X TCGA-SY-A9G0 TCGA-SY-A9G5 
       15.32        21.07        16.67        14.24        12.43        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78N TCGA-UY-A8OB TCGA-UY-A8OC 
       17.62        37.05        22.68        86.83        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PH TCGA-XF-A8HB TCGA-XF-A8HC 
        3.91        29.56         6.21        51.32        45.04         6.58 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A8HH TCGA-XF-A9SG 
       97.45       125.49        97.12        15.35         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SL TCGA-XF-A9SM 
       64.80        79.66         3.22        15.98        66.41        34.45 
TCGA-XF-A9ST TCGA-XF-A9SU TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SX TCGA-XF-A9SY 
        4.21         5.98        12.76        11.90        23.64        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T4 TCGA-XF-A9T6 TCGA-XF-AAME 
       26.27        18.90         2.24        16.27         2.10        92.98 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       10.82        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMW TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN0 TCGA-XF-AAN1 TCGA-XF-AAN2 
        8.32        98.99        44.32        56.48        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-XF-AAN8 TCGA-YC-A89H TCGA-YC-A8S6 
       86.30        27.06        75.39         3.88        18.84         9.63 
TCGA-YC-A9TC TCGA-YF-AA3M TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R4 TCGA-ZF-A9R5 
        0.66        13.64        22.36        31.20        30.28        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RC TCGA-ZF-A9RD TCGA-ZF-A9RE TCGA-ZF-A9RF TCGA-ZF-A9RG 
       21.86        94.29        13.41         3.48        64.08        58.72 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA4U TCGA-ZF-AA4V 
       20.22         2.89        34.06        19.69         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA53 TCGA-ZF-AA54 
       60.16        63.02        56.35        35.41        57.90        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-ZF-AA5P 
        8.52        54.21         5.52        12.23 

  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                          0.49                           0.10 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                        130.88                         166.03 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                        17.195                         17.195 
[1] "0.5 - 130.9 (17.2)" "0.1 - 166.0 (17.2)"
[1] "hr=" "1.4"
D69V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 36(XQ21.33) MUTATED         0       32        26       25
  DEL PEAK 36(XQ21.33) WILD-TYPE       2       97       114      110
D69V3, multiclass
           clus
vv          DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            32                             97
  STAGE III                           26                            114
  STAGE IV                            25                            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"
                                vv
clus                             T0+T1+T2  T3  T4
  DEL PEAK 36(XQ21.33) MUTATED         28  38  10
  DEL PEAK 36(XQ21.33) WILD-TYPE       95 157  48
D69V4, multiclass
          clus
vv         DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  T0+T1+T2                           28                             95
  T3                                 38                            157
  T4                                 10                             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                              N0  N1  N2  N3
  DEL PEAK 36(XQ21.33) MUTATED    52  10  15   1
  DEL PEAK 36(XQ21.33) WILD-TYPE 183  37  60   8
D69V5, multiclass
    clus
vv   DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  N0                           52                            183
  N1                           10                             37
  N2                           15                             60
  N3                            1                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED    39   0
  DEL PEAK 36(XQ21.33) WILD-TYPE 153  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED     39    0
  DEL PEAK 36(XQ21.33) WILD-TYPE  153   11
   clus
vv  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  0                           39                            153
  1                            0                             11
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED    24  60
  DEL PEAK 36(XQ21.33) WILD-TYPE  83 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED     24   60
  DEL PEAK 36(XQ21.33) WILD-TYPE   83  241
        clus
vv       DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  FEMALE                           24                             83
  MALE                             60                            241
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED    74   5
  DEL PEAK 36(XQ21.33) WILD-TYPE 290  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED     74    5
  DEL PEAK 36(XQ21.33) WILD-TYPE  290   14
     clus
vv    DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  NO                            74                            290
  YES                            5                             14
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, continuous
D69V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(XQ21.33) MUTATED       6                         7    67
  DEL PEAK 36(XQ21.33) WILD-TYPE    37                        15   260
D69V12, multiclass
                           clus
vv                          DEL PEAK 36(XQ21.33) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               67
                           clus
vv                          DEL PEAK 36(XQ21.33) WILD-TYPE
  ASIAN                                                 37
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED     4  74
  DEL PEAK 36(XQ21.33) WILD-TYPE   5 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED      4   74
  DEL PEAK 36(XQ21.33) WILD-TYPE    5  295
                        clus
vv                       DEL PEAK 36(XQ21.33) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       DEL PEAK 36(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            295
[1] 2 2
[1] FALSE
