[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/22506467/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/22507728/transformed.cor.cli.txt"

nPatients in clinical file=412, in cluster file=408, common to both=408
[1]  73 408
[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 
                          152                           256 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          152                           256 
[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 
                           74                           334 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           74                           334 
[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 
                           206                            202 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           206                            202 
[1] "AMP PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          171                           237 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          171                           237 
[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 
                           124                            284 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           124                            284 
[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(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE 
                           254                            154 
  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE 
                           254                            154 
[1] "AMP PEAK 19(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE 
                           88                           320 
  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE 
                           88                           320 
[1] "AMP PEAK 20(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE 
                         182                          226 
  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE 
                         182                          226 
[1] "AMP PEAK 21(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          51                          357 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          51                          357 
[1] "AMP PEAK 22(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                           135                            273 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                           135                            273 
[1] "AMP PEAK 23(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE 
                            71                            337 
  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE 
                            71                            337 
[1] "AMP PEAK 24(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE 
                           132                            276 
  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE 
                           132                            276 
[1] "AMP PEAK 25(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE 
                         118                          290 
  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE 
                         118                          290 
[1] "AMP PEAK 26(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                           128                            280 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                           128                            280 
[1] "AMP PEAK 27(16P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE 
                            87                            321 
  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE 
                            87                            321 
[1] "AMP PEAK 28(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE 
                            98                            310 
  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE 
                            98                            310 
[1] "AMP PEAK 29(16Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE 
                           108                            300 
  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE 
                           108                            300 
[1] "AMP PEAK 30(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE 
                            88                            320 
  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE 
                            88                            320 
[1] "AMP PEAK 31(17Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE 
                           174                            234 
  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE 
                           174                            234 
[1] "AMP PEAK 32(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         165                          243 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         165                          243 
[1] "AMP PEAK 33(17Q23.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE 
                           194                            214 
  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE 
                           194                            214 
[1] "AMP PEAK 34(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE 
                         164                          244 
  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE 
                         164                          244 
[1] "AMP PEAK 35(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE 
                            155                             253 
  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE 
                            155                             253 
[1] "AMP PEAK 36(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE 
                            263                             145 
  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE 
                            263                             145 
[1] "AMP PEAK 37(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE 
                            87                            321 
  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(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 
                           72                           336 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           72                           336 
[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 
                          207                           201 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          207                           201 
[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 
                          161                           247 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          161                           247 
[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 
                          243                           165 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          243                           165 
[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 
                        177                         231 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        177                         231 
[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 
                            168                             240 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            168                             240 
[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 
                           153                            255 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           153                            255 
[1] "DEL PEAK 23(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         144                          264 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         144                          264 
[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 
                         208                          200 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         208                          200 
[1] "DEL PEAK 32(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         179                          229 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         179                          229 
[1] "DEL PEAK 33(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           145                            263 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           145                            263 
[1] "DEL PEAK 34(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            188                             220 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            188                             220 
[1] "DEL PEAK 35(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           91                           317 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           91                           317 
[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=214,	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 
236  47  75   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
236  47  75   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
236  47  75   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
236  47  75   8 
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    49  51
  AMP PEAK  1(1P34.2) WILD-TYPE 178 127
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          100                           305 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                           51                           127 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A0YN 
       16.77        20.48        25.94         9.96         8.98        12.92 
TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-AA6L 
       16.70         8.22        23.21        17.98        64.18        38.24 
TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B7 TCGA-FD-A3NA 
      166.03        11.18        15.35        25.58         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5C0 
       24.30        23.41        19.79        12.85        15.58        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       58.92         6.15         3.06         9.67        31.07        17.23 
TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A40G TCGA-GV-A6ZA 
       21.40        24.92        10.92        32.98        19.07        22.72 
TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A9SK TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ 
       86.83        97.45        15.98         7.63        98.99        44.32 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       86.30        18.58        13.64        30.28        94.29         3.48 
TCGA-ZF-AA4T TCGA-2F-A9KP TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 
       19.69        11.97        27.62        51.16        10.22        47.80 
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HS 
       19.04         5.06        17.16        36.43         1.94        12.56 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL 
        5.19        21.86        18.41        17.95       142.78        13.58 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A97Q TCGA-FD-A3B5 
        8.15        15.02        38.83         0.56         8.09         8.94 
TCGA-FD-A43N TCGA-FD-A5BU TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3OO TCGA-GC-A3RD 
       22.98        19.33        26.93        20.12        15.81        14.07 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-A767 TCGA-GV-A3JW TCGA-HQ-A2OE 
        0.49        26.70        20.98         4.73        21.34        38.60 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-MV-A51V TCGA-UY-A78M TCGA-UY-A8OB 
       21.24        11.70        15.42        13.48        22.68        69.34 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A9SU TCGA-ZF-A9RN TCGA-ZF-AA4X 
        3.02        17.82         6.21         5.98        20.22        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       56.35        35.41        19.40        29.49 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR 
       14.89         8.35        28.70        18.58         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48        13.58         2.14        19.00       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 
       87.32        17.72        50.27        21.30         9.67        66.05 
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-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       52.01       165.73        13.64        13.64        56.15        20.32 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        0.92         1.22        33.04        17.98        29.16        46.78 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE 
        8.25         6.28        62.86        18.81        12.69        12.36 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB 
        4.31        11.08        33.01        17.62        70.32        19.13 
TCGA-GC-A3WC TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       17.75        32.78        19.82        20.28        27.35         8.58 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       33.14        51.32       125.49        97.12        15.35         3.22 
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-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 
       10.82        11.31        54.90        71.57        91.73        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4R 
       61.45         3.88         9.63        21.11        88.87        34.06 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       57.90        12.23        24.13        94.88       104.65         8.35 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       41.75        66.54         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50        14.96         5.06         8.25        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       17.56        28.41        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-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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       66.41       112.44        16.14        17.62        15.62         7.79 
TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        4.80        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        29.72         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
       22.16         2.24        16.70         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-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.32        14.37        32.02        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV 
       27.98         5.52        25.74        14.96        20.91         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       15.95        59.31         7.23        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ 
       20.71        15.91         8.94        13.91         2.10         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        2.20        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO 
        7.00        14.27        19.10         8.48        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
       19.40        64.01        12.16         9.07        17.72         1.81 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       21.07        12.23        16.67        16.54        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        35.24        29.56 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        3.85        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       27.06        75.39        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        58.72        47.84         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       60.16         8.52        54.21         5.52        10.65 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                         0.49                          0.62 
  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 
                       19.055                        16.770 
[1] "0.5 - 166.0 (19.1)" "0.6 - 165.7 (16.8)"
[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    46  18  23   2
  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                          46                           190
  N1                          18                            29
  N2                          23                            52
  N3                           2                             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  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED     88    4
  AMP PEAK  1(1P34.2) WILD-TYPE  276   16
     clus
vv    AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  NO                           88                           276
  YES                           4                            16
[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   110  91
  AMP PEAK  2(1Q21.3) WILD-TYPE 117  87
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          201                           204 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           91                            87 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
       16.27        16.77        15.12        26.14        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-DK-A1A5 
       20.48        28.70         8.98        18.58        18.48         2.14 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 
      130.88        46.68         8.22        21.30        23.21        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S 
       17.98        67.36        15.68        38.24       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DV 
       13.64        13.64        11.18        20.32        15.35         1.22 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR 
        4.01        60.66        24.30        23.41        17.98        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A62P 
       12.85        27.35        15.58        10.78        18.08         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15        12.36         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       11.08        33.01        17.62        21.40        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E 
       24.92        10.92        32.98        19.82        20.28         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AC TCGA-KQ-A41P 
       19.07        22.72         9.01        25.02         9.14        35.97 
TCGA-KQ-A41Q TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       46.98        86.83        97.45        15.35         3.22        15.98 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAML 
        4.21        11.90        66.64         2.10        13.74         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
       71.57        98.99        61.45        86.30        18.58        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       30.28        94.29         3.48        34.06        19.69        57.90 
TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       24.13         8.35        16.83        27.62         0.62        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20R 
       10.22        47.80         2.66         6.74        19.04         5.06 
TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A3MI 
        5.06        17.16        16.18         1.94        12.56        12.16 
TCGA-CF-A47V TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 
       12.46        11.34        11.34         5.19         1.84        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       18.41       112.44        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       13.58         8.15        15.02        13.58        18.81        19.00 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A5KE 
       43.59        38.83        29.72         5.36        22.16         0.56 
TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3SO 
        0.66        24.03        13.68        12.95         8.09         5.52 
TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE 
       22.98        19.33        27.45         2.27        10.65         3.25 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I3 
       20.12        66.02        29.36        15.81         0.49        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GV-A3JV TCGA-GV-A3JW 
       26.70         2.10        20.98        20.05        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI 
       19.10        36.49         1.51        38.60        64.01        11.70 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       17.72        15.42        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       15.58        13.48        12.23        16.54        38.99        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HI 
       37.05        22.68        29.56        17.82         6.58        17.88 
TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       48.62        79.66         5.98       110.60         2.96         6.77 
TCGA-XF-AAN0 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
       56.48         0.66        11.97        22.36        21.86        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       64.08        20.22        59.38        67.20        56.35        35.41 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       54.21        29.49        10.65 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YN 
      108.95        33.83        12.39        25.94         9.96        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 
        4.90        15.12        13.58        19.00        16.70        87.32 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       17.72        50.27         9.67        64.18        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA74 TCGA-E7-A541 TCGA-E7-A7DU 
       50.70        36.66        52.01        56.15        25.58         0.92 
TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       33.04        29.16        46.78         3.62        26.73        53.88 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        5.69         8.25        58.92        62.86        18.81        12.69 
TCGA-FD-A6TG TCGA-G2-AA3D TCGA-GU-A763 TCGA-GV-A3QK TCGA-K4-A3WU TCGA-K4-A4AB 
        3.06        70.32        32.78        27.35         3.45         2.76 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       27.68        52.73        50.56        14.24         1.84        33.14 
TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV 
       51.32       125.49        97.12        34.45        14.93        12.76 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMH 
       21.04        26.27        18.90         2.24        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN8 TCGA-YC-A8S6 
       54.90        91.73        44.32        30.94         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       21.11        88.87        12.23        11.97        94.88       104.65 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       44.94        17.16        34.98        50.04        51.16        66.54 
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-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-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C 
       17.56        36.43        28.41        23.01        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W 
       12.59        12.13        13.08        10.95        12.66        12.10 
TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FF 
       12.62        12.26        13.12        12.00        12.10        11.87 
TCGA-CF-A9FM TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       13.08        29.79        66.41        16.14        17.62        15.62 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A4XJ 
       20.81        10.55       163.30        15.35        12.03         2.24 
TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN 
       16.70        26.96        26.24         4.24        24.66        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       15.32        14.37        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV 
       22.52        27.98        25.74        14.96        20.91         5.36 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
        2.70         7.10        13.35        10.85        12.66         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ 
        6.94        20.71        15.91        14.07         8.94         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 
        2.20        11.31        18.97         7.63        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        7.00         8.48        19.40        12.16        21.24         9.07 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-UY-A78O TCGA-UY-A78P 
        1.81        16.27        21.07        16.67        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02       112.83        35.24         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ 
       45.04         1.87        64.80        66.41        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       16.27        92.98         8.32        27.06        75.39        18.84 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RM 
       25.41        31.20        35.84        28.41        58.72        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5N 
        2.89         8.61        60.16        19.40         8.52         5.52 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.49                          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 
                        17.82                         17.29 
[1] "0.5 - 166.0 (17.8)" "0.9 - 163.3 (17.3)"
[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 135  18  34   1
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                         101                           135
  N1                          29                            18
  N2                          41                            34
  N3                           7                             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"
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  11
  AMP PEAK  2(1Q21.3) WILD-TYPE 191   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    173   11
  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                          11                             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   121  93
  AMP PEAK  3(1Q23.3) WILD-TYPE 106  85
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                          214                           191 
  AMP PEAK  3(1Q23.3) MUTATED AMP PEAK  3(1Q23.3) WILD-TYPE 
                           93                            85 
$`AMP PEAK  3(1Q23.3) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        16.77        15.12        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
        8.35        20.48        25.94         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 
       18.58        15.12        18.48         2.14       130.88        87.32 
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-AA6R TCGA-DK-AA6S TCGA-DK-AA71 
       67.36        15.68        38.24       165.73       166.03        13.64 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA 
       11.18        20.32        25.58         1.22         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       24.30        23.41        17.98        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE 
        3.62        15.58        10.78         6.28         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY 
        3.06         4.31         9.67        31.07        17.23        17.62 
TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       21.40        17.75        24.92        10.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       20.28        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AC TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
        9.14        35.97        46.98        86.83        51.32        97.45 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T5 
       15.35         3.22        15.98         4.21        11.90        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ 
        2.10        13.74         7.63        71.57        98.99        44.32 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       86.30        18.58        13.64        30.28        94.29         3.48 
TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW 
       34.06        57.90        12.23        24.13        11.97         8.35 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.83        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J 
       10.22        47.80        40.08         2.66         6.74        19.04 
TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F0 TCGA-CF-A1HS 
        5.06        17.16        16.18         4.67         1.94        12.56 
TCGA-CF-A3MI TCGA-CF-A47V TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A5W6 
       12.16        12.46        11.34        11.34        11.87         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       21.86        18.41       112.44        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T 
        4.80        13.58         8.15        15.02        13.58        18.81 
TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       19.00        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
        0.56         0.66        24.03        13.68        12.95         8.09 
TCGA-FD-A3B4 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5BZ 
       16.77         5.52        25.74        22.98        19.33        27.45 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO 
       10.65         3.25        61.94        66.02        29.36        15.81 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 
        0.49        13.91        26.70         2.10        20.98        20.05 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO 
        4.73        14.27        21.34        19.10        36.49         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       19.40        38.60        64.01         9.07        11.70        17.72 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
       13.48        12.23        16.54        38.99        37.05        22.68 
TCGA-UY-A8OC TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SG 
        3.02        17.82         6.21         6.58        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       79.66         5.98        28.24       110.60         2.96         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R7 
       56.48        27.06         0.66        11.97        22.36        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       13.41        64.08        20.22        59.38        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       35.41        54.21        29.49        10.65 

$`AMP PEAK  3(1Q23.3) WILD-TYPE`
TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1AA 
       33.83        12.39        12.92         4.90        13.58        19.00 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW 
       16.70        46.68        17.72         9.67        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA74 
       76.60        50.70        36.66        52.01        13.64        56.15 
TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A5BR 
       15.35         0.92        33.04        29.16        46.78        26.73 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA 
       53.88         5.69         8.25        18.08        58.92        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB 
       18.81        12.69        11.08        33.01        70.32        19.13 
TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N 
       32.78        27.35         8.58         2.76        27.68        52.73 
TCGA-KQ-A41O TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HE TCGA-XF-A8HF 
       50.56        14.24         1.84        33.14       125.49        97.12 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       34.45        14.93        12.76        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAN1 
        2.24        10.82        11.31        54.90        91.73        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4T 
       61.45         3.88         9.63        21.11        88.87        19.69 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        2.50        17.42         7.33         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A42B 
       17.88        19.50         5.06        14.96         8.25        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF 
       36.43        28.41        23.01        12.79        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X 
       12.13        13.08        10.95        12.66        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A3QU 
       12.26        13.12        12.00        12.10        13.08         5.19 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3WW 
       29.79        66.41        16.14        17.62        15.62        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A4XJ TCGA-E7-A519 
       10.55       163.30        15.35        12.03         2.24        16.70 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
       26.96        26.24         4.24        24.66        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37        32.02         8.94        12.62        22.52        27.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       14.96        20.91         5.36         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK 
        2.27        10.85        12.66         8.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 
       26.93        59.31         7.23        20.12         6.94        20.71 
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-A766 TCGA-GU-AATQ TCGA-GV-A3QH TCGA-HQ-A5NE 
       18.97         7.63        15.78         7.00         8.48        12.16 
TCGA-K4-A3WV TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-UY-A78K 
       21.24         1.81        16.27        21.07        16.67        17.62 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB 
       76.01        78.25        69.34       112.83        35.24        29.56 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
        3.85        45.04         1.87        64.80        66.41        23.64 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R1 
       16.27        92.98         8.32        75.39        18.84        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       31.20        35.84        28.41        58.72        47.84         2.89 
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 
                         0.49                          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 
                       17.785                        17.560 
[1] "0.5 - 166.0 (17.8)" "0.9 - 163.3 (17.6)"
[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   111  30  43   8
  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                         111                           125
  N1                          30                            17
  N2                          43                            32
  N3                           8                             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  10
  AMP PEAK  3(1Q23.3) WILD-TYPE 173  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q23.3) MUTATED    191   10
  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                          10                            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    80  71
  AMP PEAK  4(2P25.1) WILD-TYPE 147 107
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                          151                           254 
  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                           71                           107 
$`AMP PEAK  4(2P25.1) MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
       16.77        15.12        12.39        26.14        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YR 
       20.48        25.94        28.70         8.98        18.58        15.12 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3X1 TCGA-DK-A3X2 
        2.14       130.88        87.32         8.22        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6S 
       64.18        67.36        15.68        36.66        38.24       166.03 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-FD-A3NA TCGA-FD-A3SJ 
       13.64        11.18        20.32        25.58        60.66        24.30 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A62P TCGA-FD-A6TC 
       46.78        19.79        12.85        27.35         6.28         6.15 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY 
       12.36         3.06         4.31        17.23        11.08        17.62 
TCGA-GC-A3RB TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-K4-A3WS 
       19.13        32.98        20.28        27.35        22.72        25.02 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP 
       50.56        35.97        97.45        15.35        15.98        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMZ 
        4.21        12.76        26.27        66.64         7.63        44.32 
TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-4Z-AA7R 
       61.45         3.88        94.29        34.06        19.69        17.16 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
        0.62        41.75        51.16         2.50        17.42        40.08 
TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB 
        2.66        13.15        19.04         5.06         5.06        16.18 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A47X 
       28.41        23.01        12.56        13.97        12.13        12.62 
TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       12.10        11.34        21.86        66.41        18.41       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6T 
       17.95         7.79         4.80         8.15        15.02        18.81 
TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A6ME TCGA-E7-A97Q TCGA-FD-A3B5 
       19.00        12.03        43.59        24.03         8.09         8.94 
TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FT-A3EE 
       20.91        27.45         7.10         2.27        10.85         3.25 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       66.02        29.36        14.07         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A764 TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI 
        2.10        20.98        20.05        21.34         8.48        36.49 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ 
       19.40        38.60        12.16        21.24        11.70         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-MV-A51V TCGA-UY-A78K 
       15.42        16.27        11.80        44.38        13.48        17.62 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH 
       22.68        69.34       112.83        17.82         6.21         1.87 
TCGA-XF-A9SG TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9R3 
       48.62        28.24       110.60         6.77        22.36        31.20 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       47.84        20.22        59.38        56.35        19.40         8.52 
TCGA-GU-AATO 
       10.65 

$`AMP PEAK  4(2P25.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BT-A3PK TCGA-CU-A0YN TCGA-CU-A0YO 
      108.95        16.27        33.83         9.96        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IQ 
       18.48        13.58        19.00        16.70        46.68        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 
       50.27        21.30        23.21         9.67        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ 
       50.70        52.01       165.73        13.64        56.15        15.35 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SM 
        0.92         1.22        33.04         4.01        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       29.16         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69         8.25        18.08        58.92        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM 
       12.69         9.67        31.07        33.01        70.32        21.40 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A40E 
       17.75        24.92        10.92        32.78        19.82         8.58 
TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       19.07         9.01         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       52.73        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SW 
       51.32       125.49        97.12         3.22        34.45        11.90 
TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       21.04        18.90         2.24         2.10        13.74        10.82 
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-AAN3 TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30        18.58         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
        3.48        88.87        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13I 
       27.62        50.04        66.54        10.22        47.80         7.33 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
        6.74         6.58        12.16        17.88        19.50        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
        8.25        17.16         4.67        17.56        36.43         1.94 
TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T 
       12.79        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-A8HX 
       12.46        12.10        12.26        13.12        12.00        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1AE 
       11.87        13.08         5.19        29.79         1.84        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX 
       17.62        15.62       142.78        13.58        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
      163.30        13.58        15.35        38.83        29.72         5.36 
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-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       26.24         4.24        24.66        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       15.32        14.37        32.02        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU 
       27.98         5.52        25.74        22.98        14.96        19.33 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        5.36         2.70        13.35        12.66        10.65         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW 
       20.12         6.94        20.71        15.81        15.91         0.49 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 
        3.12         2.20        11.31        18.97         7.63        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-H4-A2HO TCGA-HQ-A2OF 
        4.73         7.00        14.27        19.10         1.51        64.01 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        9.07        17.72         1.15        15.32        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78O 
       12.23        16.67        16.54        38.99        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB 
       78.25         3.02        35.24        29.56         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
        6.58        17.88        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       23.64        16.27        92.98         2.96         8.32        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       35.84        21.86        28.41        13.41        64.08        58.72 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 
        2.89         8.61        60.16        67.20        35.41        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE 
                         0.62                          0.49 
  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 
                        18.41                         16.80 
[1] "0.6 - 166.0 (18.4)" "0.5 - 165.7 (16.8)"
[1] "hr=" "1.1"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(2P25.1) MUTATED         1       42        46       62
  AMP PEAK  4(2P25.1) WILD-TYPE       1       87        94       73
D4V3, multiclass
           clus
vv          AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           42                            87
  STAGE III                          46                            94
  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  4(2P25.1) MUTATED         45  73  22
  AMP PEAK  4(2P25.1) WILD-TYPE       78 122  36
D4V4, multiclass
          clus
vv         AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  T0+T1+T2                          45                            78
  T3                                73                           122
  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
  AMP PEAK  4(2P25.1) MUTATED    76  22  34   5
  AMP PEAK  4(2P25.1) WILD-TYPE 160  25  41   3
D4V5, multiclass
    clus
vv   AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  N0                          76                           160
  N1                          22                            25
  N2                          34                            41
  N3                           5                             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    66   6
  AMP PEAK  4(2P25.1) WILD-TYPE 126   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED     66    6
  AMP PEAK  4(2P25.1) WILD-TYPE  126    5
   clus
vv  AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  0                          66                           126
  1                           6                             5
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED    48 104
  AMP PEAK  4(2P25.1) WILD-TYPE  59 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED     48  104
  AMP PEAK  4(2P25.1) WILD-TYPE   59  197
        clus
vv       AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  FEMALE                          48                            59
  MALE                           104                           197
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED   133   7
  AMP PEAK  4(2P25.1) WILD-TYPE 231  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED    133    7
  AMP PEAK  4(2P25.1) WILD-TYPE  231   13
     clus
vv    AMP PEAK  4(2P25.1) MUTATED AMP PEAK  4(2P25.1) WILD-TYPE
  NO                          133                           231
  YES                           7                            13
[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   125
  AMP PEAK  4(2P25.1) WILD-TYPE    32                        13   202
D4V12, multiclass
                           clus
vv                          AMP PEAK  4(2P25.1) MUTATED
  ASIAN                                              11
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             125
                           clus
vv                          AMP PEAK  4(2P25.1) WILD-TYPE
  ASIAN                                                32
  BLACK OR AFRICAN AMERICAN                            13
  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"
D4V13, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P25.1) MUTATED     4 133
  AMP PEAK  4(2P25.1) WILD-TYPE   5 236
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P25.1) MUTATED      4  133
  AMP PEAK  4(2P25.1) WILD-TYPE    5  236
                        clus
vv                       AMP PEAK  4(2P25.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         133
                        clus
vv                       AMP PEAK  4(2P25.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           236
[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   110  78
  AMP PEAK  5(3P25.2) WILD-TYPE 117 100
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                          188                           217 
  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                           78                           100 
$`AMP PEAK  5(3P25.2) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        12.39        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YO TCGA-CU-A0YR 
        8.35        20.48         9.96        28.70         4.90        15.12 
TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS 
        2.14       130.88        46.68        87.32         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-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 
       36.66       165.73       166.03        13.64        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.35        25.58         1.22        33.04        24.30        23.41 
TCGA-FD-A43P TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       27.35        18.08         6.28        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       17.62        70.32        19.13        10.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU 
       20.28        27.35        19.07        22.72        25.02         3.45 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       52.73        50.56        35.97        14.24         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       86.83        51.32        97.45        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ 
       15.98        12.76         2.10        10.82         7.63        71.57 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T 
       98.99        44.32        30.28        94.29        88.87        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7N 
       57.90        12.23        24.13        11.97         8.35        44.94 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       17.16        27.62         0.62        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       40.08         7.33         2.66        17.16        16.18         4.67 
TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CU-A3QU TCGA-CU-A3YL 
       12.79        12.59        12.13        12.16         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 
        1.84        21.86        66.41        18.41       112.44        17.95 
TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A3Y1 
      142.78         8.15        15.02        19.00        38.83         5.36 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       22.16         0.56         4.24        24.03        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O 
        8.09         8.94        22.98        20.91         5.36         7.10 
TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE 
        2.27        10.65         3.25        61.94        59.31        20.12 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 
       66.02        29.36        15.81        14.07         0.49        13.91 
TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10        20.98         2.20         4.73        14.27        21.34 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RH 
        8.48        36.49         1.51        38.60        21.24         9.07 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OC 
       13.48        12.23        17.62        37.05        76.01         3.02 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG 
       29.56        17.82         6.21         6.58         1.87        48.62 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9R9 
       79.66         5.98       110.60         6.77        22.36        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       64.08        47.84        59.38        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-GU-AATO 
       19.40        10.65 

$`AMP PEAK  5(3P25.2) WILD-TYPE`
TCGA-4Z-AA89 TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN 
       33.83        14.89        25.94         8.98        18.58        12.92 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IQ TCGA-DK-A3IT 
       18.48        13.58        19.00        16.70        17.72        21.30 
TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6M 
        9.67        53.29        76.60        67.36        38.24        52.01 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SM 
       13.64        56.15         0.92         4.01        60.66        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y 
       29.16        46.78        19.79        12.85         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 
       26.73        53.88        10.78         5.69         8.25        58.92 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS 
       62.86        18.81         6.15        21.40        17.75        24.92 
TCGA-GU-A763 TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       32.78         8.58         9.01         2.76         9.14        27.68 
TCGA-KQ-A41Q TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW 
       46.98       125.49        34.45        14.93         4.21        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 
       21.04        26.27        18.90         2.24        66.64        13.74 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       11.31        54.90        91.73        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE 
       18.58         3.88         9.63        13.64        21.11         3.48 
TCGA-ZF-AA4R TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       34.06        94.88       104.65        16.83        34.98        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A3JM TCGA-BT-A0S7 
       41.75        51.16        66.54        10.22         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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       14.96         5.06         8.25        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S 
        1.94        23.01        12.56        13.97        13.08        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-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL 
       16.14        17.62        15.62         7.79         4.80        13.58 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       20.81        10.55       163.30        13.58        18.81        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       12.03        43.59        29.72         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.96        26.24        24.66        14.07        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02        16.77        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S 
       25.74        14.96        19.33        27.45         2.70        13.35 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.85        12.66         8.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GD-A2C5 
        7.23         6.94        20.71        15.91         8.94        26.70 
TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        3.12        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-AATQ TCGA-GV-A3JX TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RI 
        7.00        19.10        19.40        64.01        12.16        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 
       17.72         1.81        16.27        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        35.24 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
        3.85        45.04        17.88        64.80        66.41        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       28.24        16.27        92.98         2.96         8.32        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RN 
       31.20        35.84        21.86        13.41        58.72        20.22 
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        29.49 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE 
                         0.49                          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 
                       17.885                        17.560 
[1] "0.5 - 166.0 (17.9)" "0.7 - 163.3 (17.6)"
[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 142  25  30   2
D5V5, multiclass
    clus
vv   AMP PEAK  5(3P25.2) MUTATED AMP PEAK  5(3P25.2) WILD-TYPE
  N0                          94                           142
  N1                          22                            25
  N2                          45                            30
  N3                           6                             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"
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   8
  AMP PEAK  5(3P25.2) WILD-TYPE 194  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P25.2) MUTATED    170    8
  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                           8                            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   115 101
  AMP PEAK  6(3Q26.33) WILD-TYPE 112  77
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           216                            189 
  AMP PEAK  6(3Q26.33) MUTATED AMP PEAK  6(3Q26.33) WILD-TYPE 
                           101                             77 
$`AMP PEAK  6(3Q26.33) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W 
       16.27        16.77        15.12        12.39        26.14         8.35 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       25.94         9.96        28.70        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 
       18.48       130.88        46.68        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
      165.73       166.03        13.64        13.64        56.15        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.35        25.58         1.22        33.04        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P 
       23.41        27.35        15.58         8.25        18.08         6.28 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A61P 
        6.15        12.36         3.06         4.31         9.67        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       33.01        17.62        70.32        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       10.92        20.28        27.35        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
       25.02         3.45        50.56        35.97        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       33.14        86.83        51.32        97.45        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T5 
        3.22        15.98         4.21        12.76        26.27        66.64 
TCGA-XF-A9T8 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 
       13.74         7.63        71.57        98.99        44.32        86.30 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R 
       13.64        21.11        30.28        94.29         3.48        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW 
       19.69        57.90        12.23        24.13       104.65         8.35 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       34.98        27.62         0.62         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20R 
        7.33         2.66         6.74        13.15        19.04         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E 
        5.06         8.25        17.16        16.18         4.67        36.43 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A5UA TCGA-CU-A3YL 
       12.79        12.56        12.59        12.13        12.00        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        1.84        21.86        66.41        18.41       112.44        16.14 
TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6U 
       17.95         4.80         8.15        15.02        13.58        19.00 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD 
       12.03        43.59         5.36        22.16         0.56         4.24 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 
       24.03        13.68        12.95         8.09        32.02        16.77 
TCGA-FD-A3N5 TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TF 
       22.52        20.91        19.33         5.36         7.10         2.27 
TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B 
       10.65        61.94        48.00        59.31         7.23        66.02 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       20.71        15.81        15.91        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ 
       13.91        20.98        11.31         7.63         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE 
       21.34        19.10         8.48        36.49        19.40        38.60 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO 
       12.16        21.24         9.07        11.70        15.42        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       44.38         1.15        12.23        38.99        17.62        37.05 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HC 
       69.34         3.02        29.56        17.82        45.04         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-AAMG 
        1.87        17.88        79.66         5.98        28.24       110.60 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RF 
        2.96         6.77        27.06        22.36        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        47.84        20.22         2.89        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5H TCGA-GU-AATO 
       67.20        56.35        35.41        19.40        29.49        10.65 

$`AMP PEAK  6(3Q26.33) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20T TCGA-BT-A2LD TCGA-C4-A0EZ TCGA-CF-A9FL 
      108.95        33.83        14.89        20.48         8.98        18.58 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IN 
       13.58         2.14        19.00        16.70        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       17.72        21.30         9.67        53.29        76.60        67.36 
TCGA-DK-AA6M TCGA-DK-AA75 TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3SM TCGA-FD-A3SN 
       52.01        11.18         0.92         4.01        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       46.78        19.79        12.85         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
       10.78         5.69        58.92        62.86        18.81        12.69 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       31.07        17.23        21.40        32.78        32.98        19.82 
TCGA-GV-A40E TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q 
        8.58         2.76         9.14        27.68        52.73        46.98 
TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 
      125.49        34.45        14.93        11.90        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR 
        2.24         2.10        10.82        11.31        54.90        91.73 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RL 
       30.94        61.45        18.58         3.88         9.63        88.87 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7Y 
       11.97        94.88        44.94        16.83        17.16        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BT-A0S7 
       41.75        51.16        66.54        10.22        47.80         6.58 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A42B TCGA-BT-A42F 
       12.16        17.88        19.50        14.96        17.56        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S 
        1.94        23.01        13.97        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-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW 
       17.62        15.62         7.79       142.78        13.58        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 
       10.55       163.30        18.81        15.35        38.83        29.72 
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-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.07        15.32        14.37         8.94        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BZ TCGA-FD-A62N 
        5.52        25.74        22.98        14.96        27.45         2.70 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK 
       13.35        10.85        12.66         8.94         3.25        15.95 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GD-A2C5 TCGA-GD-A3OP 
       26.93        20.12         6.94        29.36        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV 
        3.12         2.20        18.97        20.05        15.78        14.27 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R 
        1.51        64.01        17.72         1.81        16.27        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        35.24         6.21         3.85 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME 
       48.62        64.80        66.41        23.64        16.27        92.98 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
        8.32        56.48        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4U 
       25.41        31.20        35.84        21.86        28.41         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 
                          0.49                           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 
                        17.915                         17.160 
[1] "0.5 - 166.0 (17.9)" "0.7 - 163.3 (17.2)"
[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   115  25  47   5
  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                          115                            121
  N1                           25                             22
  N2                           47                             28
  N3                            5                              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   9
  AMP PEAK  6(3Q26.33) WILD-TYPE 166  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(3Q26.33) MUTATED    198    9
  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                            9                             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 178 154
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           73                           332 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           24                           154 
$`AMP PEAK  7(4P16.3) MUTATED`
TCGA-2F-A9KT TCGA-BT-A20T TCGA-BT-A3PJ TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-DK-A1A5 
      108.95        14.89        25.94        18.58        18.48         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-AA75 
      130.88        87.32        50.27        64.18        67.36        11.18 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A5C1 TCGA-FD-A6TC 
       25.58         0.92        60.66        23.41        58.92         6.15 
TCGA-FD-A6TE TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A6ZA TCGA-HQ-A5ND 
       12.36        33.01        17.62        21.40        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-UY-A78N TCGA-XF-A9T3 TCGA-XF-AAMY TCGA-XF-AAMZ 
       25.02         9.14        86.83         2.24        98.99        44.32 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-2F-A9KP TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA87 
       13.64        21.11        11.97        17.16        50.04        47.80 
TCGA-BL-A0C8 TCGA-BT-A20P TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF 
       40.08        17.88         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-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-AA76 
       11.87         1.84        66.41         7.79         8.15        12.03 
TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-G2-A2EO TCGA-G2-AA3B 
       38.83         0.56         5.36        27.45        59.31        66.02 
TCGA-GC-A3RC TCGA-GU-A42R TCGA-H4-A2HO TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41R 
       15.91        18.97         1.51         1.81        15.42        44.38 
TCGA-MV-A51V TCGA-XF-A9SZ TCGA-YF-AA3L TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA51 
       13.48        28.24        11.97        58.72         8.61        56.35 
TCGA-ZF-AA5H 
       29.49 

$`AMP PEAK  7(4P16.3) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN 
        8.35        20.48         9.96        28.70         8.98        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX 
        4.90        15.12        13.58        19.00        16.70        46.68 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
        8.22        17.72        21.30        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       56.15        20.32        15.35         1.22        33.04         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69         8.25        18.08         6.28        62.86        18.81 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       12.69         3.06         4.31         9.67        31.07        17.23 
TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       11.08        70.32        19.13        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       32.78        32.98        19.82        20.28        27.35         8.58 
TCGA-GV-A40G TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       19.07         3.45         2.76        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH 
       35.97        46.98        14.24         1.84        33.14        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.45       125.49        97.12        15.35         3.22        15.98 
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-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 
       11.31        54.90         7.63        71.57        91.73        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 
       61.45        86.30        18.58         3.88         9.63        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       12.23        24.13        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.83        34.98        27.62         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22         2.50        17.42         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q 
        6.74         6.58        13.15        19.04        12.16        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS 
        4.67        17.56        36.43        28.41        12.79        12.56 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 
       12.16        10.95        12.66        12.10        12.26        13.12 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
       12.10        11.34        13.08         5.19        29.79        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       18.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
      142.78         4.80        13.58        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC 
       15.02        13.58        18.81        19.00        15.35        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       29.72         5.36        22.16         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N 
       25.74        22.98        14.96        20.91        19.33         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
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-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.23        20.12         6.94        29.36        20.71        15.81 
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        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 
        3.12        20.98         2.20        11.31         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
        8.48        36.49        19.40        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO 
       21.24         9.07        11.70        17.72        16.27        11.80 
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-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        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        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       17.82         6.21         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
       23.64        16.27        92.98       110.60         2.96         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        6.77        56.48        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       22.36        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V 
       13.41        64.08        47.84        20.22         2.89        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        67.20        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                         0.56                          0.49 
  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 
                        17.88                         17.62 
[1] "0.6 - 130.9 (17.9)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.5"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(4P16.3) MUTATED         1       32        24       17
  AMP PEAK  7(4P16.3) WILD-TYPE       1       97       116      118
D7V3, multiclass
           clus
vv          AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  STAGE I                             1                             1
  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         33  31   8
  AMP PEAK  7(4P16.3) WILD-TYPE       90 164  50
D7V4, multiclass
          clus
vv         AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  T0+T1+T2                          33                            90
  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    53   7   8   1
  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                          53                           183
  N1                           7                            40
  N2                           8                            67
  N3                           1                             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    46   1
  AMP PEAK  7(4P16.3) WILD-TYPE 146  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     46    1
  AMP PEAK  7(4P16.3) WILD-TYPE  146   10
   clus
vv  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  0                          46                           146
  1                           1                            10
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED    20  54
  AMP PEAK  7(4P16.3) WILD-TYPE  87 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     20   54
  AMP PEAK  7(4P16.3) WILD-TYPE   87  247
        clus
vv       AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  FEMALE                          20                            87
  MALE                            54                           247
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED    64   6
  AMP PEAK  7(4P16.3) WILD-TYPE 300  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED     64    6
  AMP PEAK  7(4P16.3) WILD-TYPE  300   14
     clus
vv    AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  NO                           64                           300
  YES                           6                            14
[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    53
  AMP PEAK  7(4P16.3) WILD-TYPE    30                        20   274
D7V12, multiclass
                           clus
vv                          AMP PEAK  7(4P16.3) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              53
                           clus
vv                          AMP PEAK  7(4P16.3) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               274
[1] 3 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  64
  AMP PEAK  7(4P16.3) WILD-TYPE   7 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED      2   64
  AMP PEAK  7(4P16.3) WILD-TYPE    7  305
                        clus
vv                       AMP PEAK  7(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       AMP PEAK  7(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           305
[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    39  22
  AMP PEAK  8(4Q13.3) WILD-TYPE 188 156
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           61                           344 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           22                           156 
$`AMP PEAK  8(4Q13.3) MUTATED`
TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A3KJ 
       16.27        26.14        20.48         9.96        28.70        18.48 
TCGA-DK-A1A5 TCGA-DK-A2I6 TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
        2.14        87.32        66.05        17.98        64.18        67.36 
TCGA-DK-AA6R TCGA-E7-A541 TCGA-FD-A3NA TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5C0 
      165.73        25.58        60.66        19.79        15.58        18.08 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-A3VY TCGA-GC-A3WC TCGA-GU-A42P TCGA-GV-A6ZA 
        6.15        12.36        17.62        17.75        10.92        22.72 
TCGA-HQ-A5ND TCGA-KQ-A41Q TCGA-XF-AAMZ TCGA-ZF-A9R2 TCGA-ZF-AA4T TCGA-4Z-AA7W 
        9.01        46.98        44.32        21.11        19.69        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A47X TCGA-CF-A8HX 
        0.62        51.16        36.43        23.01        12.62        11.34 
TCGA-CF-A8HY TCGA-DK-A1A7 TCGA-DK-A2I2 TCGA-E5-A4U1 TCGA-E7-A6MD TCGA-FD-A5BV 
       11.34        18.41         7.79        38.83         4.24         5.36 
TCGA-FD-A5BZ TCGA-FD-A62S TCGA-G2-A2EJ TCGA-G2-AA3B TCGA-GC-A4ZW TCGA-GD-A2C5 
       27.45        13.35        48.00        66.02         0.49        26.70 
TCGA-GV-A3JW TCGA-K4-A3WV TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K 
       21.34        21.24        44.38        15.58        13.48        17.62 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OD TCGA-XF-A9T4 TCGA-YF-AA3L TCGA-ZF-A9RN 
       37.05        76.01       112.83        16.27        11.97        20.22 
TCGA-ZF-AA5H 
       29.49 

$`AMP PEAK  8(4Q13.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.77        15.12        33.83        12.39        14.89 
TCGA-BT-A20W TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
        8.35        25.94         8.98        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       15.12        13.58        19.00        16.70       130.88        46.68 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L 
       53.29        76.60        15.68        50.70        36.66        38.24 
TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
       52.01       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       20.32        15.35         0.92         1.22        33.04         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS 
       24.30        23.41        17.98        29.16        46.78        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
        8.25        58.92         6.28        62.86        18.81        12.69 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A763 
       33.01        70.32        21.40        19.13        24.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       25.02         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       50.56        35.97        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       51.32        97.45       125.49        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       15.98        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 
       21.04        26.27        18.90         2.24        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       13.74        10.82        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       91.73        98.99        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
        3.88         9.63        13.64        30.28        94.29         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       88.87        34.06        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       34.98        50.04        41.75        66.54        10.22        47.80 
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-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
        5.06        14.96         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
        4.67        17.56        28.41         1.94        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-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       21.86        66.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95       142.78         4.80        13.58         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.35        12.03        43.59        29.72         5.36        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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66        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-A3B8 
       14.37         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FD-A6TK 
       20.91        19.33         2.70         7.10         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EK 
       12.66        10.65         8.94         3.25        61.94        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93        59.31         7.23        20.12         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       64.01        12.16         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       15.42        16.27        11.80         1.15        15.32        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78P 
       12.23        16.67        16.54        38.99        22.68        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       69.34         3.02        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        3.85        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ 
       64.80        79.66        66.41         5.98        23.64        28.24 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       92.98       110.60         2.96         8.32         6.77        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        47.84         2.89         8.61        59.38        60.16 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
       67.20        56.35        35.41        19.40         8.52        54.21 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                         0.49                          0.56 
  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 
                        20.22                         16.77 
[1] "0.5 - 165.7 (20.2)" "0.6 - 166.0 (16.8)"
[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 199  37  65   7
D8V5, multiclass
    clus
vv   AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  N0                          37                           199
  N1                          10                            37
  N2                          10                            65
  N3                           1                             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"
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  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED     54    2
  AMP PEAK  8(4Q13.3) WILD-TYPE  310   18
     clus
vv    AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  NO                           54                           310
  YES                           2                            18
[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 109  91
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           205                            200 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                            87                             91 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ 
      108.95        16.27        12.39        14.89         8.35        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A2I6 
        9.96        28.70         8.98        12.92        15.12        87.32 
TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B5 
        8.22        23.21         9.67        64.18        67.36        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       36.66        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3NA 
       13.64        56.15        15.35        25.58         1.22        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY 
       24.30        29.16        19.79        15.58        26.73         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         6.28        18.81         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D 
        3.06         4.31        17.23        11.08        17.62        70.32 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E 
       19.13        24.92        10.92        19.82        20.28         8.58 
TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O 
       19.07         9.01         2.76         9.14        52.73        50.56 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HF TCGA-XF-A9SJ 
       46.98        14.24         1.84        86.83        97.12         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 
       15.98        34.45        14.93        26.27         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN3 TCGA-XF-AAN7 
        2.10        10.82        54.90         7.63        86.30        18.58 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.64        21.11        30.28        94.29        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       19.69        57.90        12.23         8.35        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A3JM 
        0.62        41.75        10.22         2.50        40.08         6.74 
TCGA-BT-A20P TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HS 
       17.88         5.06        17.16        36.43        23.01        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A5UA TCGA-CU-A3QU 
       12.59        12.13        13.08        10.95        12.00         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3WX 
        1.84        21.86       112.44       142.78         8.15        10.55 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       15.02        13.58        19.00        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A97Q 
       29.72        22.16         4.24        24.03        12.95         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP 
       32.02        16.77         8.94        22.52         5.52        25.74 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
       19.33         5.36         2.70         7.10        13.35        10.85 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
        3.25        61.94        59.31         7.23        20.12        66.02 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW 
       29.36        20.71        15.81        15.91        14.07         0.49 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 
       13.91         2.10        20.98         7.63        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ 
        7.00        14.27        19.10         8.48        36.49        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ 
       38.60        64.01        12.16         9.07        11.70         1.81 
TCGA-K4-A6MB TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FN 
       15.42        44.38         1.15        15.32        13.48        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB 
       38.99        17.62        37.05        69.34       112.83        29.56 
TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SZ 
        6.21         6.58        48.62        79.66        23.64        28.24 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-ZF-A9R3 TCGA-ZF-A9R7 
       92.98       110.60         2.96         6.77        31.20        21.86 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X 
       58.72        47.84        20.22         2.89        59.38        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-GU-AATO 
       10.65 

$`AMP PEAK  9(5P15.33) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A2LD TCGA-CF-A9FL 
       16.77        15.12        33.83        26.14        20.48        18.58 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
        4.90        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
      130.88        46.68        17.72        50.27        21.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA75 TCGA-DK-AA77 
       17.98        53.29        76.60        15.68        11.18        20.32 
TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ 
        0.92        33.04         4.01        23.41        17.98        46.78 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       12.85        27.35         3.62        53.88        10.78         5.69 
TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-GC-A3BM 
       18.08        62.86         9.67        31.07        33.01        21.40 
TCGA-GC-A3WC TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-K4-A3WS 
       17.75        32.78        32.98        27.35        22.72        25.02 
TCGA-K4-A3WU TCGA-K4-A54R TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD 
        3.45        27.68        35.97        33.14        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
      125.49        15.35         4.21        12.76        11.90        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       18.90        13.74        11.31        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RE 
       44.32        30.94        61.45         3.88         9.63         3.48 
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-AA7R TCGA-4Z-AA7S TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM 
       17.16        34.98        51.16        66.54        47.80        17.42 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        7.33         2.66         6.58        13.15        19.04        12.16 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50         5.06        14.96         8.25        16.18         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-A9FM TCGA-CU-A3YL 
       12.10        11.34        11.34        11.87        13.08        29.79 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       66.41        18.41        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6T 
        7.79         4.80        13.58        20.81       163.30        18.81 
TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       43.59         5.36         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       26.96        26.24        24.66        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       14.37        12.62        27.98        22.98        14.96        20.91 
TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EJ 
       27.45         2.27        12.66        10.65         8.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-AA3C TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       15.95        26.93         6.94         8.94        26.70         3.12 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GV-A3JW TCGA-H4-A2HO 
        2.20        11.31        18.97        20.05        21.34         1.51 
TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT 
       21.24        17.72        16.27        11.80        15.58        21.07 
TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       12.23        16.54        22.68        76.01        78.25         3.02 
TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        17.82         3.85        45.04         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAMW TCGA-XF-AAN0 
       64.80        66.41         5.98        16.27         8.32        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       27.06        75.39        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-AA4U 
       25.41        35.84        28.41        13.41        64.08         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA5N 
       60.16         5.52 

  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                          0.49                           0.56 
  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 
                         17.62                          17.72 
[1] "0.5 - 166.0 (17.6)" "0.6 - 163.3 (17.7)"
[1] "hr=" "1.1"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(5P15.33) MUTATED         1       65        74       65
  AMP PEAK  9(5P15.33) WILD-TYPE       1       64        66       70
D9V3, multiclass
           clus
vv          AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  STAGE I                              1                              1
  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         58 98 29
  AMP PEAK  9(5P15.33) WILD-TYPE       65 97 29
D9V4, multiclass
          clus
vv         AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  T0+T1+T2                           58                             65
  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   114  26  36   3
  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                          114                            122
  N1                           26                             21
  N2                           36                             39
  N3                            3                              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    91   2
  AMP PEAK  9(5P15.33) WILD-TYPE 101   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     91    2
  AMP PEAK  9(5P15.33) WILD-TYPE  101    9
   clus
vv  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  0                           91                            101
  1                            2                              9
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED    54 152
  AMP PEAK  9(5P15.33) WILD-TYPE  53 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED     54  152
  AMP PEAK  9(5P15.33) WILD-TYPE   53  149
        clus
vv       AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  FEMALE                           54                             53
  MALE                            152                            149
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED   185   8
  AMP PEAK  9(5P15.33) WILD-TYPE 179  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED    185    8
  AMP PEAK  9(5P15.33) WILD-TYPE  179   12
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  NO                           185                            179
  YES                            8                             12
[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   168
  AMP PEAK  9(5P15.33) WILD-TYPE    28                         9   159
D9V12, multiclass
                           clus
vv                          AMP PEAK  9(5P15.33) MUTATED
  ASIAN                                               15
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              168
                           clus
vv                          AMP PEAK  9(5P15.33) WILD-TYPE
  ASIAN                                                 28
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                159
[1] 3 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     5 186
  AMP PEAK  9(5P15.33) WILD-TYPE   4 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      5  186
  AMP PEAK  9(5P15.33) WILD-TYPE    4  183
                        clus
vv                       AMP PEAK  9(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          186
                        clus
vv                       AMP PEAK  9(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            183
[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   110  61
  AMP PEAK 10(6P22.3) WILD-TYPE 117 117
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          171                           234 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                           61                           117 
$`AMP PEAK 10(6P22.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       16.27        15.12         8.35        20.48        25.94        28.70 
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IS 
        8.98        12.92         2.14       130.88        87.32        50.27 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       64.18        67.36        15.68       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV 
       13.64        56.15        11.18        15.35        25.58         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A5C1 
       33.04         4.01        24.30        19.79        27.35        58.92 
TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       62.86         6.15        12.36         3.06        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS 
       11.08        17.62        70.32        21.40        19.13        24.92 
TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       10.92        32.98        19.82         8.58        19.07        22.72 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N 
        9.14        27.68        52.73        46.98        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP 
       51.32        97.45        97.12         3.22        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ 
        4.21        26.27         2.24        10.82         7.63        71.57 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       98.99        44.32        18.58        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-4Z-AA7R TCGA-4Z-AA7W 
       94.29        34.06        19.69        12.23        17.16        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A0S7 
        0.62        41.75        51.16        47.80         2.66         6.58 
TCGA-BT-A20R TCGA-BT-A2LA TCGA-CF-A1HS TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5UA 
        5.06        17.16        12.56        12.46        12.62        12.00 
TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 
        5.19        66.41        18.41       112.44        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6U TCGA-DK-AA76 
      142.78        13.58         8.15        10.55        19.00        12.03 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       43.59        22.16         0.56        24.03        13.68        12.95 
TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A6TF 
       32.02        22.52        25.74        22.98        19.33         2.27 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 
       10.65         3.25        61.94        66.02        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        15.91        14.07         0.49        13.91        26.70 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3QH 
       18.97         7.63        20.05         4.73        21.34         8.48 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-A83P 
       38.60        12.16        21.24         9.07        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI 
       11.80        44.38         1.15        15.32        15.58        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        38.99        17.62        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02        29.56        17.82         6.21         3.85 
TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-AAMG TCGA-YF-AA3L TCGA-ZF-A9RD TCGA-ZF-A9RF 
        6.58        48.62       110.60        11.97        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA56 
       58.72        47.84        59.38        67.20        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       54.21        29.49        10.65 

$`AMP PEAK 10(6P22.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.77        33.83        12.39        26.14        14.89 
TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
        9.96        18.58         4.90        15.12        18.48        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       19.00        16.70        46.68         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        66.05        17.98        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA77 TCGA-E7-A7DU 
       50.70        36.66        38.24        52.01        20.32         0.92 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS 
       60.66        23.41        17.98        29.16        46.78        12.85 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TH 
        8.25        18.08         6.28        18.81        12.69         4.31 
TCGA-FD-A6TI TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK 
        9.67        33.01        17.75        32.78        20.28        27.35 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41O TCGA-KQ-A41P 
        9.01        25.02         3.45         2.76        50.56        35.97 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SV 
       14.24         1.84       125.49        15.35        15.98        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       11.90        21.04        18.90        66.64         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       11.31        54.90        91.73        30.94        61.45        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-2F-A9KO 
        3.88         9.63         3.48        88.87        57.90        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM 
       34.98        50.04        66.54        10.22         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33         6.74        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB 
       17.88        19.50        14.96         5.06         8.25        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        13.97        12.59        12.13        13.08        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-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3WW 
       21.86        16.14        17.62        15.62         4.80        20.81 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A4U1 
      163.30        15.02        13.58        18.81        15.35        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       29.72         5.36         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24         4.24        24.66        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO 
        8.09        16.77         8.94        12.62        27.98         5.52 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O 
       14.96        20.91         5.36        27.45         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EK 
       13.35        10.85        12.66         8.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A6I1 
       26.93        59.31         7.23        20.12         6.94         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A766 
        2.10         3.12        20.98         2.20        11.31        15.78 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.00        14.27        19.10        36.49         1.51        19.40 
TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-LT-A8JT TCGA-MV-A51V 
       64.01        11.70        17.72         1.81        21.07        13.48 
TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HH 
       16.54        78.25       112.83        35.24        45.04         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       17.88        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       28.24        16.27        92.98         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 
       56.48        27.06        75.39        18.84         0.66        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RN 
       25.41        31.20        35.84        21.86        28.41        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA5N 
        2.89         8.61        60.16        56.35        35.41         5.52 

  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                         0.49                          0.66 
  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 
                        19.07                         16.70 
[1] "0.5 - 166.0 (19.1)" "0.7 - 163.3 (16.7)"
[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       64
  AMP PEAK 10(6P22.3) WILD-TYPE       2       74        89       71
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                           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
  AMP PEAK 10(6P22.3) MUTATED         59  75  25
  AMP PEAK 10(6P22.3) WILD-TYPE       64 120  33
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                                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 10(6P22.3) MUTATED    93  23  37   4
  AMP PEAK 10(6P22.3) WILD-TYPE 143  24  38   4
D10V5, multiclass
    clus
vv   AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  N0                          93                           143
  N1                          23                            24
  N2                          37                            38
  N3                           4                             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    74   4
  AMP PEAK 10(6P22.3) WILD-TYPE 118   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     74    4
  AMP PEAK 10(6P22.3) WILD-TYPE  118    7
   clus
vv  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  0                          74                           118
  1                           4                             7
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED    38 133
  AMP PEAK 10(6P22.3) WILD-TYPE  69 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED     38  133
  AMP PEAK 10(6P22.3) WILD-TYPE   69  168
        clus
vv       AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  FEMALE                          38                            69
  MALE                           133                           168
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED   152   8
  AMP PEAK 10(6P22.3) WILD-TYPE 212  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED    152    8
  AMP PEAK 10(6P22.3) WILD-TYPE  212   12
     clus
vv    AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  NO                          152                           212
  YES                           8                            12
[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   143
  AMP PEAK 10(6P22.3) WILD-TYPE    30                        13   184
D10V12, multiclass
                           clus
vv                          AMP PEAK 10(6P22.3) MUTATED
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             143
                           clus
vv                          AMP PEAK 10(6P22.3) WILD-TYPE
  ASIAN                                                30
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               184
[1] 3 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     6 150
  AMP PEAK 10(6P22.3) WILD-TYPE   3 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED      6  150
  AMP PEAK 10(6P22.3) WILD-TYPE    3  219
                        clus
vv                       AMP PEAK 10(6P22.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         150
                        clus
vv                       AMP PEAK 10(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           219
[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 204 166
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         35                         370 
  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                         12                         166 
$`AMP PEAK 11(6Q21) MUTATED`
TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A6B5 TCGA-DK-AA75 TCGA-FD-A43P TCGA-FJ-A3Z7 
       15.12       130.88        50.70        11.18        27.35        31.07 
TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3YS TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9T5 
       17.23        21.40        24.92        86.83        51.32        66.64 
TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-4Z-AA7R TCGA-BL-A0C8 TCGA-BT-A0S7 TCGA-BT-A20J 
       71.57        30.28        17.16        40.08         6.58        19.04 
TCGA-BT-A2LA TCGA-CF-A47V TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A3WX TCGA-E7-A6ME 
       17.16        12.46        21.86        18.41        10.55        24.03 
TCGA-FJ-A3ZE TCGA-GC-A3OO TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-K4-A5RH TCGA-UY-A78K 
       10.65        15.81        13.91        26.70         9.07        17.62 
TCGA-XF-AAMG TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-GU-AATO 
      110.60        58.72        59.38        56.35        10.65 

$`AMP PEAK 11(6Q21) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       26.14        14.89         8.35        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       28.70         8.98        18.58        12.92         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 
       13.58         2.14        19.00        16.70        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        17.72        50.27        21.30        23.21         9.67 
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-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       15.68        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
       13.64        13.64        56.15        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
        0.92         1.22        33.04         4.01        60.66        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        8.25        18.08        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI 
        6.15        12.69        12.36         3.06         4.31         9.67 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       11.08        33.01        17.62        70.32        19.13        17.75 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
        8.58        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HD TCGA-XF-A8HE 
       46.98        14.24         1.84        33.14        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        7.63        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       86.30        18.58         3.88         9.63        13.64        21.11 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         8.35 
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-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       41.75        51.16        66.54        10.22        47.80         2.50 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20O 
       17.42         7.33         2.66         6.74        13.15        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-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       16.18         4.67        17.56        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       23.01        12.79        12.56        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47W TCGA-CF-A47X 
       13.08        12.16        10.95        12.66        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
       11.87        13.08         5.19        29.79         1.84        66.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY 
      142.78         4.80        13.58         8.15        20.81       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       15.02        13.58        18.81        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       43.59        38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       27.98         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S 
       19.33         5.36        27.45         2.70         7.10        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
        2.27        10.85        12.66         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       66.02         6.94        29.36        20.71        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
        0.49         8.94         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        7.00        14.27        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       11.70        17.72         1.81        15.42        16.27        11.80 
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-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M 
       12.23        16.67        16.54        38.99        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       76.01        78.25        69.34         3.02       112.83        35.24 
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-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-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
        5.98        23.64        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32         6.77        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN 
       21.86        28.41        13.41        64.08        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 
        2.89         8.61        60.16        67.20        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
        8.52        54.21        29.49         5.52 

  AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE 
                       6.58                        0.49 
  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 
                     21.860                      17.125 
[1] "6.6 - 130.9 (21.9)" "0.5 - 166.0 (17.1)"
[1] "hr=" "1.7"
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 218  43  67   7
D11V5, multiclass
    clus
vv   AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  N0                        18                         218
  N1                         4                          43
  N2                         8                          67
  N3                         1                           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"
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  18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(6Q21) MUTATED     30    2
  AMP PEAK 11(6Q21) WILD-TYPE  334   18
     clus
vv    AMP PEAK 11(6Q21) MUTATED AMP PEAK 11(6Q21) WILD-TYPE
  NO                         30                         334
  YES                         2                          18
[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 201 158
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           46                           359 
  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                           20                           158 
$`AMP PEAK 12(6Q23.3) MUTATED`
TCGA-BT-A20T TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1AC TCGA-DK-A6B6 TCGA-DK-AA75 
       14.89        15.12        18.48       130.88        36.66        11.18 
TCGA-E7-A541 TCGA-FD-A3SS TCGA-FD-A6TD TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3RB 
       25.58        12.85        12.69        17.23        21.40        19.13 
TCGA-GC-A3YS TCGA-GV-A40G TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A9SV TCGA-XF-A9T5 
       24.92        19.07        86.83        51.32        12.76        66.64 
TCGA-XF-AAMQ TCGA-XF-AAN8 TCGA-ZF-A9R4 TCGA-4Z-AA7S TCGA-BT-A0S7 TCGA-BT-A2LA 
       71.57         3.88        30.28        34.98         6.58        17.16 
TCGA-CF-A1HS TCGA-CF-A47V TCGA-DK-A1A7 TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P 
       12.56        12.46        18.41         8.15        10.55        15.02 
TCGA-E7-A97Q TCGA-FJ-A3ZE TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GV-A3JV 
        8.09        10.65        29.36        15.81         0.49        14.27 
TCGA-HQ-A2OE TCGA-K4-A5RH TCGA-UY-A9PE TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-ZF-A9RF 
       38.60         9.07         6.21        28.24       110.60        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-GU-AATO 
       58.72        20.22        59.38        10.65 

$`AMP PEAK 12(6Q23.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       26.14         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A5 
        8.98        18.58        12.92         4.90        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       19.00        16.70        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       56.15        20.32        15.35         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        4.01        60.66        24.30        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       46.78        19.79        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        4.31         9.67        31.07        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       70.32        17.75        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       20.28        27.35         8.58        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HD 
       35.97        46.98        14.24         1.84        33.14        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
      125.49        97.12        15.35         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       14.93         4.21        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
        7.63        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       86.30        18.58         9.63        13.64        21.11        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        17.16        27.62        50.04         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.74        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        8.25        16.18         4.67        17.56        36.43        28.41 
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-A47W TCGA-CF-A47X 
       13.08        12.16        10.95        12.66        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       66.41       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79       142.78         4.80        13.58        20.81       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58        18.81        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        13.68        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       10.85        12.66         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
        6.94        20.71        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       18.97         7.63        20.05        15.78         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       21.34        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       64.01        12.16        21.24        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       15.42        16.27        11.80        44.38         1.15        15.32 
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-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        35.24        29.56        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        3.85        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 
       64.80        79.66        66.41         5.98        23.64        16.27 
TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RM 
       31.20        35.84        21.86        28.41        13.41        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.40         8.52        54.21        29.49         5.52 

  AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE 
                         0.49                          0.56 
  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 
                        17.82                         17.62 
[1] "0.5 - 130.9 (17.8)" "0.6 - 166.0 (17.6)"
[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 210  41  68   5
D12V5, multiclass
    clus
vv   AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  N0                          26                           210
  N1                           6                            41
  N2                           7                            68
  N3                           3                             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"
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  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(6Q23.3) MUTATED     42    2
  AMP PEAK 12(6Q23.3) WILD-TYPE  322   18
     clus
vv    AMP PEAK 12(6Q23.3) MUTATED AMP PEAK 12(6Q23.3) WILD-TYPE
  NO                           42                           322
  YES                           2                            18
[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   104  97
  AMP PEAK 13(7P21.1) WILD-TYPE 123  81
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                          201                           204 
  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                           97                            81 
$`AMP PEAK 13(7P21.1) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        12.39        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-CU-A0YN 
        8.35        20.48        25.94         9.96        28.70        12.92 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 
        4.90        18.48        13.58         2.14       130.88        87.32 
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-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R 
       64.18        67.36        15.68        36.66        38.24       165.73 
TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
      166.03        11.18        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       33.04         4.01        24.30        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A5C1 
       27.35         3.62        26.73        10.78        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.28        12.69        12.36         3.06         9.67        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       17.23        11.08        17.62        70.32        21.40        19.13 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
       24.92        10.92        32.98        19.82        27.35         8.58 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 
       22.72         9.01        35.97        46.98         1.84        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       86.83        51.32        97.45        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T0 
       15.98        34.45        14.93         4.21        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ 
        2.24        66.64         7.63        71.57        98.99        44.32 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P 
       61.45        18.58        13.64        34.06        19.69        12.23 
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       11.97         8.35        17.16        27.62         0.62        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20O 
       10.22        47.80        40.08         2.66         6.58        12.16 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E TCGA-BT-A42F 
        5.06         8.25        17.16        16.18        36.43        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5U8 TCGA-CU-A3QU 
       23.01        12.79        12.13        12.16        13.12         5.19 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       21.86        18.41        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-E5-A2PC TCGA-E7-A4IJ 
       13.58         8.15        15.02        19.00        43.59        22.16 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       24.03        13.68         8.09        32.02        16.77         8.94 
TCGA-FD-A3N5 TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O 
       22.52        22.98        20.91         5.36        27.45         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-AA3B 
       13.35         2.27        10.65         3.25        59.31        66.02 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 
       29.36        20.71        15.91        14.07        13.91        26.70 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       20.98         2.20        11.31        15.78         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI 
       21.34        36.49        19.40        12.16         9.07        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V 
        1.81        15.42        16.27         1.15        15.32        13.48 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       17.62        37.05        22.68        76.01        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SU 
       35.24        29.56         6.21        48.62        79.66         5.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-ZF-A9R0 
      110.60         2.96         6.77        56.48        75.39        22.36 
TCGA-ZF-A9R3 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V 
       31.20        13.41        64.08        58.72         2.89        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5H 
       67.20         8.52        29.49 

$`AMP PEAK 13(7P21.1) WILD-TYPE`
TCGA-4Z-AA89 TCGA-BT-A20T TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YR TCGA-DK-A1AA 
       33.83        14.89         8.98        18.58        15.12        19.00 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A6AW TCGA-DK-A6B0 
       16.70        46.68        17.72        21.30        53.29        76.60 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       50.70        52.01        13.64        13.64        56.15        20.32 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A43Y TCGA-FD-A5BS 
       60.66        23.41        17.98        29.16        15.58        53.88 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TH 
        5.69         8.25        62.86        18.81         6.15         4.31 
TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A40G TCGA-K4-A3WS 
       33.01        17.75        32.78        20.28        19.07        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        3.45         2.76         9.14        27.68        52.73        50.56 
TCGA-R3-A69X TCGA-XF-A8HE TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T2 TCGA-XF-A9T6 
       14.24       125.49        12.76        11.90        18.90         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAN1 
       13.74        10.82        11.31        54.90        91.73        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       86.30         3.88         9.63        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR 
        3.48        88.87        57.90        24.13        94.88       104.65 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       44.94        16.83        34.98        50.04        51.16        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J 
        2.50        17.42         7.33         6.74        13.15        19.04 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42B 
       17.88        19.50         5.06        14.96         4.67        17.56 
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-A9FM TCGA-CU-A3YL 
       12.10        11.34        11.34        11.87        13.08        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        1.84        66.41       112.44        16.14        17.62        15.62 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       20.81        10.55       163.30        13.58        18.81        15.35 
TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       12.03        38.83        29.72         5.36         2.24        16.70 
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-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.07        12.95        15.32        14.37        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A6TK 
        5.52        25.74        14.96        19.33         2.70        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       12.66         8.94        61.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I1 
        7.23        20.12         6.94        15.81         0.49         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GV-A3JV 
        2.10         3.12        18.97         7.63        20.05        14.27 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
       19.10         8.48         1.51        38.60        64.01        21.24 
TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI 
       17.72        11.80        44.38        15.58        21.07        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       16.67        16.54        38.99        78.25       112.83        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH 
        3.85        45.04         6.58         1.87        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW 
       66.41        23.64        28.24        16.27        92.98         8.32 
TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R5 
       27.06        18.84         0.66        11.97        25.41        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W 
       21.86        28.41        47.84        20.22         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        35.41        19.40        54.21         5.52        10.65 

  AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE 
                         0.62                          0.49 
  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 
                        17.95                         17.59 
[1] "0.6 - 166.0 (17.9)" "0.5 - 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   102  29  44   7
  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                         102                           134
  N1                          29                            18
  N2                          44                            31
  N3                           7                             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  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(7P21.1) MUTATED    185    5
  AMP PEAK 13(7P21.1) WILD-TYPE  179   15
     clus
vv    AMP PEAK 13(7P21.1) MUTATED AMP PEAK 13(7P21.1) WILD-TYPE
  NO                          185                           179
  YES                           5                            15
[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   102  88
  AMP PEAK 14(7P11.2) WILD-TYPE 125  90
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                          190                           215 
  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                           88                            90 
$`AMP PEAK 14(7P11.2) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A0YO 
        8.35        20.48        25.94        28.70        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
       18.48        13.58         2.14       130.88        46.68        87.32 
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-AA6R TCGA-DK-AA6S 
       64.18        67.36        36.66        38.24       165.73       166.03 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       11.18        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
        4.01        24.30        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TD 
        3.62        26.73        18.08        58.92         6.28        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY 
       12.36         3.06         9.67        17.23        11.08        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       70.32        21.40        19.13        10.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       20.28        27.35         8.58        19.07        22.72         9.01 
TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       35.97         1.84        33.14        86.83        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       97.12        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY 
       21.04         2.24        66.64         7.63        71.57        98.99 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       61.45        18.58        13.64        27.62         0.62        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J 
       10.22        47.80        40.08         2.66         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E 
       12.16         5.06         8.25        17.16        16.18        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5U8 
       28.41        23.01        12.56        12.13        12.16        13.12 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       21.86        18.41       112.44        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
        4.80        13.58         8.15        15.02        18.81        19.00 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q 
       43.59        22.16        24.03        13.68        12.95         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV 
       32.02         8.94        22.52        22.98        20.91         5.36 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE 
       27.45         7.10        13.35         2.27        10.65         3.25 
TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       59.31        66.02        29.36        20.71        15.91        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A764 
       13.91        26.70        20.98         2.20        11.31        20.05 
TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE 
       15.78         7.00        21.34         8.48        19.40        38.60 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P 
       12.16        21.24         9.07        11.70         1.81        16.27 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
        1.15        15.32        13.48        22.68        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SI 
        3.02        35.24        29.56         6.21        48.62        79.66 
TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
        5.98       110.60         2.96         6.77        56.48        75.39 
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        67.20        56.35        29.49 

$`AMP PEAK 14(7P11.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-BT-A20T TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YR 
      108.95        14.89         9.96         8.98        18.58        15.12 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A6AW TCGA-DK-A6B0 
       19.00        16.70        17.72        21.30        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       15.68        50.70        52.01        13.64        13.64        56.15 
TCGA-DK-AA77 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A43Y 
       20.32        60.66        23.41        17.98        29.16        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TB 
       53.88        10.78         5.69         8.25        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GC-A3YS 
        6.15         4.31        31.07        33.01        17.75        24.92 
TCGA-GU-A763 TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       32.78        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-XF-A8HE TCGA-XF-A9ST 
       52.73        50.56        46.98        14.24       125.49         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 
       12.76        11.90        26.27        18.90         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 
       10.82        11.31        54.90        91.73        44.32        30.94 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       86.30         3.88         9.63        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N 
       24.13        11.97        94.88       104.65         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       16.83        17.16        34.98        50.04        51.16        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20P 
        2.50        17.42         7.33         6.74        13.15        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F0 
       19.50         5.06        14.96         4.67        17.56         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       12.79        13.97        12.59        13.08        10.95        12.66 
TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 
       12.46        12.10        12.62        12.26        12.00        12.10 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3WW 
        1.84        66.41        16.14        17.62        15.62        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       10.55       163.30        13.58        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72         5.36         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
       26.96        26.24         4.24        24.66        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
       14.37        16.77        12.62        27.98         5.52        25.74 
TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
       14.96        19.33         2.70        10.85        12.66         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        48.00        15.95        26.93         7.23        20.12 
TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ 
        6.94        15.81         0.49         8.94         2.10         3.12 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI 
       18.97         7.63         4.73        14.27        19.10        36.49 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R 
        1.51        64.01        17.72        15.42        11.80        44.38 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.58        21.07        12.23        16.67        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-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL 
       45.04         6.58         1.87        17.88        64.80        66.41 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN4 
       23.64        28.24        16.27        92.98         8.32        27.06 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.84         0.66        11.97        25.41        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA52 
       28.41        47.84        20.22         8.61        60.16        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21         5.52        10.65 

  AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE 
                         0.62                          0.49 
  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 
                       18.905                        16.700 
[1] "0.6 - 166.0 (18.9)" "0.5 - 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    98  23  41   7
  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                          98                           138
  N1                          23                            24
  N2                          41                            34
  N3                           7                             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  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(7P11.2) MUTATED    174    6
  AMP PEAK 14(7P11.2) WILD-TYPE  190   14
     clus
vv    AMP PEAK 14(7P11.2) MUTATED AMP PEAK 14(7P11.2) WILD-TYPE
  NO                          174                           190
  YES                           6                            14
[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    66  57
  AMP PEAK 15(8P11.23) WILD-TYPE 161 121
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                           123                            282 
  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                            57                            121 
$`AMP PEAK 15(8P11.23) MUTATED`
TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A2LD TCGA-CU-A72E TCGA-DK-A1A5 
       33.83        12.39        26.14        20.48        13.58         2.14 
TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6B6 
       87.32        17.72        50.27        23.21        17.98        36.66 
TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA71 TCGA-DK-AA74 TCGA-FD-A3B7 TCGA-FD-A3NA 
       38.24       165.73        13.64        56.15         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       24.30        17.98        46.78        19.79        12.85        27.35 
TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES 
       53.88        58.92        12.69         9.67        11.08        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU 
       17.62        21.40         8.58        22.72         9.01         3.45 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HF 
       27.68        52.73        33.14        86.83        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9T5 TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN7 
       15.35        15.98        66.64        71.57        98.99        18.58 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
       13.64        21.11         3.48        34.06        57.90        12.23 
TCGA-2F-A9KO TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-BL-A13J 
       24.13        44.94        16.83        17.16        41.75         2.66 
TCGA-BL-A3JM TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A27C 
        6.74         5.06        17.16        36.43        23.01        13.97 
TCGA-CF-A3MG TCGA-CU-A3QU TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3WX 
       12.13         5.19       112.44        17.95         4.80        10.55 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW 
       43.59        29.72        22.16        26.96        24.03        13.68 
TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A43U TCGA-FD-A62O TCGA-FJ-A3ZE TCGA-FT-A3EE 
       12.95         8.09        20.91         7.10        10.65         3.25 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 
       20.12        66.02        20.71        14.07        13.91        26.70 
TCGA-GD-A6C6 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI 
        2.20         7.00        14.27        21.34        19.10        36.49 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
       38.60        12.16        21.24        11.70         1.81        15.42 
TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PE 
        1.15        21.07        12.23         3.02       112.83         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SU TCGA-XF-AAMG 
        3.85        45.04        48.62        64.80         5.98       110.60 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X 
       22.36        31.20        58.72         2.89         8.61        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA56 TCGA-ZF-AA58 
       56.35         8.52        54.21 

$`AMP PEAK 15(8P11.23) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20T TCGA-BT-A20W 
      108.95        16.27        16.77        15.12        14.89         8.35 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN 
       25.94         9.96        28.70         8.98        18.58        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        4.90        15.12        18.48        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
       46.68         8.22        21.30         9.67        66.05        64.18 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M 
       53.29        76.60        67.36        15.68        50.70        52.01 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 
      166.03        13.64        11.18        20.32        15.35        25.58 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43X 
        0.92         1.22        33.04        23.41        29.16         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       15.58        26.73        10.78         5.69         8.25        18.08 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
        4.31        31.07        17.23        70.32        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41O 
       27.35        19.07        25.02         2.76         9.14        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HE 
       35.97        46.98        14.24         1.84        51.32       125.49 
TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
        3.22        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        26.27        18.90         2.24         2.10        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMZ 
       10.82        11.31        54.90         7.63        91.73        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 
       30.94        61.45        86.30         3.88         9.63        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       94.29        88.87        19.69        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 
        8.35        34.98        27.62        50.04         0.62        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       66.54        10.22        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       19.50         5.06        14.96         8.25        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF 
       17.56        28.41         1.94        12.79        12.56        12.59 
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-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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.87        13.08        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       66.41        18.41        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P 
      142.78        13.58         8.15        20.81       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       13.58        18.81        19.00        15.35        12.03        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
        5.36         2.24        16.70         0.56         0.66        26.24 
TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 
        4.24        24.66        14.07        15.32        14.37        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       25.74        22.98        14.96        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 
        2.70        13.35         2.27        10.85        12.66         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I1 
        6.94        29.36        15.81        15.91         0.49         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
        2.10         3.12        20.98        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ 
       20.05        15.78         4.73         8.48         1.51        19.40 
TCGA-HQ-A2OF TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       64.01         9.07        17.72        16.27        11.80        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       15.32        15.58        13.48        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       17.62        37.05        22.68        76.01        78.25        69.34 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
       35.24        29.56        17.82         6.58         1.87        17.88 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       79.66        66.41        23.64        28.24        16.27        92.98 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
        2.96         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       18.84         0.66        11.97        25.41        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4V 
       28.41        13.41        64.08        47.84        20.22        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       60.16        35.41        19.40        29.49         5.52        10.65 

  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE 
                          1.15                           0.49 
  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 
                        20.480                         16.685 
[1] "1.1 - 165.7 (20.5)" "0.5 - 166.0 (16.7)"
[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       43
  AMP PEAK 15(8P11.23) WILD-TYPE       2       88       101       92
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                            43                             92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 15(8P11.23) MUTATED         42  56  19
  AMP PEAK 15(8P11.23) WILD-TYPE       81 139  39
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                                 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 15(8P11.23) MUTATED    63  20  19   3
  AMP PEAK 15(8P11.23) WILD-TYPE 173  27  56   5
D15V5, multiclass
    clus
vv   AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  N0                           63                            173
  N1                           20                             27
  N2                           19                             56
  N3                            3                              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"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED    55   2
  AMP PEAK 15(8P11.23) WILD-TYPE 137   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED     55    2
  AMP PEAK 15(8P11.23) WILD-TYPE  137    9
   clus
vv  AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  0                           55                            137
  1                            2                              9
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED    32  92
  AMP PEAK 15(8P11.23) WILD-TYPE  75 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED     32   92
  AMP PEAK 15(8P11.23) WILD-TYPE   75  209
        clus
vv       AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  FEMALE                           32                             75
  MALE                             92                            209
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(8P11.23) MUTATED   114   6
  AMP PEAK 15(8P11.23) WILD-TYPE 250  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED    114    6
  AMP PEAK 15(8P11.23) WILD-TYPE  250   14
     clus
vv    AMP PEAK 15(8P11.23) MUTATED AMP PEAK 15(8P11.23) WILD-TYPE
  NO                           114                            250
  YES                            6                             14
[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    99
  AMP PEAK 15(8P11.23) WILD-TYPE    34                        14   228
D15V12, multiclass
                           clus
vv                          AMP PEAK 15(8P11.23) MUTATED
  ASIAN                                                9
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               99
                           clus
vv                          AMP PEAK 15(8P11.23) WILD-TYPE
  ASIAN                                                 34
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                228
[1] 3 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     5 107
  AMP PEAK 15(8P11.23) WILD-TYPE   4 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(8P11.23) MUTATED      5  107
  AMP PEAK 15(8P11.23) WILD-TYPE    4  262
                        clus
vv                       AMP PEAK 15(8P11.23) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          107
                        clus
vv                       AMP PEAK 15(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            262
[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    84  55
  AMP PEAK 16(8P11.21) WILD-TYPE 143 123
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                           139                            266 
  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                            55                            123 
$`AMP PEAK 16(8P11.21) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD 
      108.95        33.83        12.39        26.14         8.35        20.48 
TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A72E TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS 
       25.94        12.92        13.58        87.32        17.72        50.27 
TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       23.21        17.98        36.66        38.24        52.01       165.73 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SQ 
       13.64        56.15         0.92         1.22        60.66        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5C1 TCGA-FD-A6TI 
       19.79        12.85        27.35        53.88        58.92         9.67 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.08        33.01        21.40        19.13        19.82        20.28 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-KQ-A41N 
        8.58        22.72         9.01        25.02         3.45        52.73 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       33.14        86.83        51.32        97.45        97.12        15.35 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 
        7.63        71.57        98.99        18.58        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       30.28         3.48        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-4Z-AA86 
       11.97        44.94        16.83        17.16        41.75        10.22 
TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A2LA TCGA-BT-A42E TCGA-C4-A0F6 
       47.80         2.66         6.74        17.16        36.43        23.01 
TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.97        12.13        12.62         5.19        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WX TCGA-DK-AA6U 
      112.44        17.95       142.78         4.80        10.55        19.00 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       43.59        22.16        26.96        24.03        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A62O TCGA-FT-A3EE 
        8.09        22.98        20.91         2.70         7.10         3.25 
TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-AATQ 
       66.02        20.71         0.49        20.98         2.20         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A2OF 
       14.27        19.10         8.48        36.49        38.60        64.01 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI 
       11.70         1.81        15.42         1.15        21.07        12.23 
TCGA-SY-A9G5 TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB 
       38.99         3.02       112.83        17.82         6.21        45.04 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SU TCGA-XF-AAMG TCGA-YC-A89H 
        1.87        48.62        64.80         5.98       110.60        18.84 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N 
       22.36        25.41        31.20        64.08        58.72         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 
        8.61        67.20        56.35        19.40         8.52        54.21 
TCGA-ZF-AA5H 
       29.49 

$`AMP PEAK 16(8P11.21) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20T TCGA-BT-A3PK TCGA-BT-A42C 
       16.27        16.77        15.12        14.89         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 
        8.98        18.58         4.90        15.12        18.48         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IT 
       19.00        16.70       130.88        46.68         8.22        21.30 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
        9.67        66.05        64.18        53.29        76.60        67.36 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 
       15.68        50.70       166.03        13.64        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.35        25.58        33.04         4.01        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT 
       17.98        29.16         3.62        15.58        26.73        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69         8.25        18.08         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
        6.15        12.69        12.36         3.06         4.31        31.07 
TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       17.23        17.62        70.32        17.75        24.92        10.92 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A4AB TCGA-K4-A4AC 
       32.78        32.98        27.35        19.07         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        50.56        35.97        46.98        14.24         1.84 
TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
      125.49         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 
       91.73        44.32        30.94        61.45        86.30         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-2F-A9KQ TCGA-2F-A9KR 
        9.63        94.29        88.87        34.06        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 
        8.35        34.98        27.62        50.04         0.62        51.16 
TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 
       66.54         2.50        17.42        40.08         7.33         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-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         5.06         8.25        16.18         4.67        17.56 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MH 
       28.41         1.94        12.79        12.56        12.59        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-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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AE TCGA-DK-A1AF 
       13.08        29.79         1.84        21.86        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY 
       15.62         7.79        13.58         8.15        20.81       163.30 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       15.02        13.58        18.81        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72         5.36         2.24        16.70         0.56         0.66 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24         4.24        24.66        14.07        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
        5.52        25.74        14.96        19.33         5.36        27.45 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        12.66        10.65         8.94 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         6.94        29.36        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42Q 
        8.94        13.91        26.70         2.10         3.12        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW 
       18.97         7.63        20.05        15.78         4.73        21.34 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ 
        1.51        19.40        12.16        21.24         9.07        17.72 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       16.27        11.80        44.38        15.32        15.58        13.48 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        16.54        17.62        37.05        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HC 
       78.25        69.34        35.24        29.56         3.85         6.58 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       17.88        79.66        66.41        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98         2.96         8.32         6.77        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       75.39         0.66        11.97        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA52 
       13.41        47.84        20.22        59.38        60.16        35.41 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE 
                          0.49                           0.56 
  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 
                         20.48                          16.16 
[1] "0.5 - 165.7 (20.5)" "0.6 - 166.0 (16.2)"
[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    76  19  20   4
  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                           76                            160
  N1                           19                             28
  N2                           20                             55
  N3                            4                              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  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(8P11.21) MUTATED    128    5
  AMP PEAK 16(8P11.21) WILD-TYPE  236   15
     clus
vv    AMP PEAK 16(8P11.21) MUTATED AMP PEAK 16(8P11.21) WILD-TYPE
  NO                           128                            236
  YES                            5                             15
[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   144 119
  AMP PEAK 17(8Q22.3) WILD-TYPE  83  59
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          263                           142 
  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                          119                            59 
$`AMP PEAK 17(8Q22.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
       16.27        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN 
        8.35        20.48        25.94        28.70         8.98        12.92 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2I6 
       15.12        18.48        13.58         2.14       130.88        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        17.72        50.27        23.21        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       64.18        15.68        36.66        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       24.30        46.78        26.73        53.88        10.78         5.69 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       18.08        58.92         6.28        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31         9.67        31.07        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       21.40        19.13        17.75        10.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       20.28         8.58        22.72         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
        2.76         9.14        52.73        35.97        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       33.14        86.83        51.32        97.45        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
        3.22        15.98        34.45        14.93         4.21        12.76 
TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
       26.27         2.24         2.10        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3M 
       71.57        98.99        44.32        61.45        18.58        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T 
       21.11        30.28        94.29         3.48        88.87        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW 
       57.90        12.23        24.13        11.97       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       44.94        17.16        34.98         0.62        41.75        51.16 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J 
       10.22        47.80        40.08         2.66         6.74        19.04 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16        16.18        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG 
       28.41         1.94        23.01        12.56        13.97        12.13 
TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF 
       13.08        10.95        12.62        12.00        11.34        11.87 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
        5.19         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WX 
       16.14        17.95       142.78         4.80         8.15        10.55 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ 
       15.02        19.00        12.03        43.59        38.83        22.16 
TCGA-E7-A4XJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW 
        2.24         0.56        26.96         4.24        24.03        13.68 
TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A3SP 
       12.95        14.37         8.09         8.94        27.98        25.74 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S 
       22.98        20.91         5.36        27.45         7.10        13.35 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EO 
       10.85        12.66        10.65         3.25        15.95        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I1 
       20.12        66.02        29.36        20.71        14.07         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A766 
        2.10         3.12        20.98         2.20        18.97        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       36.49         1.51        19.40        38.60        64.01        12.16 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R 
        9.07        11.70         1.81        15.42        16.27        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        1.15        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       16.67        38.99        17.62        22.68        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
        3.02       112.83        17.82         6.21         3.85        45.04 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAME 
        1.87        48.62        64.80        79.66         5.98        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 
      110.60         2.96         8.32        75.39        18.84        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN 
       25.41        31.20        28.41        64.08        58.72        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       19.40         8.52        54.21        29.49         5.52 

$`AMP PEAK 17(8Q22.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO TCGA-DK-A1AA 
      108.95        16.77         9.96        18.58         4.90        19.00 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 
       16.70        46.68        21.30         9.67        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       67.36        50.70        38.24        23.41        17.98        29.16 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BY 
       19.79        12.85        27.35         3.62        15.58         8.25 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-GC-A3YS 
       62.86        18.81         6.15        17.23        11.08        24.92 
TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41Q 
       32.78        27.35        19.07        27.68        50.56        46.98 
TCGA-XF-A8HE TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T8 
      125.49        11.90        21.04        18.90        66.64        13.74 
TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 
       10.82        91.73        30.94        86.30         3.88         9.63 
TCGA-ZF-AA4R TCGA-2F-A9KQ TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 
       34.06        94.88        16.83        27.62        50.04        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        2.50        17.42         7.33         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH TCGA-CF-A1HR 
       17.88        19.50         5.06        14.96         4.67        12.79 
TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       12.59        12.16        12.66        12.46        12.10        12.26 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FM TCGA-CU-A3YL TCGA-DK-A1AF 
       13.12        12.10        11.34        13.08        29.79        17.62 
TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q 
       15.62         7.79        13.58        20.81       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KF 
       18.81        15.35        29.72         5.36        16.70         0.66 
TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 
       26.24        24.66        14.07        15.32        32.02        16.77 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62N 
       12.62        22.52         5.52        14.96        19.33         2.70 
TCGA-FD-A6TF TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3IB 
        2.27         8.94        61.94        48.00        26.93         7.23 
TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
        6.94        15.81        15.91         0.49        13.91        26.70 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-AAQO 
       11.31         7.63        20.05        21.24        17.72        11.80 
TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HC 
       16.54        37.05        78.25        35.24        29.56         6.58 
TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAMX 
       17.88        66.41        23.64        28.24        16.27         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       56.48        27.06         0.66        11.97        35.84        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-AA4V TCGA-GU-AATO 
       13.41        47.84        59.38        10.65 

  AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE 
                         0.56                          0.49 
  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 
                       17.750                        17.325 
[1] "0.6 - 166.0 (17.8)" "0.5 - 163.3 (17.3)"
[1] "hr=" "1.1"
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   146  35  46   5
  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                         146                            90
  N1                          35                            12
  N2                          46                            29
  N3                           5                             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   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(8Q22.3) MUTATED    236   13
  AMP PEAK 17(8Q22.3) WILD-TYPE  128    7
     clus
vv    AMP PEAK 17(8Q22.3) MUTATED AMP PEAK 17(8Q22.3) WILD-TYPE
  NO                          236                           128
  YES                          13                             7
[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(8Q24.21) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(8Q24.21) MUTATED   138 115
  AMP PEAK 18(8Q24.21) WILD-TYPE  89  63
  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE 
                           253                            152 
  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE 
                           115                             63 
$`AMP PEAK 18(8Q24.21) MUTATED`
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
       15.12        33.83        12.39        26.14        14.89         8.35 
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
        8.98        12.92        15.12        18.48        13.58         2.14 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
      130.88        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B6 
       23.21        66.05        17.98        64.18        15.68        36.66 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SQ TCGA-FD-A5BR TCGA-FD-A5BS 
       33.04         4.01        24.30        46.78        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TD 
       10.78         5.69        18.08        58.92         6.28        12.69 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES 
       12.36         3.06         4.31         9.67        17.23        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       17.62        70.32        21.40        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A6ZA 
       10.92        32.98        19.82        20.28         8.58        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N 
        9.01        25.02         3.45         2.76         9.14        52.73 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       97.45        97.12        15.35         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 
       14.93         4.21        12.76        21.04        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       66.64         2.10        11.31        54.90         7.63        71.57 
TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       98.99        61.45        18.58        13.64        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP 
        3.48        88.87        19.69        57.90        24.13        11.97 
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
      104.65        44.94        17.16         0.62        41.75        51.16 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX 
       10.22        47.80        40.08         2.66         6.74        13.15 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B 
       19.04         5.06         8.25        17.16        16.18        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C 
       36.43        28.41         1.94        23.01        12.56        13.97 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47X TCGA-CF-A5UA 
       12.13        13.08        12.16        10.95        12.62        12.00 
TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       11.34        11.87         5.19         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK 
       18.41       112.44        16.14        17.95       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC 
        8.15        10.55        15.02        19.00        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME 
       38.83        22.16         2.24        26.96         4.24        24.03 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3N6 TCGA-FD-A43N 
       13.68        12.95        14.37         8.09        27.98        22.98 
TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
       20.91         5.36        27.45         7.10        13.35        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO 
       12.66        10.65         3.25        61.94        15.95        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I1 
       20.12        66.02        29.36        20.71        14.07         8.94 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A766 
        2.10         3.12        20.98         2.20        11.31        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        4.73         7.00        14.27        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH 
       36.49        19.40        38.60        64.01        12.16         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
       11.70         1.81        15.42        44.38         1.15        15.32 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       13.48        12.23        16.67        38.99        17.62        22.68 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34         3.02       112.83        29.56         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAME 
       45.04        48.62        64.80        79.66         5.98        92.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN5 TCGA-YC-A89H 
      110.60         2.96         8.32         6.77        75.39        18.84 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG 
       22.36        25.41        31.20        28.41        64.08        58.72 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N 
        5.52 

$`AMP PEAK 18(8Q24.21) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
      108.95        16.27        16.77        20.48        25.94         9.96 
TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX 
       28.70        18.58         4.90        19.00        16.70        46.68 
TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L 
        9.67        53.29        76.60        67.36        50.70        38.24 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        23.41        17.98        29.16        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TB 
       27.35         3.62        15.58         8.25        62.86        18.81 
TCGA-FD-A6TC TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40G 
        6.15        31.07        11.08        32.78        27.35        19.07 
TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-XF-A8HE TCGA-XF-A9SW TCGA-XF-A9T2 
       27.68        50.56        46.98       125.49        11.90        18.90 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 
       13.74        10.82        91.73        44.32        30.94        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KQ 
        3.88         9.63        94.29        34.06        12.23        94.88 
TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 
        8.35        16.83        34.98        27.62        50.04        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P 
        2.50        17.42         7.33         6.58        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A3PH TCGA-CF-A1HR TCGA-CF-A3MF 
       19.50         5.06        14.96         4.67        12.79        12.59 
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-A9FM TCGA-CU-A3YL TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       11.34        13.08        29.79        17.62        15.62         7.79 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       13.58        20.81       163.30        13.58        18.81        15.35 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 
       29.72         5.36        16.70         0.56         0.66        26.24 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       24.66        14.07        15.32        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU 
       12.62        22.52         5.52        25.74        14.96        19.33 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FJ-A871 TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3IB 
        2.70         2.27         8.94        48.00        26.93         7.23 
TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
        6.94        15.81        15.91         0.49        13.91        26.70 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-H4-A2HO TCGA-K4-A3WV TCGA-K4-A5RJ 
       18.97         7.63        20.05         1.51        21.24        17.72 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78L 
       16.27        11.80        15.58        21.07        16.54        37.05 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A9PA TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A8HH 
       76.01        78.25        35.24        17.82         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAN0 
       17.88        66.41        23.64        28.24        16.27        56.48 
TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
       27.06         0.66        11.97        35.84        21.86        13.41 
TCGA-ZF-A9RM TCGA-GU-AATO 
       47.84        10.65 

  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE 
                          0.62                           0.49 
  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE 
                         17.72                          17.52 
[1] "0.6 - 166.0 (17.7)" "0.5 - 163.3 (17.5)"
[1] "hr=" "1.1"
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 18(8Q24.21) MUTATED         1       77        89       85
  AMP PEAK 18(8Q24.21) WILD-TYPE       1       52        51       50
D18V3, multiclass
           clus
vv          AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            77                             52
  STAGE III                           89                             51
  STAGE IV                            85                             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 18(8Q24.21) MUTATED         76 124  34
  AMP PEAK 18(8Q24.21) WILD-TYPE       47  71  24
D18V4, multiclass
          clus
vv         AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE
  T0+T1+T2                           76                             47
  T3                                124                             71
  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
  AMP PEAK 18(8Q24.21) MUTATED   142  34  42   5
  AMP PEAK 18(8Q24.21) WILD-TYPE  94  13  33   3
D18V5, multiclass
    clus
vv   AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE
  N0                          142                             94
  N1                           34                             13
  N2                           42                             33
  N3                            5                              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"
D18V6, binary
                                cls
clus                               0   1
  AMP PEAK 18(8Q24.21) MUTATED   120   7
  AMP PEAK 18(8Q24.21) WILD-TYPE  72   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(8Q24.21) MUTATED    120    7
  AMP PEAK 18(8Q24.21) WILD-TYPE   72    4
   clus
vv  AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE
  0                          120                             72
  1                            7                              4
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(8Q24.21) MUTATED    64 190
  AMP PEAK 18(8Q24.21) WILD-TYPE  43 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(8Q24.21) MUTATED     64  190
  AMP PEAK 18(8Q24.21) WILD-TYPE   43  111
        clus
vv       AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE
  FEMALE                           64                             43
  MALE                            190                            111
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(8Q24.21) MUTATED   226  13
  AMP PEAK 18(8Q24.21) WILD-TYPE 138   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(8Q24.21) MUTATED    226   13
  AMP PEAK 18(8Q24.21) WILD-TYPE  138    7
     clus
vv    AMP PEAK 18(8Q24.21) MUTATED AMP PEAK 18(8Q24.21) WILD-TYPE
  NO                           226                            138
  YES                           13                              7
[1] 2 2
[1] FALSE
D18V9, continuous
D18V10, continuous
D18V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(8Q24.21) MUTATED      23                        12   206
  AMP PEAK 18(8Q24.21) WILD-TYPE    20                        10   121
D18V12, multiclass
                           clus
vv                          AMP PEAK 18(8Q24.21) MUTATED
  ASIAN                                               23
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              206
                           clus
vv                          AMP PEAK 18(8Q24.21) WILD-TYPE
  ASIAN                                                 20
  BLACK OR AFRICAN AMERICAN                             10
  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"
D18V13, binary
                                cls
clus                               0   1
  AMP PEAK 18(8Q24.21) MUTATED     5 227
  AMP PEAK 18(8Q24.21) WILD-TYPE   4 142
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(8Q24.21) MUTATED      5  227
  AMP PEAK 18(8Q24.21) WILD-TYPE    4  142
                        clus
vv                       AMP PEAK 18(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          227
                        clus
vv                       AMP PEAK 18(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            142
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(9P24.1) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 19(9P24.1) MUTATED    49  39
  AMP PEAK 19(9P24.1) WILD-TYPE 178 139
  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE 
                           88                           317 
  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE 
                           39                           139 
$`AMP PEAK 19(9P24.1) MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A3PJ TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AC 
       16.77        15.12        25.94        15.12         2.14       130.88 
TCGA-DK-A2I6 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL 
       87.32        36.66       165.73        33.04         4.01        23.41 
TCGA-FD-A43P TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3Z7 
       27.35        10.78         5.69        12.69         4.31        31.07 
TCGA-GC-A3BM TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       21.40        32.78        19.82        20.28         8.58        19.07 
TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP 
       33.14        97.12        15.35         3.22        34.45        14.93 
TCGA-XF-A9SY TCGA-XF-A9T5 TCGA-XF-AAML TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-AA4T 
       21.04        66.64         7.63        13.64        30.28        19.69 
TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-4Z-AA87 TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20V 
       57.90        24.13        47.80         6.74         6.58         5.06 
TCGA-CU-A3QU TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-E7-A85H TCGA-FD-A3B3 
        5.19       112.44       142.78         8.15        12.95        32.02 
TCGA-FD-A3N5 TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A6TF TCGA-G2-A2EF TCGA-G2-A2EJ 
       22.52        19.33         2.70         2.27        61.94        48.00 
TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       20.12        20.71        15.91         0.49        13.91        26.70 
TCGA-GD-A3OP TCGA-GU-A764 TCGA-GV-A3QI TCGA-HQ-A5NE TCGA-K4-A6FZ TCGA-LC-A66R 
        2.10        20.05        36.49        12.16         1.81        15.32 
TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A9PB TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-A9SI 
       17.62        78.25        29.56         6.58        48.62        79.66 
TCGA-XF-A9T4 TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-ZF-A9R0 
       16.27       110.60         2.96        27.06        75.39        22.36 
TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA58 
       59.38        60.16        67.20        54.21 

$`AMP PEAK 19(9P24.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL 
        8.35        20.48         9.96        28.70         8.98        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
       12.92         4.90        18.48        13.58        19.00        16.70 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6S 
       67.36        15.68        50.70        38.24        52.01       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM 
       25.58         0.92         1.22        60.66        24.30        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y 
       29.16        46.78        19.79        12.85         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       26.73        53.88         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI 
       62.86        18.81         6.15        12.36         3.06         9.67 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB 
       17.23        11.08        33.01        17.62        70.32        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3QK TCGA-GV-A6ZA 
       17.75        24.92        10.92        32.98        27.35        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
       52.73        50.56        35.97        46.98        14.24         1.84 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9ST 
       86.83        51.32        97.45       125.49        15.98         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 
       12.76        11.90        26.27        18.90         2.24         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
        3.88         9.63        21.11        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       34.06        12.23        11.97        94.88       104.65         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-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI 
        0.62        41.75        51.16        66.54        10.22         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20J 
       17.42        40.08         7.33         2.66        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       12.16        17.88        19.50         5.06        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       21.86        66.41        18.41        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX 
       17.95         7.79         4.80        13.58        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
        4.24        24.03        24.66        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.37         8.09        16.77         8.94        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV 
        5.52        25.74        22.98        14.96        20.91         5.36 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       27.45         7.10        13.35        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
        8.94         3.25        15.95        26.93        59.31         7.23 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I1 
       66.02         6.94        29.36        15.81        14.07         8.94 
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-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
        8.48         1.51        19.40        38.60        64.01        21.24 
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-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-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        16.54        38.99        37.05        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE 
       69.34         3.02       112.83        35.24        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL 
        3.85        45.04         1.87        17.88        64.80        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAMX 
        5.98        23.64        28.24        92.98         8.32         6.77 
TCGA-XF-AAN0 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       56.48        18.84         0.66        11.97        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-AA4U TCGA-ZF-AA51 TCGA-ZF-AA52 
       35.84        28.41        13.41         8.61        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        29.49         5.52        10.65 

  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE 
                         0.49                          0.56 
  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE 
                       165.73                        166.03 
  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE 
                       20.875                        16.700 
[1] "0.5 - 165.7 (20.9)" "0.6 - 166.0 (16.7)"
[1] "hr=" "1.2"
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 19(9P24.1) MUTATED         0       26        33       29
  AMP PEAK 19(9P24.1) WILD-TYPE       2      103       107      106
D19V3, multiclass
           clus
vv          AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(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 19(9P24.1) MUTATED         23  44  13
  AMP PEAK 19(9P24.1) WILD-TYPE      100 151  45
D19V4, multiclass
          clus
vv         AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(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 19(9P24.1) MUTATED    46   9  19   1
  AMP PEAK 19(9P24.1) WILD-TYPE 190  38  56   7
D19V5, multiclass
    clus
vv   AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE
  N0                          46                           190
  N1                           9                            38
  N2                          19                            56
  N3                           1                             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"
D19V6, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P24.1) MUTATED    34   3
  AMP PEAK 19(9P24.1) WILD-TYPE 158   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P24.1) MUTATED     34    3
  AMP PEAK 19(9P24.1) WILD-TYPE  158    8
   clus
vv  AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE
  0                          34                           158
  1                           3                             8
[1] 2 2
[1] FALSE
D19V7, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P24.1) MUTATED    20  68
  AMP PEAK 19(9P24.1) WILD-TYPE  87 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P24.1) MUTATED     20   68
  AMP PEAK 19(9P24.1) WILD-TYPE   87  233
        clus
vv       AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE
  FEMALE                          20                            87
  MALE                            68                           233
[1] 2 2
[1] FALSE
D19V8, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P24.1) MUTATED    80   1
  AMP PEAK 19(9P24.1) WILD-TYPE 284  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P24.1) MUTATED     80    1
  AMP PEAK 19(9P24.1) WILD-TYPE  284   19
     clus
vv    AMP PEAK 19(9P24.1) MUTATED AMP PEAK 19(9P24.1) WILD-TYPE
  NO                           80                           284
  YES                           1                            19
[1] 2 2
[1] FALSE
D19V9, continuous
D19V10, continuous
D19V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(9P24.1) MUTATED       4                         7    74
  AMP PEAK 19(9P24.1) WILD-TYPE    39                        15   253
D19V12, multiclass
                           clus
vv                          AMP PEAK 19(9P24.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              74
                           clus
vv                          AMP PEAK 19(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"
D19V13, binary
                               cls
clus                              0   1
  AMP PEAK 19(9P24.1) MUTATED     3  79
  AMP PEAK 19(9P24.1) WILD-TYPE   6 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(9P24.1) MUTATED      3   79
  AMP PEAK 19(9P24.1) WILD-TYPE    6  290
                        clus
vv                       AMP PEAK 19(9P24.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          79
                        clus
vv                       AMP PEAK 19(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           290
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(10P14) MUTATION ANALYSIS
D20V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 20(10P14) MUTATED    99  83
  AMP PEAK 20(10P14) WILD-TYPE 128  95
  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE 
                         182                          223 
  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE 
                          83                           95 
$`AMP PEAK 20(10P14) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD 
       16.27        16.77        15.12        26.14         8.35        20.48 
TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AC 
       25.94         8.98        12.92        18.48         2.14       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV 
       46.68        87.32         8.22         9.67        66.05        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA74 
       67.36        15.68        36.66       165.73       166.03        56.15 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS 
        1.22        33.04        60.66        24.30        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5C0 TCGA-FD-A5C1 
       27.35        15.58        26.73        53.88        18.08        58.92 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES 
       12.36         3.06         9.67        31.07        11.08        33.01 
TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.62        19.13        10.92        32.98        19.82        20.28 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R 
        8.58        22.72         9.01        25.02         9.14        27.68 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       35.97        46.98        33.14        86.83        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST 
       97.12        15.35         3.22        15.98        14.93         4.21 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMZ 
        2.10        10.82        11.31        54.90         7.63        44.32 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       13.64        30.28        94.29        34.06        19.69        57.90 
TCGA-2F-A9KO TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA87 
       24.13        17.16        27.62         0.62        41.75        47.80 
TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R 
        2.50        40.08         2.66         6.58        19.50         5.06 
TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MF 
        5.06        16.18        36.43        23.01        12.56        12.59 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3QU TCGA-CU-A5W6 
       12.13        12.16        12.00        11.34         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-AA6P 
       21.86        66.41       112.44        17.95        13.58        15.02 
TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       19.00        38.83         4.24        24.03        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A43N 
       14.37         8.09        32.02         8.94        22.52        22.98 
TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F 
       27.45         2.27         3.25        20.12        66.02        29.36 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OS 
       14.07         0.49         8.94        13.91        26.70        20.98 
TCGA-GD-A6C6 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QH 
        2.20        15.78         4.73         7.00        21.34         8.48 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI 
       19.40        38.60        64.01        12.16         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
       17.72         1.81        16.27        11.80         1.15        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       15.58        13.48        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SH 
       76.01        69.34        35.24         6.21        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       79.66        23.64        28.24       110.60         2.96         6.77 
TCGA-XF-AAN4 TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
       27.06        22.36        25.41        31.20        28.41        64.08 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
       47.84        20.22        59.38        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-GU-AATO 
       19.40        10.65 

$`AMP PEAK 20(10P14) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A3PK TCGA-BT-A42C 
      108.95        33.83        12.39        14.89         9.96        28.70 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
       18.58         4.90        15.12        13.58        19.00        16.70 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AW 
       17.72        50.27        21.30        23.21        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA71 
       76.60        50.70        38.24        52.01        13.64        13.64 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B7 
       11.18        20.32        15.35        25.58         0.92         4.01 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BT 
       23.41        17.98        29.16        46.78         3.62        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        5.69         8.25         6.28        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC 
       12.69         4.31        17.23        70.32        21.40        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40G TCGA-K4-A3WU TCGA-K4-A4AB 
       24.92        32.78        27.35        19.07         3.45         2.76 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A8HE TCGA-XF-A9SM 
       52.73        50.56        14.24         1.84       125.49        34.45 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 
       66.64        13.74        71.57        91.73        98.99        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 
       61.45        86.30        18.58         3.88         9.63        21.11 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
        3.48        88.87        12.23        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 
        8.35        44.94        16.83        34.98        50.04        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX 
       66.54        10.22        17.42         7.33         6.74        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       19.04        12.16        17.88        14.96         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C 
        4.67        17.56        28.41         1.94        12.79        13.97 
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-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        13.12        12.10        11.34        11.87        13.08 
TCGA-CU-A3YL TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       29.79        18.41        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
      142.78         4.80         8.15        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
       13.58        18.81        15.35        12.03        43.59        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        22.16         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B4 
       26.96        26.24        24.66        14.07        15.32        16.77 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U 
       12.62        27.98         5.52        25.74        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
       19.33         5.36         2.70         7.10        13.35        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66        10.65         8.94        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO 
       26.93        59.31         7.23         6.94        20.71        15.81 
TCGA-GC-A3RC TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       15.91         2.10         3.12        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-K4-A3WV 
       20.05        14.27        19.10        36.49         1.51        21.24 
TCGA-K4-A6MB TCGA-KQ-A41R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 
       15.42        44.38        21.07        12.23        16.67        16.54 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF 
       78.25         3.02       112.83        29.56        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SL TCGA-XF-A9SU 
       45.04         6.58         1.87        17.88        66.41         5.98 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A89H 
       16.27        92.98         8.32        56.48        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RG 
        0.66        11.97        35.84        21.86        13.41        58.72 
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        29.49 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE 
                        0.49                         0.56 
  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE 
                      166.03                       163.30 
  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE 
                      19.595                       16.670 
[1] "0.5 - 166.0 (19.6)" "0.6 - 163.3 (16.7)"
[1] "hr=" "1.1"
D20V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 20(10P14) MUTATED         1       53        61       66
  AMP PEAK 20(10P14) WILD-TYPE       1       76        79       69
D20V3, multiclass
           clus
vv          AMP PEAK 20(10P14) MUTATED AMP PEAK 20(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 20(10P14) MUTATED         53  88  28
  AMP PEAK 20(10P14) WILD-TYPE       70 107  30
D20V4, multiclass
          clus
vv         AMP PEAK 20(10P14) MUTATED AMP PEAK 20(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 20(10P14) MUTATED    89  26  34   5
  AMP PEAK 20(10P14) WILD-TYPE 147  21  41   3
D20V5, multiclass
    clus
vv   AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE
  N0                         89                          147
  N1                         26                           21
  N2                         34                           41
  N3                          5                            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"
D20V6, binary
                              cls
clus                             0   1
  AMP PEAK 20(10P14) MUTATED    81   5
  AMP PEAK 20(10P14) WILD-TYPE 111   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(10P14) MUTATED     81    5
  AMP PEAK 20(10P14) WILD-TYPE  111    6
   clus
vv  AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE
  0                         81                          111
  1                          5                            6
[1] 2 2
[1] FALSE
D20V7, binary
                              cls
clus                             0   1
  AMP PEAK 20(10P14) MUTATED    44 138
  AMP PEAK 20(10P14) WILD-TYPE  63 163
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(10P14) MUTATED     44  138
  AMP PEAK 20(10P14) WILD-TYPE   63  163
        clus
vv       AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE
  FEMALE                         44                           63
  MALE                          138                          163
[1] 2 2
[1] FALSE
D20V8, binary
                              cls
clus                             0   1
  AMP PEAK 20(10P14) MUTATED   161   6
  AMP PEAK 20(10P14) WILD-TYPE 203  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(10P14) MUTATED    161    6
  AMP PEAK 20(10P14) WILD-TYPE  203   14
     clus
vv    AMP PEAK 20(10P14) MUTATED AMP PEAK 20(10P14) WILD-TYPE
  NO                         161                          203
  YES                          6                           14
[1] 2 2
[1] FALSE
D20V9, continuous
D20V10, continuous
D20V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(10P14) MUTATED      16                         9   147
  AMP PEAK 20(10P14) WILD-TYPE    27                        13   180
D20V12, multiclass
                           clus
vv                          AMP PEAK 20(10P14) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            147
                           clus
vv                          AMP PEAK 20(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"
D20V13, binary
                              cls
clus                             0   1
  AMP PEAK 20(10P14) MUTATED     4 159
  AMP PEAK 20(10P14) WILD-TYPE   5 210
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(10P14) MUTATED      4  159
  AMP PEAK 20(10P14) WILD-TYPE    5  210
                        clus
vv                       AMP PEAK 20(10P14) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        159
                        clus
vv                       AMP PEAK 20(10P14) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          210
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(11P13) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(11P13) MUTATED    28  23
  AMP PEAK 21(11P13) WILD-TYPE 199 155
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          51                          354 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                          23                          155 
$`AMP PEAK 21(11P13) MUTATED`
TCGA-4Z-AA7M TCGA-BT-A3PJ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-DK-A3IV TCGA-DK-AA6R 
       16.27        25.94        12.92         4.90         9.67       165.73 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A5BT TCGA-FD-A62P TCGA-FD-A6TI TCGA-FJ-A3Z7 
        1.22        33.04        10.78         6.28         9.67        31.07 
TCGA-GV-A3JZ TCGA-GV-A40E TCGA-K4-A3WS TCGA-K4-A4AC TCGA-KQ-A41P TCGA-XF-A9SP 
       19.82         8.58        25.02         9.14        35.97        14.93 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-AAMH TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-AA4T 
       21.04         2.24        11.31        18.58        13.64        19.69 
TCGA-ZF-AA5P TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A2LA TCGA-DK-A2I2 TCGA-DK-A3WX 
       12.23         6.74         5.06        17.16         7.79        10.55 
TCGA-E5-A2PC TCGA-E7-A5KE TCGA-E7-A6ME TCGA-FD-A62N TCGA-GC-A3RC TCGA-GU-A762 
       43.59         0.56        24.03         2.70        15.91         7.63 
TCGA-GU-A766 TCGA-GV-A3QI TCGA-LC-A66R TCGA-PQ-A6FI TCGA-UY-A78K TCGA-UY-A78M 
       15.78        36.49        15.32        12.23        17.62        22.68 
TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT 
      112.83        29.56         3.85        23.64       110.60         2.96 
TCGA-ZF-A9RD TCGA-ZF-AA51 TCGA-ZF-AA5H 
       13.41        56.35        29.49 

$`AMP PEAK 21(11P13) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        20.48         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       16.70       130.88        46.68        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV 
       50.27        21.30        23.21        66.05        17.98        64.18 
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-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       38.24        52.01       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B7 
       11.18        20.32        15.35        25.58         0.92         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       19.79        12.85        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA 
       53.88         5.69         8.25        18.08        58.92        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
       17.23        11.08        33.01        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       19.13        17.75        24.92        10.92        32.78        32.98 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WU 
       20.28        27.35        19.07        22.72         9.01         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X 
        2.76        27.68        52.73        50.56        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
        1.84        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST 
       97.12        15.35         3.22        15.98        34.45         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 
       12.76        11.90        26.27        18.90        66.64         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        86.30         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL 
        9.63        21.11        30.28        94.29         3.48        88.87 
TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       34.06        57.90        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        17.16        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         5.06         8.25        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       36.43        28.41         1.94        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-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-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 
      112.44        16.14        17.62        15.62        17.95       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P 
        4.80        13.58         8.15        20.81       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       13.58        18.81        19.00        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       29.72         5.36        22.16         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN 
       26.96        26.24         4.24        24.66        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-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        7.10        13.35         2.27        10.85        12.66        10.65 
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-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       59.31         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        14.07         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       18.97        20.05         4.73         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10         8.48         1.51        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 
       15.42        16.27        11.80        44.38         1.15        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L 
       21.07        13.48        16.67        16.54        38.99        37.05 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PD 
       76.01        78.25        69.34         3.02        35.24        17.82 
TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        6.21        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41         5.98        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
       92.98         8.32         6.77        56.48        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       35.84        21.86        28.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       20.22         2.89         8.61        59.38        60.16        67.20 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       35.41        19.40         8.52        54.21         5.52        10.65 

  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                        0.56                         0.49 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                      165.73                       166.03 
  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE 
                       15.32                        17.88 
[1] "0.6 - 165.7 (15.3)" "0.5 - 166.0 (17.9)"
[1] "hr=" "1.2"
D21V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 21(11P13) MUTATED         0       13        13       25
  AMP PEAK 21(11P13) WILD-TYPE       2      116       127      110
D21V3, multiclass
           clus
vv          AMP PEAK 21(11P13) MUTATED AMP PEAK 21(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 21(11P13) MUTATED         14  25   9
  AMP PEAK 21(11P13) WILD-TYPE      109 170  49
D21V4, multiclass
          clus
vv         AMP PEAK 21(11P13) MUTATED AMP PEAK 21(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 21(11P13) MUTATED    21   6  15   4
  AMP PEAK 21(11P13) WILD-TYPE 215  41  60   4
D21V5, multiclass
    clus
vv   AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  N0                         21                          215
  N1                          6                           41
  N2                         15                           60
  N3                          4                            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"
D21V6, binary
                              cls
clus                             0   1
  AMP PEAK 21(11P13) MUTATED    16   1
  AMP PEAK 21(11P13) WILD-TYPE 176  10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(11P13) MUTATED     16    1
  AMP PEAK 21(11P13) WILD-TYPE  176   10
   clus
vv  AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  0                         16                          176
  1                          1                           10
[1] 2 2
[1] FALSE
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(11P13) MUTATED    14  37
  AMP PEAK 21(11P13) WILD-TYPE  93 264
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(11P13) MUTATED     14   37
  AMP PEAK 21(11P13) WILD-TYPE   93  264
        clus
vv       AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  FEMALE                         14                           93
  MALE                           37                          264
[1] 2 2
[1] FALSE
D21V8, binary
                              cls
clus                             0   1
  AMP PEAK 21(11P13) MUTATED    45   1
  AMP PEAK 21(11P13) WILD-TYPE 319  19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(11P13) MUTATED     45    1
  AMP PEAK 21(11P13) WILD-TYPE  319   19
     clus
vv    AMP PEAK 21(11P13) MUTATED AMP PEAK 21(11P13) WILD-TYPE
  NO                          45                          319
  YES                          1                           19
[1] 2 2
[1] FALSE
D21V9, continuous
D21V10, continuous
D21V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(11P13) MUTATED       4                         1    45
  AMP PEAK 21(11P13) WILD-TYPE    39                        21   282
D21V12, multiclass
                           clus
vv                          AMP PEAK 21(11P13) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             45
                           clus
vv                          AMP PEAK 21(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"
D21V13, binary
                              cls
clus                             0   1
  AMP PEAK 21(11P13) MUTATED     2  48
  AMP PEAK 21(11P13) WILD-TYPE   7 321
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(11P13) MUTATED      2   48
  AMP PEAK 21(11P13) WILD-TYPE    7  321
                        clus
vv                       AMP PEAK 21(11P13) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         48
                        clus
vv                       AMP PEAK 21(11P13) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          321
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(11Q13.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(11Q13.3) MUTATED    76  59
  AMP PEAK 22(11Q13.3) WILD-TYPE 151 119
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                           135                            270 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                            59                            119 
$`AMP PEAK 22(11Q13.3) MUTATED`
TCGA-BT-A20N TCGA-BT-A3PJ TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       26.14        25.94        28.70        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3X1 TCGA-DK-A3X2 
       18.48         2.14        87.32        17.72        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3B6 
       64.18        36.66        56.15        20.32         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
        4.01        60.66        24.30        27.35        15.58        26.73 
TCGA-FD-A5BT TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-AA3D 
       10.78         3.06         9.67        31.07        33.01        70.32 
TCGA-GC-A3BM TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       21.40        19.82        20.28        27.35         8.58        19.07 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        9.01         2.76         9.14        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HF 
       46.98        14.24         1.84        33.14        51.32        97.12 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
       12.76        21.04         2.10        11.31         7.63        71.57 
TCGA-XF-AAMZ TCGA-XF-AAN8 TCGA-YF-AA3M TCGA-ZF-AA53 TCGA-4Z-AA7O TCGA-4Z-AA7S 
       44.32         3.88        13.64        57.90        16.83        34.98 
TCGA-4Z-AA80 TCGA-BL-A13J TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        0.62         2.66        17.16         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A47V TCGA-CF-A8HX 
       28.41        23.01        12.56        12.13        12.46        11.34 
TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AF TCGA-DK-A2I1 
       11.34         1.84        21.86        66.41        17.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA76 
        7.79        13.58         8.15        10.55        15.02        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A97Q 
       43.59        38.83         0.56         0.66         4.24         8.09 
TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S 
        8.94        22.98        20.91         5.36         2.70        13.35 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC 
        7.23        20.12        66.02        29.36        20.71        15.91 
TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 
       14.07         8.94        26.70        20.98         2.20         7.63 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       15.78         4.73         7.00        14.27        21.34         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-LC-A66R TCGA-LT-A8JT 
       36.49        19.40        38.60        21.24        15.32        21.07 
TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A8OD 
       12.23        16.54        22.68        76.01         3.02       112.83 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A9T4 TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       29.56         3.85        16.27         2.96         8.32         6.77 
TCGA-XF-AAN4 TCGA-ZF-A9R7 TCGA-ZF-AA51 
       27.06        21.86        56.35 

$`AMP PEAK 22(11Q13.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL 
       14.89         8.35        20.48         9.96         8.98        18.58 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN 
       13.58        19.00        16.70       130.88        46.68         8.22 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 
       50.27        21.30        23.21         9.67        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        50.70        38.24        52.01       165.73 
TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 
      166.03        13.64        13.64        11.18        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
        0.92        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       12.85         3.62        53.88         5.69         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
       58.92         6.28        62.86        18.81         6.15        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3RB 
       12.36         4.31        17.23        11.08        17.62        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A6ZA 
       17.75        24.92        10.92        32.78        32.98        22.72 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       25.02         3.45        27.68        86.83        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       15.35         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 
       11.90        26.27        18.90         2.24        66.64        13.74 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       10.82        54.90        91.73        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       86.30        18.58         9.63        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO 
        3.48        88.87        34.06        19.69        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R 
       11.97        94.88       104.65         8.35        44.94        17.16 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62        50.04        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM 
       47.80         2.50        17.42        40.08         7.33         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-C4-A0F0 
        5.06        14.96         5.06         8.25        16.18         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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A7 
       12.10        11.87        13.08         5.19        29.79        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WW 
      112.44        16.14        15.62       142.78         4.80        20.81 
TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E7-A3X6 
      163.30        13.58        18.81        19.00        15.35        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 
        5.36        22.16         2.24        16.70        26.96        26.24 
TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66        13.68        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-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62O 
        5.52        25.74        14.96        19.33        27.45         7.10 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.27        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3C 
       61.94        48.00        15.95        26.93        59.31         6.94 
TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42Q 
       15.81         0.49        13.91         2.10         3.12        11.31 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GV-A3JX TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE 
       18.97        20.05        19.10         1.51        64.01        12.16 
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-A78P TCGA-UY-A8OB TCGA-UY-A9PA 
       38.99        17.62        37.05        78.25        69.34        35.24 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
       17.82         6.21        45.04         6.58         1.87        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A89H 
       28.24        92.98       110.60        56.48        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       28.41        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 
        2.89         8.61        59.38        60.16        67.20        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                        112.83                         166.03 
  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE 
                        17.560                         17.735 
[1] "0.6 - 112.8 (17.6)" "0.5 - 166.0 (17.7)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 22(11Q13.3) MUTATED         0       47        38       49
  AMP PEAK 22(11Q13.3) WILD-TYPE       2       82       102       86
D22V3, multiclass
           clus
vv          AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(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 22(11Q13.3) MUTATED         46  58  20
  AMP PEAK 22(11Q13.3) WILD-TYPE       77 137  38
D22V4, multiclass
          clus
vv         AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(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 22(11Q13.3) MUTATED    75  16  27   5
  AMP PEAK 22(11Q13.3) WILD-TYPE 161  31  48   3
D22V5, multiclass
    clus
vv   AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  N0                           75                            161
  N1                           16                             31
  N2                           27                             48
  N3                            5                              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"
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q13.3) MUTATED    59   3
  AMP PEAK 22(11Q13.3) WILD-TYPE 133   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q13.3) MUTATED     59    3
  AMP PEAK 22(11Q13.3) WILD-TYPE  133    8
   clus
vv  AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  0                           59                            133
  1                            3                              8
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q13.3) MUTATED    40  95
  AMP PEAK 22(11Q13.3) WILD-TYPE  67 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q13.3) MUTATED     40   95
  AMP PEAK 22(11Q13.3) WILD-TYPE   67  206
        clus
vv       AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  FEMALE                           40                             67
  MALE                             95                            206
[1] 2 2
[1] FALSE
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q13.3) MUTATED   121   4
  AMP PEAK 22(11Q13.3) WILD-TYPE 243  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q13.3) MUTATED    121    4
  AMP PEAK 22(11Q13.3) WILD-TYPE  243   16
     clus
vv    AMP PEAK 22(11Q13.3) MUTATED AMP PEAK 22(11Q13.3) WILD-TYPE
  NO                           121                            243
  YES                            4                             16
[1] 2 2
[1] FALSE
D22V9, continuous
D22V10, continuous
D22V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(11Q13.3) MUTATED      10                        12   106
  AMP PEAK 22(11Q13.3) WILD-TYPE    33                        10   221
D22V12, multiclass
                           clus
vv                          AMP PEAK 22(11Q13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              106
                           clus
vv                          AMP PEAK 22(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"
D22V13, binary
                                cls
clus                               0   1
  AMP PEAK 22(11Q13.3) MUTATED     2 124
  AMP PEAK 22(11Q13.3) WILD-TYPE   7 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(11Q13.3) MUTATED      2  124
  AMP PEAK 22(11Q13.3) WILD-TYPE    7  245
                        clus
vv                       AMP PEAK 22(11Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          124
                        clus
vv                       AMP PEAK 22(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            245
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(11Q22.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(11Q22.2) MUTATED    44  27
  AMP PEAK 23(11Q22.2) WILD-TYPE 183 151
  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE 
                            71                            334 
  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE 
                            27                            151 
$`AMP PEAK 23(11Q22.2) MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20W TCGA-BT-A3PJ TCGA-CU-A0YR TCGA-DK-A2I6 TCGA-DK-A3X1 
       15.12         8.35        25.94        15.12        87.32        66.05 
TCGA-DK-A3X2 TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A43P 
       17.98        20.32         1.22        33.04        60.66        27.35 
TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5C1 TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 
       26.73        10.78        58.92         3.06         9.67        31.07 
TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GV-A3QF TCGA-GV-A40E TCGA-K4-A4AB TCGA-K4-A4AC 
       70.32        24.92        20.28         8.58         2.76         9.14 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A9SY 
       52.73        35.97         1.84        33.14        97.12        21.04 
TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-YF-AA3M TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-4Z-AA80 
        2.10        11.31        13.64        12.23        24.13         0.62 
TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A3 
       36.43         1.94        23.01        11.34         1.84        21.86 
TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3WX TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A5KF 
       17.95        13.58        10.55        12.03        43.59         0.66 
TCGA-E7-A97Q TCGA-FD-A5BZ TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC 
        8.09        27.45        66.02        29.36        20.71        15.91 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3QI TCGA-K4-A6MB 
       20.98         2.20         7.63        15.78        36.49        15.42 
TCGA-LC-A66R TCGA-PQ-A6FI TCGA-UY-A78M TCGA-UY-A8OC TCGA-UY-A9PB TCGA-UY-A9PF 
       15.32        12.23        22.68         3.02        29.56         3.85 
TCGA-XF-AAMX TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-AA51 TCGA-ZF-AA5H 
        6.77        21.86        64.08        56.35        29.49 

$`AMP PEAK 23(11Q22.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL 
       14.89        20.48         9.96        28.70         8.98        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       12.92         4.90        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       16.70       130.88        46.68         8.22        17.72        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30        23.21         9.67        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL 
       15.35        25.58         0.92         4.01        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X 
       17.98        29.16        46.78        19.79        12.85         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P 
       15.58        53.88         5.69         8.25        18.08         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
       62.86        18.81         6.15        12.69        12.36         4.31 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB 
       17.23        11.08        33.01        17.62        21.40        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK 
       17.75        10.92        32.78        32.98        19.82        27.35 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R 
       19.07        22.72         9.01        25.02         3.45        27.68 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       50.56        46.98        14.24        86.83        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
      125.49        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       66.64        13.74        10.82        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       18.58         3.88         9.63        21.11        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KP 
        3.48        88.87        34.06        19.69        57.90        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         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-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A1HR 
       17.16        16.18         4.67        17.56        28.41        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-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
        5.19        29.79        66.41        18.41       112.44        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-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
       16.70         0.56        26.96        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        13.68        14.07        12.95        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
        5.36         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C 
       15.95        26.93        59.31         7.23        20.12         6.94 
TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A767 
        2.10         3.12        11.31        18.97        20.05         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO 
        7.00        14.27        21.34        19.10         8.48         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
       19.40        38.60        64.01        12.16        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       11.70        17.72         1.81        16.27        11.80        44.38 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 
        1.15        15.58        21.07        13.48        16.67        16.54 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB 
       38.99        17.62        37.05        76.01        78.25        69.34 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC 
      112.83        35.24        17.82         6.21        45.04         6.58 
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-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        2.96         8.32        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       28.41        13.41        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 
        8.61        59.38        60.16        67.20        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21         5.52        10.65 

  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE 
                          0.62                           0.49 
  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE 
                         97.12                         166.03 
  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE 
                         17.98                          17.62 
[1] "0.6 - 97.1 (18.0)"  "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 23(11Q22.2) MUTATED         0       23        17       31
  AMP PEAK 23(11Q22.2) WILD-TYPE       2      106       123      104
D23V3, multiclass
           clus
vv          AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(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 23(11Q22.2) MUTATED         24  32  11
  AMP PEAK 23(11Q22.2) WILD-TYPE       99 163  47
D23V4, multiclass
          clus
vv         AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(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 23(11Q22.2) MUTATED    34  11  17   3
  AMP PEAK 23(11Q22.2) WILD-TYPE 202  36  58   5
D23V5, multiclass
    clus
vv   AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE
  N0                           34                            202
  N1                           11                             36
  N2                           17                             58
  N3                            3                              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(11Q22.2) MUTATED    33   2
  AMP PEAK 23(11Q22.2) WILD-TYPE 159   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11Q22.2) MUTATED     33    2
  AMP PEAK 23(11Q22.2) WILD-TYPE  159    9
   clus
vv  AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE
  0                           33                            159
  1                            2                              9
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(11Q22.2) MUTATED    19  52
  AMP PEAK 23(11Q22.2) WILD-TYPE  88 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11Q22.2) MUTATED     19   52
  AMP PEAK 23(11Q22.2) WILD-TYPE   88  249
        clus
vv       AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE
  FEMALE                           19                             88
  MALE                             52                            249
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(11Q22.2) MUTATED    63   1
  AMP PEAK 23(11Q22.2) WILD-TYPE 301  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11Q22.2) MUTATED     63    1
  AMP PEAK 23(11Q22.2) WILD-TYPE  301   19
     clus
vv    AMP PEAK 23(11Q22.2) MUTATED AMP PEAK 23(11Q22.2) WILD-TYPE
  NO                            63                            301
  YES                            1                             19
[1] 2 2
[1] FALSE
D23V9, continuous
D23V10, continuous
D23V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(11Q22.2) MUTATED       3                         3    62
  AMP PEAK 23(11Q22.2) WILD-TYPE    40                        19   265
D23V12, multiclass
                           clus
vv                          AMP PEAK 23(11Q22.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               62
                           clus
vv                          AMP PEAK 23(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"
D23V13, binary
                                cls
clus                               0   1
  AMP PEAK 23(11Q22.2) MUTATED     1  66
  AMP PEAK 23(11Q22.2) WILD-TYPE   8 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(11Q22.2) MUTATED      1   66
  AMP PEAK 23(11Q22.2) WILD-TYPE    8  303
                        clus
vv                       AMP PEAK 23(11Q22.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       AMP PEAK 23(11Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            303
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(12P12.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(12P12.1) MUTATED    76  56
  AMP PEAK 24(12P12.1) WILD-TYPE 151 122
  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE 
                           132                            273 
  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE 
                            56                            122 
$`AMP PEAK 24(12P12.1) MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YN 
       15.12        26.14        20.48        25.94         9.96        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV 
        4.90        15.12        18.48        50.27        66.05        64.18 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA71 
       67.36        15.68        36.66       165.73       166.03        13.64 
TCGA-DK-AA75 TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BS 
       11.18        33.04        60.66        12.85        27.35        53.88 
TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TB TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A3VY 
        5.69         6.28        18.81        31.07        11.08        17.62 
TCGA-GC-A3BM TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND 
       21.40        19.82        27.35         8.58        19.07         9.01 
TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41P TCGA-UY-A9PH TCGA-XF-A9SK TCGA-XF-A9SV 
        3.45         9.14        35.97        51.32        15.98        12.76 
TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
        7.63        98.99        44.32        86.30        18.58        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-4Z-AA7W TCGA-4Z-AA81 
       21.11        30.28        57.90        24.13        27.62        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J 
       10.22        47.80        40.08         2.66         6.74        19.04 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42E 
       17.88         5.06         5.06         8.25        16.18        36.43 
TCGA-C4-A0F0 TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A5UA TCGA-CF-A8HX 
        1.94        12.13        13.08        12.16        12.00        11.34 
TCGA-CF-A8HY TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P 
       11.34        66.41        18.41         8.15        10.55        15.02 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME 
       18.81        19.00        15.35        22.16         0.56        24.03 
TCGA-FD-A3B3 TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3Z9 
       32.02         5.36        27.45        13.35         2.27        12.66 
TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD 
       59.31        66.02        29.36        20.71        15.81        14.07 
TCGA-GC-A6I3 TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3QH TCGA-GV-A3QI 
       13.91         7.63        20.05         7.00         8.48        36.49 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A83P TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78K 
       16.27        15.32        13.48        12.23        38.99        17.62 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A9SI 
       76.01        78.25         3.02        35.24        29.56        79.66 
TCGA-XF-A9SU TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN5 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        5.98         2.96         6.77        75.39        25.41        31.20 
TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       13.41         2.89        59.38        60.16        56.35        19.40 

$`AMP PEAK 24(12P12.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.27        16.77        33.83        12.39        14.89 
TCGA-BT-A20W TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A72E TCGA-DK-A1A5 
        8.35        28.70         8.98        18.58        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       19.00        16.70       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW 
       17.72        21.30        23.21         9.67        17.98        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA74 
       76.60        50.70        38.24        52.01        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 
       20.32        15.35        25.58         0.92         1.22         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 
        3.62        15.58        26.73        10.78         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       58.92        62.86         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB 
        4.31         9.67        17.23        33.01        70.32        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF 
       17.75        24.92        10.92        32.78        32.98        20.28 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       22.72        25.02         2.76        27.68        52.73        50.56 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD 
       46.98        14.24         1.84        33.14        86.83        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP 
      125.49        97.12        15.35         3.22        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 
       71.57        91.73        30.94        61.45         3.88         9.63 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P 
       94.29         3.48        88.87        34.06        19.69        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 
       17.16        34.98        50.04         0.62        51.16        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
        2.50        17.42         7.33         6.58        13.15        12.16 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F 
       19.50        14.96        17.16         4.67        17.56        28.41 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A47S 
       23.01        12.79        12.56        13.97        12.59        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-A7I0 TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       12.10        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 
       21.86       112.44        16.14        17.62        15.62        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79       142.78         4.80        13.58        20.81       163.30 
TCGA-DK-AA6Q TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       13.58        12.03        43.59        38.83        29.72         5.36 
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-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        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-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
        2.70         7.10        10.85        10.65         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        48.00        15.95        26.93         7.23        20.12 
TCGA-G2-AA3C TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
        6.94        15.91         0.49         8.94        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A766 
        3.12        20.98         2.20        11.31        18.97        15.78 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.73        14.27        21.34        19.10         1.51        19.40 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
       17.72         1.81        15.42        11.80        44.38         1.15 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A78M 
       15.58        21.07        16.67        16.54        37.05        22.68 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       69.34       112.83        17.82         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL 
        6.58         1.87        17.88        48.62        64.80        66.41 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW 
       23.64        28.24        16.27        92.98       110.60         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       35.84        21.86        28.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 
       20.22         8.61        67.20        35.41         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE 
                        18.445                         17.420 
[1] "0.6 - 166.0 (18.4)" "0.5 - 163.3 (17.4)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 24(12P12.1) MUTATED         1       50        39       40
  AMP PEAK 24(12P12.1) WILD-TYPE       1       79       101       95
D24V3, multiclass
           clus
vv          AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            50                             79
  STAGE III                           39                            101
  STAGE IV                            40                             95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1+T2  T3  T4
  AMP PEAK 24(12P12.1) MUTATED         45  60  16
  AMP PEAK 24(12P12.1) WILD-TYPE       78 135  42
D24V4, multiclass
          clus
vv         AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE
  T0+T1+T2                           45                             78
  T3                                 60                            135
  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
  AMP PEAK 24(12P12.1) MUTATED    77  18  20   3
  AMP PEAK 24(12P12.1) WILD-TYPE 159  29  55   5
D24V5, multiclass
    clus
vv   AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE
  N0                           77                            159
  N1                           18                             29
  N2                           20                             55
  N3                            3                              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"
D24V6, binary
                                cls
clus                               0   1
  AMP PEAK 24(12P12.1) MUTATED    67   4
  AMP PEAK 24(12P12.1) WILD-TYPE 125   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(12P12.1) MUTATED     67    4
  AMP PEAK 24(12P12.1) WILD-TYPE  125    7
   clus
vv  AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE
  0                           67                            125
  1                            4                              7
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(12P12.1) MUTATED    35  97
  AMP PEAK 24(12P12.1) WILD-TYPE  72 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(12P12.1) MUTATED     35   97
  AMP PEAK 24(12P12.1) WILD-TYPE   72  204
        clus
vv       AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE
  FEMALE                           35                             72
  MALE                             97                            204
[1] 2 2
[1] FALSE
D24V8, binary
                                cls
clus                               0   1
  AMP PEAK 24(12P12.1) MUTATED   123   5
  AMP PEAK 24(12P12.1) WILD-TYPE 241  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(12P12.1) MUTATED    123    5
  AMP PEAK 24(12P12.1) WILD-TYPE  241   15
     clus
vv    AMP PEAK 24(12P12.1) MUTATED AMP PEAK 24(12P12.1) WILD-TYPE
  NO                           123                            241
  YES                            5                             15
[1] 2 2
[1] FALSE
D24V9, continuous
D24V10, continuous
D24V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(12P12.1) MUTATED      12                         7   106
  AMP PEAK 24(12P12.1) WILD-TYPE    31                        15   221
D24V12, multiclass
                           clus
vv                          AMP PEAK 24(12P12.1) MUTATED
  ASIAN                                               12
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              106
                           clus
vv                          AMP PEAK 24(12P12.1) WILD-TYPE
  ASIAN                                                 31
  BLACK OR AFRICAN AMERICAN                             15
  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"
D24V13, binary
                                cls
clus                               0   1
  AMP PEAK 24(12P12.1) MUTATED     2 118
  AMP PEAK 24(12P12.1) WILD-TYPE   7 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(12P12.1) MUTATED      2  118
  AMP PEAK 24(12P12.1) WILD-TYPE    7  251
                        clus
vv                       AMP PEAK 24(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          118
                        clus
vv                       AMP PEAK 24(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            251
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(12Q15) MUTATION ANALYSIS
D25V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 25(12Q15) MUTATED    66  52
  AMP PEAK 25(12Q15) WILD-TYPE 161 126
  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE 
                         118                          287 
  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE 
                          52                          126 
$`AMP PEAK 25(12Q15) MUTATED`
TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A5 
        9.96        28.70        18.58         4.90        15.12         2.14 
TCGA-DK-A1AC TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6S TCGA-DK-AA71 
      130.88        64.18        67.36        15.68       166.03        13.64 
TCGA-DK-AA75 TCGA-E7-A541 TCGA-FD-A43Y TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P 
       11.18        25.58        15.58         5.69        58.92         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A3VY 
       18.81         6.15         3.06        31.07        11.08        17.62 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A3WU TCGA-KQ-A41P 
       70.32        21.40        27.35         8.58         3.45        35.97 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A9SJ TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-AAMY 
        1.84        33.14         3.22        12.76        11.90        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 
       44.32        61.45        86.30        18.58        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW 
       30.28        94.29        57.90        24.13        11.97         8.35 
TCGA-4Z-AA80 TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J 
        0.62        40.08         2.66         6.74         6.58        19.04 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42E 
       17.88         5.06         5.06         8.25        16.18        36.43 
TCGA-C4-A0F6 TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A5UA 
       23.01        12.59        12.13        13.08        12.16        12.00 
TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       12.10        11.34        11.34         1.84        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A2I4 TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       18.41       142.78        10.55        15.02        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       15.35        12.03         0.56        24.03        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A5BZ TCGA-FD-A62S TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO 
        8.09        27.45        13.35        61.94        15.95        59.31 
TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3QH 
       20.71        14.07        13.91        18.97        21.34         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV 
       36.49         1.51        19.40        38.60        64.01        21.24 
TCGA-K4-A5RI TCGA-K4-A83P TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PE 
       11.70        16.27        13.48        38.99        76.01         6.21 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN4 
       64.80        79.66         5.98         2.96         6.77        27.06 
TCGA-ZF-A9R1 TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V 
       25.41        20.22         8.61        59.38 

$`AMP PEAK 25(12Q15) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0EZ 
       26.14        14.89         8.35        20.48        25.94         8.98 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX 
       12.92        18.48        13.58        19.00        16.70        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
        9.67        66.05        17.98        53.29        76.60        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 
       36.66        38.24        52.01       165.73        13.64        56.15 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       20.32        15.35         0.92         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       60.66        24.30        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85        27.35         3.62        26.73        53.88 
TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE 
       10.78         8.25        18.08        62.86        12.69        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GC-A3WC 
        4.31         9.67        17.23        33.01        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       24.92        10.92        32.78        32.98        19.82        20.28 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
       19.07        22.72         9.01        25.02         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N 
       27.68        52.73        50.56        46.98        14.24        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK 
       51.32        97.45       125.49        97.12        15.35        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       34.45        14.93         4.21        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN8 
       54.90         7.63        71.57        91.73        30.94         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P 
        9.63         3.48        88.87        34.06        19.69        12.23 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
       94.88       104.65        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       27.62        50.04        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O 
       47.80         2.50        17.42         7.33        13.15        12.16 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F 
       19.50        14.96        17.16         4.67        17.56        28.41 
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-A3QU TCGA-CU-A3YL TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       13.08         5.19        29.79       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       15.62        17.95         7.79         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       20.81       163.30        13.58        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
        5.36        22.16         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24         4.24        24.66        14.07        15.32        14.37 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
        5.52        25.74        22.98        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        5.36         2.70         7.10         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A3IB 
       10.65         8.94         3.25        48.00        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC 
       20.12        66.02         6.94        29.36        15.81        15.91 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
        0.49         8.94        26.70         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
        2.20        11.31         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ 
        7.00        14.27        19.10        12.16         9.07        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R 
        1.81        15.42        11.80        44.38         1.15        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       15.58        21.07        12.23        16.67        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       37.05        22.68        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       35.24        29.56        17.82         3.85        45.04         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ 
        1.87        17.88        48.62        66.41        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN5 
       16.27        92.98       110.60         8.32        56.48        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       18.84         0.66        11.97        22.36        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
        2.89        60.16        67.20        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE 
                        0.56                         0.49 
  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE 
                      166.03                       165.73 
  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE 
                      16.065                       17.750 
[1] "0.6 - 166.0 (16.1)" "0.5 - 165.7 (17.8)"
[1] "hr=" "1.1"
D25V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 25(12Q15) MUTATED         1       40        39       37
  AMP PEAK 25(12Q15) WILD-TYPE       1       89       101       98
D25V3, multiclass
           clus
vv          AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(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 25(12Q15) MUTATED         34  53  19
  AMP PEAK 25(12Q15) WILD-TYPE       89 142  39
D25V4, multiclass
          clus
vv         AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(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 25(12Q15) MUTATED    68  12  23   2
  AMP PEAK 25(12Q15) WILD-TYPE 168  35  52   6
D25V5, multiclass
    clus
vv   AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE
  N0                         68                          168
  N1                         12                           35
  N2                         23                           52
  N3                          2                            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"
D25V6, binary
                              cls
clus                             0   1
  AMP PEAK 25(12Q15) MUTATED    65   3
  AMP PEAK 25(12Q15) WILD-TYPE 127   8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(12Q15) MUTATED     65    3
  AMP PEAK 25(12Q15) WILD-TYPE  127    8
   clus
vv  AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE
  0                         65                          127
  1                          3                            8
[1] 2 2
[1] FALSE
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(12Q15) MUTATED    34  84
  AMP PEAK 25(12Q15) WILD-TYPE  73 217
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(12Q15) MUTATED     34   84
  AMP PEAK 25(12Q15) WILD-TYPE   73  217
        clus
vv       AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE
  FEMALE                         34                           73
  MALE                           84                          217
[1] 2 2
[1] FALSE
D25V8, binary
                              cls
clus                             0   1
  AMP PEAK 25(12Q15) MUTATED   110   6
  AMP PEAK 25(12Q15) WILD-TYPE 254  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(12Q15) MUTATED    110    6
  AMP PEAK 25(12Q15) WILD-TYPE  254   14
     clus
vv    AMP PEAK 25(12Q15) MUTATED AMP PEAK 25(12Q15) WILD-TYPE
  NO                         110                          254
  YES                          6                           14
[1] 2 2
[1] FALSE
D25V9, continuous
D25V10, continuous
D25V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(12Q15) MUTATED      17                         5    92
  AMP PEAK 25(12Q15) WILD-TYPE    26                        17   235
D25V12, multiclass
                           clus
vv                          AMP PEAK 25(12Q15) MUTATED
  ASIAN                                             17
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             92
                           clus
vv                          AMP PEAK 25(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"
D25V13, binary
                              cls
clus                             0   1
  AMP PEAK 25(12Q15) MUTATED     2 110
  AMP PEAK 25(12Q15) WILD-TYPE   7 259
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(12Q15) MUTATED      2  110
  AMP PEAK 25(12Q15) WILD-TYPE    7  259
                        clus
vv                       AMP PEAK 25(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        110
                        clus
vv                       AMP PEAK 25(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          259
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(13Q22.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(13Q22.1) MUTATED    75  53
  AMP PEAK 26(13Q22.1) WILD-TYPE 152 125
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                           128                            277 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                            53                            125 
$`AMP PEAK 26(13Q22.1) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-CU-A0YN 
      108.95        16.77        26.14        20.48        25.94        12.92 
TCGA-CU-A0YR TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       15.12        46.68        87.32        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-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 
      165.73       166.03        13.64        25.58         0.92        33.04 
TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A5BT TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
       17.98         3.62        10.78         6.15        12.36         3.06 
TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P 
        4.31        11.08        70.32        19.13        17.75        10.92 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AC 
       19.82        20.28        27.35         9.01         3.45         9.14 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       52.73        35.97        14.24        86.83        51.32        97.45 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9T0 TCGA-XF-A9T6 
       97.12        15.35        15.98        14.93        26.27         2.10 
TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN2 
       10.82         7.63        71.57        91.73        98.99        61.45 
TCGA-ZF-A9R2 TCGA-2F-A9KO TCGA-4Z-AA7O TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A3JM 
       21.11        24.13        16.83        41.75        47.80         6.74 
TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20Q TCGA-BT-A20U TCGA-C4-A0F0 TCGA-CF-A1HR 
        6.58        19.04        19.50        14.96         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A8HX TCGA-CU-A3YL TCGA-DK-A3IK 
       12.56        12.13        12.16        11.34        29.79         4.80 
TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A97Q 
       13.58        15.02        19.00        12.03        43.59         8.09 
TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A62O TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EK 
        8.94        22.52         7.10        10.65        61.94        15.95 
TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GD-A3OS 
       66.02        15.81        15.91         0.49         2.10        20.98 
TCGA-GU-A42R TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A5NE 
       18.97         7.00        19.10         8.48        19.40        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
       21.24         9.07        15.42        11.80         1.15        15.32 
TCGA-MV-A51V TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OB 
       13.48        38.99        17.62        37.05        78.25        69.34 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HC TCGA-XF-A9SG 
        3.02        35.24        29.56        17.82         6.58        48.62 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-AA4X TCGA-ZF-AA56 
        6.77        56.48        22.36        25.41        67.20         8.52 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

$`AMP PEAK 26(13Q22.1) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W 
       16.27        15.12        33.83        12.39        14.89         8.35 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ 
        9.96        28.70         8.98        18.58         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IN 
       13.58         2.14        19.00        16.70       130.88         8.22 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B6 
        9.67        17.98        64.18        53.29        76.60        36.66 
TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       52.01        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        1.22         4.01        60.66        24.30        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
       46.78        19.79        12.85        27.35        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       53.88         5.69         8.25        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       62.86        18.81        12.69         9.67        31.07        17.23 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP 
       33.01        17.62        21.40        24.92        32.78        32.98 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A54R 
        8.58        19.07        22.72        25.02         2.76        27.68 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HE TCGA-XF-A9SJ 
       50.56        46.98         1.84        33.14       125.49         3.22 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 
       34.45         4.21        12.76        11.90        21.04        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMZ 
        2.24        66.64        13.74        11.31        54.90        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       30.94        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       57.90        12.23        11.97        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       44.94        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       51.16        66.54        10.22         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R 
        7.33         2.66        13.15        12.16        17.88         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
        5.06         8.25        17.16        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH 
       36.43        28.41        23.01        13.97        12.59        13.08 
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-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
        5.19         1.84        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       15.35        38.83        29.72         5.36        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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66        13.68        14.07        12.95        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO 
       14.37        32.02        16.77        12.62        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70        13.35         2.27        10.85        12.66 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
        8.94         3.25        48.00        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A6I1 
       20.12         6.94        29.36        20.71        14.07         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
       13.91        26.70         3.12         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI 
       20.05        15.78         4.73        14.27        21.34        36.49 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
        1.51        38.60        64.01        11.70        17.72         1.81 
TCGA-K4-A83P TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       16.27        44.38        15.58        21.07        12.23        16.67 
TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF 
       16.54        22.68        76.01       112.83         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
       45.04         1.87        17.88        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
        5.98        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        2.96         8.32        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       11.97        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
       59.38        60.16        56.35        35.41        19.40        54.21 
TCGA-ZF-AA5N 
        5.52 

  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                          0.49                           0.56 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE 
                        17.785                         17.560 
[1] "0.5 - 166.0 (17.8)" "0.6 - 163.3 (17.6)"
[1] "hr=" "1.2"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 26(13Q22.1) MUTATED         0       36        46       46
  AMP PEAK 26(13Q22.1) WILD-TYPE       2       93        94       89
D26V3, multiclass
           clus
vv          AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(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 26(13Q22.1) MUTATED         34  63  20
  AMP PEAK 26(13Q22.1) WILD-TYPE       89 132  38
D26V4, multiclass
          clus
vv         AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(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 26(13Q22.1) MUTATED    76  17  24   4
  AMP PEAK 26(13Q22.1) WILD-TYPE 160  30  51   4
D26V5, multiclass
    clus
vv   AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  N0                           76                            160
  N1                           17                             30
  N2                           24                             51
  N3                            4                              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"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(13Q22.1) MUTATED    62   4
  AMP PEAK 26(13Q22.1) WILD-TYPE 130   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(13Q22.1) MUTATED     62    4
  AMP PEAK 26(13Q22.1) WILD-TYPE  130    7
   clus
vv  AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  0                           62                            130
  1                            4                              7
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(13Q22.1) MUTATED    26 102
  AMP PEAK 26(13Q22.1) WILD-TYPE  81 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(13Q22.1) MUTATED     26  102
  AMP PEAK 26(13Q22.1) WILD-TYPE   81  199
        clus
vv       AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  FEMALE                           26                             81
  MALE                            102                            199
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  AMP PEAK 26(13Q22.1) MUTATED   114   5
  AMP PEAK 26(13Q22.1) WILD-TYPE 250  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(13Q22.1) MUTATED    114    5
  AMP PEAK 26(13Q22.1) WILD-TYPE  250   15
     clus
vv    AMP PEAK 26(13Q22.1) MUTATED AMP PEAK 26(13Q22.1) WILD-TYPE
  NO                           114                            250
  YES                            5                             15
[1] 2 2
[1] FALSE
D26V9, continuous
D26V10, continuous
D26V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(13Q22.1) MUTATED       6                         7   110
  AMP PEAK 26(13Q22.1) WILD-TYPE    37                        15   217
D26V12, multiclass
                           clus
vv                          AMP PEAK 26(13Q22.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                              110
                           clus
vv                          AMP PEAK 26(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"
D26V13, binary
                                cls
clus                               0   1
  AMP PEAK 26(13Q22.1) MUTATED     3 116
  AMP PEAK 26(13Q22.1) WILD-TYPE   6 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(13Q22.1) MUTATED      3  116
  AMP PEAK 26(13Q22.1) WILD-TYPE    6  253
                        clus
vv                       AMP PEAK 26(13Q22.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       AMP PEAK 26(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            253
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(16P13.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(16P13.2) MUTATED    42  44
  AMP PEAK 27(16P13.2) WILD-TYPE 185 134
  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE 
                            86                            319 
  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE 
                            44                            134 
$`AMP PEAK 27(16P13.2) MUTATED`
TCGA-4Z-AA7M TCGA-C4-A0EZ TCGA-CU-A0YR TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IV 
       16.27         8.98        15.12         8.22        50.27         9.67 
TCGA-DK-A3X1 TCGA-DK-A6B1 TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-FD-A3NA 
       66.05        67.36       166.03        11.18        15.35        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI 
       24.30        19.79         8.25        12.69         3.06         9.67 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-HQ-A5ND 
       17.62        21.40        10.92        32.98        19.82         9.01 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A9SJ 
        3.45         2.76        14.24         1.84        51.32         3.22 
TCGA-XF-A9SM TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMR 
       34.45        26.27        66.64         2.10         7.63        91.73 
TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-ZF-AA4T TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA80 
       44.32        18.58        19.69         8.35        17.16         0.62 
TCGA-5N-A9KI TCGA-BT-A0S7 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-CF-A47X 
        2.50         6.58         5.06         8.25        17.16        12.62 
TCGA-CU-A3QU TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6U TCGA-DK-AA6X 
        5.19         7.79        13.58         8.15        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A97Q 
       12.03        43.59        22.16        24.03        12.95         8.09 
TCGA-FD-A43U TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO TCGA-G2-A3IE 
       20.91         2.27        10.65         3.25        59.31        20.12 
TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HQ TCGA-HQ-A2OE 
       66.02        20.71        15.78        14.27        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A83P TCGA-LC-A66R TCGA-SY-A9G5 TCGA-UY-A9PD TCGA-XF-A9SU 
       64.01        16.27        15.32        38.99        17.82         5.98 
TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       28.24       110.60         6.77        22.36        13.41        64.08 
TCGA-ZF-AA4V TCGA-ZF-AA4W 
       59.38        60.16 

$`AMP PEAK 27(16P13.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       18.58        12.92         4.90        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ 
       19.00        16.70       130.88        46.68        87.32        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30        23.21        17.98        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       15.68        50.70        36.66        38.24        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU 
       13.64        13.64        56.15        20.32        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        1.22        33.04         4.01        23.41        17.98        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       46.78        12.85        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       53.88        10.78         5.69        18.08        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
       62.86        18.81         6.15        12.36         4.31        31.07 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       17.23        11.08        33.01        70.32        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       24.92        32.78        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       22.72        25.02         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       35.97        46.98        33.14        86.83        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       97.12        15.35        15.98        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF 
       11.90        21.04        18.90         2.24        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       11.31        54.90        71.57        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29         3.48        88.87        34.06        57.90        12.23 
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-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       10.22        47.80        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06        14.96        16.18         4.67        17.56        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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A3WX 
       15.62        17.95       142.78         4.80        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-E5-A4U1 TCGA-E7-A3X6 
      163.30        15.02        13.58        18.81        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
        5.36         2.24        16.70         0.56         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       26.24         4.24        24.66        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU 
       27.98         5.52        25.74        22.98        14.96        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
        5.36        27.45         2.70         7.10        13.35        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       12.66         8.94        61.94        48.00        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        7.23         6.94        29.36        15.81        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
        0.49         8.94        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        21.34        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
        1.51        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 
        1.81        15.42        11.80        44.38         1.15        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       21.07        13.48        12.23        16.67        16.54        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       37.05        22.68        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
      112.83        35.24        29.56         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        6.58         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW 
       66.41        23.64        16.27        92.98         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RG 
       25.41        31.20        35.84        21.86        28.41        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 
       47.84        20.22         2.89         8.61        67.20        56.35 
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        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE 
                          0.62                           0.49 
  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE 
                        16.025                         17.880 
[1] "0.6 - 166.0 (16.0)" "0.5 - 165.7 (17.9)"
[1] "hr=" "1.3"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 27(16P13.2) MUTATED         0       20        31       35
  AMP PEAK 27(16P13.2) WILD-TYPE       2      109       109      100
D27V3, multiclass
           clus
vv          AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(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 27(16P13.2) MUTATED         20  38  21
  AMP PEAK 27(16P13.2) WILD-TYPE      103 157  37
D27V4, multiclass
          clus
vv         AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(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 27(16P13.2) MUTATED    44  11  19   4
  AMP PEAK 27(16P13.2) WILD-TYPE 192  36  56   4
D27V5, multiclass
    clus
vv   AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE
  N0                           44                            192
  N1                           11                             36
  N2                           19                             56
  N3                            4                              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(16P13.2) MUTATED    37   4
  AMP PEAK 27(16P13.2) WILD-TYPE 155   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16P13.2) MUTATED     37    4
  AMP PEAK 27(16P13.2) WILD-TYPE  155    7
   clus
vv  AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE
  0                           37                            155
  1                            4                              7
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(16P13.2) MUTATED    23  64
  AMP PEAK 27(16P13.2) WILD-TYPE  84 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16P13.2) MUTATED     23   64
  AMP PEAK 27(16P13.2) WILD-TYPE   84  237
        clus
vv       AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE
  FEMALE                           23                             84
  MALE                             64                            237
[1] 2 2
[1] FALSE
D27V8, binary
                                cls
clus                               0   1
  AMP PEAK 27(16P13.2) MUTATED    79   3
  AMP PEAK 27(16P13.2) WILD-TYPE 285  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16P13.2) MUTATED     79    3
  AMP PEAK 27(16P13.2) WILD-TYPE  285   17
     clus
vv    AMP PEAK 27(16P13.2) MUTATED AMP PEAK 27(16P13.2) WILD-TYPE
  NO                            79                            285
  YES                            3                             17
[1] 2 2
[1] FALSE
D27V9, continuous
D27V10, continuous
D27V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(16P13.2) MUTATED       5                         4    74
  AMP PEAK 27(16P13.2) WILD-TYPE    38                        18   253
D27V12, multiclass
                           clus
vv                          AMP PEAK 27(16P13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               74
                           clus
vv                          AMP PEAK 27(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"
D27V13, binary
                                cls
clus                               0   1
  AMP PEAK 27(16P13.2) MUTATED     1  79
  AMP PEAK 27(16P13.2) WILD-TYPE   8 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(16P13.2) MUTATED      1   79
  AMP PEAK 27(16P13.2) WILD-TYPE    8  290
                        clus
vv                       AMP PEAK 27(16P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       AMP PEAK 27(16P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(16P11.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(16P11.2) MUTATED    51  46
  AMP PEAK 28(16P11.2) WILD-TYPE 176 132
  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE 
                            97                            308 
  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE 
                            46                            132 
$`AMP PEAK 28(16P11.2) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ 
       16.27        15.12        28.70         8.98        12.92        18.48 
TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-AA6S 
       87.32        50.27         9.67        66.05        15.68       166.03 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A43Y 
       11.18        15.35        33.04        24.30        19.79        15.58 
TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FT-A61P TCGA-GC-A3BM 
        8.25        12.69         3.06         9.67        11.08        21.40 
TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       24.92        32.98        19.82        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A9SJ 
        3.45         2.76        14.24         1.84        51.32         3.22 
TCGA-XF-A9SM TCGA-XF-A9T5 TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       34.45        66.64         7.63        91.73        98.99        44.32 
TCGA-ZF-A9RL TCGA-4Z-AA80 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 
       88.87         0.62         2.50        40.08         2.66         6.58 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42E TCGA-CF-A47X 
        5.06         5.06         8.25        17.16        36.43        12.62 
TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-AA6P 
        5.19        18.41         7.79         4.80        13.58        15.02 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE 
       19.00        15.35        43.59        38.83        22.16         0.56 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A6TF TCGA-FJ-A3ZE 
        8.09        32.02        20.91         5.36         2.27        10.65 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3I6 
        3.25        61.94        59.31        20.12        66.02        20.71 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-K4-A83P 
       14.27        21.34        19.40        64.01        15.42        16.27 
TCGA-SY-A9G5 TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-AAMG 
       38.99         3.85         6.58         5.98        28.24       110.60 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-AA4V 
        6.77        56.48        22.36        13.41        64.08        59.38 
TCGA-ZF-AA4W 
       60.16 

$`AMP PEAK 28(16P11.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.77        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO 
        8.35        20.48        25.94         9.96        18.58         4.90 
TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       15.12        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X2 
       46.68         8.22        17.72        21.30        23.21        17.98 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       64.18        53.29        76.60        67.36        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       38.24        52.01       165.73        13.64        13.64        56.15 
TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA 
       20.32        25.58         0.92         1.22         4.01        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        17.98        29.16        46.78        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 
        3.62        26.73        53.88        10.78         5.69        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
       58.92         6.28        62.86        18.81         6.15        12.36 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31        31.07        17.23        33.01        17.62        70.32 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK 
       19.13        17.75        10.92        32.78        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
        8.58        19.07         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       35.97        46.98        33.14        86.83        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV 
       97.12        15.35        15.98        14.93         4.21        12.76 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 
       11.90        21.04        26.27        18.90         2.24         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAN1 
       13.74        10.82        11.31        54.90        71.57        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T 
       21.11        30.28        94.29         3.48        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
       57.90        12.23        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
        8.35        44.94        16.83        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-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       17.42         7.33         6.74        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       17.88        19.50        14.96        16.18         4.67        17.56 
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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       21.86        66.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       17.95       142.78         8.15        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       13.58        18.81        12.03        29.72         5.36         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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        13.68        14.07        12.95        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N 
       25.74        22.98        14.96        19.33        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-G2-A2EJ 
        7.10        13.35        10.85        12.66         8.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO 
       15.95        26.93         7.23         6.94        29.36        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.91        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JX 
        7.63        20.05        15.78         4.73         7.00        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV 
        8.48        36.49         1.51        38.60        12.16        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41R 
        9.07        11.70        17.72         1.81        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI 
        1.15        15.32        15.58        21.07        13.48        12.23 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.67        16.54        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        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       17.82         6.21        45.04         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME 
       64.80        79.66        66.41        23.64        16.27        92.98 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        2.96         8.32        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X 
       58.72        47.84        20.22         2.89         8.61        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       56.35        35.41        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE 
                         16.27                          17.72 
[1] "0.6 - 166.0 (16.3)" "0.5 - 165.7 (17.7)"
[1] "hr=" "1.1"
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 28(16P11.2) MUTATED         1       23        32       42
  AMP PEAK 28(16P11.2) WILD-TYPE       1      106       108       93
D28V3, multiclass
           clus
vv          AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            23                            106
  STAGE III                           32                            108
  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 28(16P11.2) MUTATED         21  47  20
  AMP PEAK 28(16P11.2) WILD-TYPE      102 148  38
D28V4, multiclass
          clus
vv         AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE
  T0+T1+T2                           21                            102
  T3                                 47                            148
  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 28(16P11.2) MUTATED    47  14  23   4
  AMP PEAK 28(16P11.2) WILD-TYPE 189  33  52   4
D28V5, multiclass
    clus
vv   AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE
  N0                           47                            189
  N1                           14                             33
  N2                           23                             52
  N3                            4                              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"
D28V6, binary
                                cls
clus                               0   1
  AMP PEAK 28(16P11.2) MUTATED    44   5
  AMP PEAK 28(16P11.2) WILD-TYPE 148   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(16P11.2) MUTATED     44    5
  AMP PEAK 28(16P11.2) WILD-TYPE  148    6
   clus
vv  AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE
  0                           44                            148
  1                            5                              6
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(16P11.2) MUTATED    26  72
  AMP PEAK 28(16P11.2) WILD-TYPE  81 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(16P11.2) MUTATED     26   72
  AMP PEAK 28(16P11.2) WILD-TYPE   81  229
        clus
vv       AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE
  FEMALE                           26                             81
  MALE                             72                            229
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  AMP PEAK 28(16P11.2) MUTATED    91   4
  AMP PEAK 28(16P11.2) WILD-TYPE 273  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(16P11.2) MUTATED     91    4
  AMP PEAK 28(16P11.2) WILD-TYPE  273   16
     clus
vv    AMP PEAK 28(16P11.2) MUTATED AMP PEAK 28(16P11.2) WILD-TYPE
  NO                            91                            273
  YES                            4                             16
[1] 2 2
[1] FALSE
D28V9, continuous
D28V10, continuous
D28V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(16P11.2) MUTATED       4                         3    87
  AMP PEAK 28(16P11.2) WILD-TYPE    39                        19   240
D28V12, multiclass
                           clus
vv                          AMP PEAK 28(16P11.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               87
                           clus
vv                          AMP PEAK 28(16P11.2) WILD-TYPE
  ASIAN                                                 39
  BLACK OR AFRICAN AMERICAN                             19
  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"
D28V13, binary
                                cls
clus                               0   1
  AMP PEAK 28(16P11.2) MUTATED     1  91
  AMP PEAK 28(16P11.2) WILD-TYPE   8 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(16P11.2) MUTATED      1   91
  AMP PEAK 28(16P11.2) WILD-TYPE    8  278
                        clus
vv                       AMP PEAK 28(16P11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       AMP PEAK 28(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            278
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(16Q22.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(16Q22.1) MUTATED    56  51
  AMP PEAK 29(16Q22.1) WILD-TYPE 171 127
  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE 
                           107                            298 
  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE 
                            51                            127 
$`AMP PEAK 29(16Q22.1) MUTATED`
TCGA-2F-A9KT TCGA-BT-A20N TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A3KJ 
      108.95        26.14        25.94        28.70         8.98        18.48 
TCGA-DK-A1A5 TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 
        2.14        50.27         9.67        66.05        64.18        15.68 
TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SL 
       38.24       166.03        11.18         1.22        24.30        23.41 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P 
       27.35        15.58        10.78         8.25        18.08         6.28 
TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        6.15         3.06         9.67        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-AATP TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       21.40        24.92        32.98         9.01        25.02         3.45 
TCGA-K4-A4AB TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A9SK TCGA-XF-A9SM 
        2.76        14.24         1.84        51.32        15.98        34.45 
TCGA-XF-A9T3 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-ZF-A9RC 
        2.24        71.57        91.73        98.99        44.32        94.29 
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A0S7 
       11.97         8.35         0.62        47.80         2.66         6.58 
TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42E TCGA-CF-A1HS 
        5.06         5.06         8.25        17.16        36.43        12.56 
TCGA-CF-A47X TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6X TCGA-E5-A2PC 
       12.62         7.79        13.58         8.15        15.35        43.59 
TCGA-E5-A4U1 TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A5BV TCGA-FD-A5BZ 
       38.83        13.68         8.09        32.02         5.36        27.45 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EO 
       13.35         2.27        10.85        10.65         3.25        59.31 
TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OS 
       66.02        20.71         0.49         8.94        26.70        20.98 
TCGA-GU-A762 TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A6MB 
        7.63        21.34        19.40        64.01        12.16        15.42 
TCGA-K4-AAQO TCGA-LC-A66R TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD 
       11.80        15.32        38.99        22.68        69.34       112.83 
TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SU TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9R7 
        6.21        48.62         5.98         6.77        22.36        21.86 
TCGA-ZF-A9RD TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA5H TCGA-GU-AATO 
       13.41        60.16        19.40        29.49        10.65 

$`AMP PEAK 29(16Q22.1) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
       16.27        16.77        15.12        33.83        12.39        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
        8.35        20.48         9.96        18.58        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       15.12        13.58        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X2 
       87.32         8.22        17.72        21.30        23.21        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M 
       53.29        76.60        67.36        50.70        36.66        52.01 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ 
      165.73        13.64        13.64        56.15        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SM 
       25.58         0.92        33.04         4.01        60.66        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR 
       29.16        46.78        19.79        12.85         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
       53.88         5.69        58.92        62.86        18.81        12.69 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-GC-A3RB 
       12.36         4.31        31.07        17.23        11.08        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       17.75        10.92        32.78        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
        8.58        19.07        22.72         9.14        27.68        52.73 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD 
       50.56        35.97        46.98        33.14        86.83        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9ST 
      125.49        97.12        15.35         3.22        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 
       12.76        11.90        21.04        26.27        18.90        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       30.94        61.45        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
       13.64        21.11        30.28         3.48        88.87        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        57.90        12.23        24.13        94.88       104.65 
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-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM 
       41.75        51.16        66.54        10.22         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       40.08         7.33         6.74        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       17.88        19.50        14.96        16.18         4.67        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 
       11.34        11.87        13.08         5.19        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3WW TCGA-DK-A3WX 
       15.62        17.95       142.78         4.80        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 
      163.30        15.02        13.58        18.81        19.00        12.03 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        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-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        12.95        15.32        14.37        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N 
       12.62        22.52        27.98         5.52        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62O TCGA-FJ-A3Z9 
       14.96        20.91        19.33         2.70         7.10        12.66 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        8.94        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12         6.94        29.36        15.81        15.91        14.07 
TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
       13.91         2.10         3.12         2.20        11.31        18.97 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX 
       20.05        15.78         4.73         7.00        14.27        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RH 
        8.48        36.49         1.51        38.60        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S 
       11.70        17.72         1.81        16.27        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-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       17.62        37.05        76.01        78.25         3.02        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       29.56        17.82         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ 
       17.88        64.80        79.66        66.41        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       16.27        92.98       110.60         2.96         8.32        56.48 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       31.20        35.84        28.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 
       20.22         2.89         8.61        59.38        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       35.41         8.52        54.21         5.52 

  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE 
                          0.49                           0.56 
  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE 
                        15.980                         17.735 
[1] "0.5 - 166.0 (16.0)" "0.6 - 165.7 (17.7)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 29(16Q22.1) MUTATED         0       25        42       41
  AMP PEAK 29(16Q22.1) WILD-TYPE       2      104        98       94
D29V3, multiclass
           clus
vv          AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(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 29(16Q22.1) MUTATED         23  58  19
  AMP PEAK 29(16Q22.1) WILD-TYPE      100 137  39
D29V4, multiclass
          clus
vv         AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(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 29(16Q22.1) MUTATED    59  13  23   4
  AMP PEAK 29(16Q22.1) WILD-TYPE 177  34  52   4
D29V5, multiclass
    clus
vv   AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE
  N0                           59                            177
  N1                           13                             34
  N2                           23                             52
  N3                            4                              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"
D29V6, binary
                                cls
clus                               0   1
  AMP PEAK 29(16Q22.1) MUTATED    43   5
  AMP PEAK 29(16Q22.1) WILD-TYPE 149   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(16Q22.1) MUTATED     43    5
  AMP PEAK 29(16Q22.1) WILD-TYPE  149    6
   clus
vv  AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE
  0                           43                            149
  1                            5                              6
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(16Q22.1) MUTATED    36  72
  AMP PEAK 29(16Q22.1) WILD-TYPE  71 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(16Q22.1) MUTATED     36   72
  AMP PEAK 29(16Q22.1) WILD-TYPE   71  229
        clus
vv       AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE
  FEMALE                           36                             71
  MALE                             72                            229
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  AMP PEAK 29(16Q22.1) MUTATED    95   4
  AMP PEAK 29(16Q22.1) WILD-TYPE 269  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(16Q22.1) MUTATED     95    4
  AMP PEAK 29(16Q22.1) WILD-TYPE  269   16
     clus
vv    AMP PEAK 29(16Q22.1) MUTATED AMP PEAK 29(16Q22.1) WILD-TYPE
  NO                            95                            269
  YES                            4                             16
[1] 2 2
[1] FALSE
D29V9, continuous
D29V10, continuous
D29V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(16Q22.1) MUTATED       6                         7    88
  AMP PEAK 29(16Q22.1) WILD-TYPE    37                        15   239
D29V12, multiclass
                           clus
vv                          AMP PEAK 29(16Q22.1) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               88
                           clus
vv                          AMP PEAK 29(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"
D29V13, binary
                                cls
clus                               0   1
  AMP PEAK 29(16Q22.1) MUTATED     2  99
  AMP PEAK 29(16Q22.1) WILD-TYPE   7 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(16Q22.1) MUTATED      2   99
  AMP PEAK 29(16Q22.1) WILD-TYPE    7  270
                        clus
vv                       AMP PEAK 29(16Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       AMP PEAK 29(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(17P11.2) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 30(17P11.2) MUTATED    42  45
  AMP PEAK 30(17P11.2) WILD-TYPE 185 133
  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE 
                            87                            318 
  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE 
                            45                            133 
$`AMP PEAK 30(17P11.2) MUTATED`
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YR 
        8.35        20.48        25.94        28.70         8.98        15.12 
TCGA-DK-A1A5 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-E7-A541 TCGA-FD-A3B6 
        2.14        67.36        36.66        38.24        25.58        33.04 
TCGA-FD-A3SQ TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A6TE TCGA-FD-A6TH TCGA-G2-A3VY 
       46.78        10.78        18.08        12.36         4.31        17.62 
TCGA-GC-A3YS TCGA-GV-A3JZ TCGA-K4-A3WU TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A9SP 
       24.92        19.82         3.45         1.84        86.83        14.93 
TCGA-XF-A9T0 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL 
       26.27         7.63        71.57        30.28        94.29        88.87 
TCGA-2F-A9KP TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A13J TCGA-BL-A3JM 
       11.97        17.16        41.75        10.22         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA TCGA-CF-A1HR 
        6.58        19.50         5.06        14.96        17.16        12.79 
TCGA-CF-A3MF TCGA-CF-A8HY TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       12.59        11.34        29.79        66.41        18.41       112.44 
TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6U TCGA-E7-A5KE TCGA-E7-A677 
        7.79         4.80         8.15        19.00         0.56        26.96 
TCGA-E7-A85H TCGA-FD-A3SP TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ 
       12.95        25.74         2.27        10.65         3.25        48.00 
TCGA-G2-A2EO TCGA-GD-A3OP TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI 
       59.31         2.10        14.27        21.34         8.48        36.49 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-SY-A9G5 TCGA-UY-A8OB TCGA-UY-A9PE 
       21.24        11.70         1.81        38.99        69.34         6.21 
TCGA-XF-A8HI TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-AAMT TCGA-XF-AAMX TCGA-ZF-A9R7 
       17.88        79.66        23.64         2.96         6.77        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4X TCGA-ZF-AA52 
       28.41        13.41        58.72        47.84        67.20        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA5H TCGA-GU-AATO 
       19.40        29.49        10.65 

$`AMP PEAK 30(17P11.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO 
       26.14        14.89         9.96        18.58        12.92         4.90 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       18.48        13.58        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       15.68        50.70        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU 
       13.64        56.15        11.18        20.32        15.35         0.92 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        1.22         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       29.16        19.79        12.85        27.35         3.62        15.58 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P 
       26.73        53.88         5.69         8.25        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI 
       62.86        18.81         6.15        12.69         3.06         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM 
       31.07        17.23        11.08        33.01        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF 
       19.13        17.75        10.92        32.78        32.98        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        2.76         9.14        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
       46.98        14.24        33.14        51.32        97.45       125.49 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST 
       97.12        15.35         3.22        15.98        34.45         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       12.76        11.90        21.04        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMR 
        2.10        13.74        10.82        11.31        54.90        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 
       98.99        44.32        30.94        61.45        86.30        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA4R 
        3.88         9.63        13.64        21.11         3.48        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR 
       19.69        57.90        12.23        24.13        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
        8.35        44.94        16.83        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
        0.62        51.16        66.54        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
       40.08         7.33        13.15        19.04        12.16        17.88 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG 
       28.41         1.94        23.01        12.56        13.97        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-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-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1AE 
       11.87        13.08         5.19         1.84        21.86        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW 
       17.62        15.62        17.95       142.78        13.58        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       10.55       163.30        15.02        13.58        18.81        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       12.03        43.59        38.83        29.72         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME 
        2.24        16.70         0.66        26.24         4.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        13.68        14.07        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       32.02        16.77         8.94        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
        5.52        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70         7.10        13.35        10.85        12.66 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
        8.94        61.94        15.95        26.93         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
       66.02         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
       14.07         0.49         8.94        13.91        26.70         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ 
       15.78         4.73         7.00        19.10         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
       38.60        64.01        12.16         9.07        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       16.27        11.80        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       21.07        13.48        12.23        16.67        16.54        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-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       35.24        29.56        17.82         3.85        45.04         6.58 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ 
        1.87        48.62        64.80        66.41         5.98        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
       16.27        92.98       110.60         8.32        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 
       75.39        18.84         0.66        11.97        22.36        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       31.20        35.84        64.08        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       59.38        60.16        56.35         8.52        54.21         5.52 

  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE 
                        112.44                         166.03 
  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE 
                         18.08                          17.59 
[1] "0.6 - 112.4 (18.1)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.3"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 30(17P11.2) MUTATED         0       26        26       36
  AMP PEAK 30(17P11.2) WILD-TYPE       2      103       114       99
D30V3, multiclass
           clus
vv          AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            26                            103
  STAGE III                           26                            114
  STAGE IV                            36                             99
[1] 4 2
[1] 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(17P11.2) MUTATED         23  45  11
  AMP PEAK 30(17P11.2) WILD-TYPE      100 150  47
D30V4, multiclass
          clus
vv         AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE
  T0+T1+T2                           23                            100
  T3                                 45                            150
  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 30(17P11.2) MUTATED    43  10  22   3
  AMP PEAK 30(17P11.2) WILD-TYPE 193  37  53   5
D30V5, multiclass
    clus
vv   AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE
  N0                           43                            193
  N1                           10                             37
  N2                           22                             53
  N3                            3                              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"
D30V6, binary
                                cls
clus                               0   1
  AMP PEAK 30(17P11.2) MUTATED    37   3
  AMP PEAK 30(17P11.2) WILD-TYPE 155   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(17P11.2) MUTATED     37    3
  AMP PEAK 30(17P11.2) WILD-TYPE  155    8
   clus
vv  AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE
  0                           37                            155
  1                            3                              8
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(17P11.2) MUTATED    25  63
  AMP PEAK 30(17P11.2) WILD-TYPE  82 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(17P11.2) MUTATED     25   63
  AMP PEAK 30(17P11.2) WILD-TYPE   82  238
        clus
vv       AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE
  FEMALE                           25                             82
  MALE                             63                            238
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  AMP PEAK 30(17P11.2) MUTATED    79   4
  AMP PEAK 30(17P11.2) WILD-TYPE 285  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(17P11.2) MUTATED     79    4
  AMP PEAK 30(17P11.2) WILD-TYPE  285   16
     clus
vv    AMP PEAK 30(17P11.2) MUTATED AMP PEAK 30(17P11.2) WILD-TYPE
  NO                            79                            285
  YES                            4                             16
[1] 2 2
[1] FALSE
D30V9, continuous
D30V10, continuous
D30V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(17P11.2) MUTATED       8                         3    76
  AMP PEAK 30(17P11.2) WILD-TYPE    35                        19   251
D30V12, multiclass
                           clus
vv                          AMP PEAK 30(17P11.2) MUTATED
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               76
                           clus
vv                          AMP PEAK 30(17P11.2) WILD-TYPE
  ASIAN                                                 35
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                251
[1] 3 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(17P11.2) MUTATED     2  80
  AMP PEAK 30(17P11.2) WILD-TYPE   7 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(17P11.2) MUTATED      2   80
  AMP PEAK 30(17P11.2) WILD-TYPE    7  289
                        clus
vv                       AMP PEAK 30(17P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       AMP PEAK 30(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            289
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(17Q11.2) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 31(17Q11.2) MUTATED    93  79
  AMP PEAK 31(17Q11.2) WILD-TYPE 134  99
  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE 
                           172                            233 
  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE 
                            79                             99 
$`AMP PEAK 31(17Q11.2) MUTATED`
TCGA-4Z-AA7M TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C 
       16.27        12.39        14.89         8.35        20.48        28.70 
TCGA-C4-A0EZ TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A3IS TCGA-DK-A3X1 
        8.98        15.12         2.14       130.88        50.27        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-DK-AA71 
       17.98        67.36        50.70        36.66       166.03        13.64 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ 
       11.18        15.35        25.58        33.04        60.66        24.30 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5C1 
       46.78        27.35         3.62        26.73        10.78        58.92 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
       62.86        18.81        12.36         3.06         4.31        31.07 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P 
       17.62        70.32        21.40        19.13        24.92        10.92 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N 
        9.01         3.45        46.98        14.24         1.84        86.83 
TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9T0 
       97.45        97.12        15.35         3.22        14.93        26.27 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-YF-AA3M 
       11.31         7.63        71.57        91.73        86.30        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KP TCGA-4Z-AA7R 
       30.28        94.29        19.69        24.13        11.97        17.16 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13J 
        0.62        41.75        10.22        47.80        17.42         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
        6.74         6.58        17.88        19.50         5.06        14.96 
TCGA-BT-A3PH TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X 
        4.67        12.79        12.59        12.13        12.16        12.62 
TCGA-CF-A8HY TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       11.34        29.79         1.84        66.41        18.41       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U 
       17.95         7.79         4.80         8.15        15.02        19.00 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A677 
       15.35        43.59        38.83        22.16         0.56        26.96 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FD-A43N 
       24.03        13.68         8.94        22.52        25.74        22.98 
TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TF TCGA-FT-A3EE TCGA-G2-A2EO 
       20.91         5.36         7.10         2.27         3.25        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 
       20.12        66.02        29.36         0.49        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        2.10         2.20        18.97         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       21.34         8.48        36.49        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO 
       12.16        21.24        11.70         1.81        15.42        11.80 
TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OC TCGA-UY-A8OD 
        1.15        12.23        38.99        76.01         3.02       112.83 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SU 
       17.82         6.21         1.87        17.88        48.62         5.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
      110.60         2.96         8.32         6.77        56.48        11.97 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X 
       28.41        13.41        47.84        20.22        59.38        67.20 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-GU-AATO 
       35.41         8.52        29.49        10.65 

$`AMP PEAK 31(17Q11.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A3PJ 
      108.95        16.77        15.12        33.83        26.14        25.94 
TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E 
        9.96        18.58        12.92         4.90        18.48        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       19.00        16.70        46.68        87.32         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30        23.21         9.67        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 
       15.68        38.24        52.01       165.73        13.64        56.15 
TCGA-DK-AA77 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SM 
       20.32         0.92         1.22         4.01        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX 
       29.16        19.79        12.85        15.58        53.88         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI 
        8.25        18.08         6.28         6.15        12.69         9.67 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GU-A763 TCGA-GV-A6ZA 
       17.23        11.08        33.01        17.75        32.78        22.72 
TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O 
       25.02         2.76         9.14        27.68        52.73        50.56 
TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9SM 
       35.97        33.14        51.32       125.49        15.98        34.45 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        21.04        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMY 
       66.64         2.10        13.74        10.82        54.90        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       44.32        30.94        61.45        18.58         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
       21.11         3.48        88.87        34.06        57.90        12.23 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       94.88       104.65         8.35        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KI TCGA-BL-A0C8 
       27.62        50.04        51.16        66.54         2.50        40.08 
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20X 
        7.33        13.15        19.04        12.16         5.06         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
       17.16        16.18        17.56        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       23.01        12.56        13.97        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-A9FM TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1AE 
       11.34        11.87        13.08         5.19        21.86        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX 
       17.62        15.62       142.78        13.58        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A3Y1 
      163.30        13.58        18.81        12.03        29.72         5.36 
TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
        2.24        16.70         0.66        26.24         4.24        24.66 
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-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A5BU 
       16.77        12.62        27.98         5.52        14.96        19.33 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       27.45         2.70        13.35        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB 
        8.94        61.94        48.00        15.95        26.93         7.23 
TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 
        6.94        20.71        15.81        15.91        14.07         8.94 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        3.12        20.98        11.31         7.63        20.05        15.78 
TCGA-GV-A3JX TCGA-H4-A2HO TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A83P TCGA-KQ-A41R 
       19.10         1.51         9.07        17.72        16.27        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 
       15.32        15.58        21.07        13.48        16.67        16.54 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A9PA 
       17.62        37.05        22.68        78.25        69.34        35.24 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A9SH TCGA-XF-A9SI 
       29.56         3.85        45.04         6.58        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAN4 
       66.41        23.64        28.24        16.27        92.98        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4U 
       35.84        21.86        64.08        58.72         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       60.16        56.35        19.40        54.21         5.52 

  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE 
                          0.49                           0.66 
  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE 
                         17.88                          17.56 
[1] "0.5 - 166.0 (17.9)" "0.7 - 165.7 (17.6)"
[1] "hr=" "1.1"
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 31(17Q11.2) MUTATED         0       51        55       67
  AMP PEAK 31(17Q11.2) WILD-TYPE       2       78        85       68
D31V3, multiclass
           clus
vv          AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE
  STAGE I                              0                              2
  STAGE II                            51                             78
  STAGE III                           55                             85
  STAGE IV                            67                             68
[1] 4 2
[1] 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(17Q11.2) MUTATED         53  84  27
  AMP PEAK 31(17Q11.2) WILD-TYPE       70 111  31
D31V4, multiclass
          clus
vv         AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE
  T0+T1+T2                           53                             70
  T3                                 84                            111
  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(17Q11.2) MUTATED    93  20  43   2
  AMP PEAK 31(17Q11.2) WILD-TYPE 143  27  32   6
D31V5, multiclass
    clus
vv   AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE
  N0                           93                            143
  N1                           20                             27
  N2                           43                             32
  N3                            2                              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"
D31V6, binary
                                cls
clus                               0   1
  AMP PEAK 31(17Q11.2) MUTATED    75   3
  AMP PEAK 31(17Q11.2) WILD-TYPE 117   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(17Q11.2) MUTATED     75    3
  AMP PEAK 31(17Q11.2) WILD-TYPE  117    8
   clus
vv  AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE
  0                           75                            117
  1                            3                              8
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  AMP PEAK 31(17Q11.2) MUTATED    44 130
  AMP PEAK 31(17Q11.2) WILD-TYPE  63 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(17Q11.2) MUTATED     44  130
  AMP PEAK 31(17Q11.2) WILD-TYPE   63  171
        clus
vv       AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE
  FEMALE                           44                             63
  MALE                            130                            171
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                               0   1
  AMP PEAK 31(17Q11.2) MUTATED   160   6
  AMP PEAK 31(17Q11.2) WILD-TYPE 204  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(17Q11.2) MUTATED    160    6
  AMP PEAK 31(17Q11.2) WILD-TYPE  204   14
     clus
vv    AMP PEAK 31(17Q11.2) MUTATED AMP PEAK 31(17Q11.2) WILD-TYPE
  NO                           160                            204
  YES                            6                             14
[1] 2 2
[1] FALSE
D31V9, continuous
D31V10, continuous
D31V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 31(17Q11.2) MUTATED      13                        10   142
  AMP PEAK 31(17Q11.2) WILD-TYPE    30                        12   185
D31V12, multiclass
                           clus
vv                          AMP PEAK 31(17Q11.2) MUTATED
  ASIAN                                               13
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              142
                           clus
vv                          AMP PEAK 31(17Q11.2) WILD-TYPE
  ASIAN                                                 30
  BLACK OR AFRICAN AMERICAN                             12
  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"
D31V13, binary
                                cls
clus                               0   1
  AMP PEAK 31(17Q11.2) MUTATED     5 154
  AMP PEAK 31(17Q11.2) WILD-TYPE   4 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(17Q11.2) MUTATED      5  154
  AMP PEAK 31(17Q11.2) WILD-TYPE    4  215
                        clus
vv                       AMP PEAK 31(17Q11.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          154
                        clus
vv                       AMP PEAK 31(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            215
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(17Q12) MUTATION ANALYSIS
D32V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 32(17Q12) MUTATED    85  78
  AMP PEAK 32(17Q12) WILD-TYPE 142 100
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                         163                          242 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                          78                          100 
$`AMP PEAK 32(17Q12) MUTATED`
TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C 
       15.12        12.39         8.35        20.48         9.96        28.70 
TCGA-C4-A0EZ TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3X1 
        8.98        15.12         2.14        87.32        50.27        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA75 
       17.98        67.36        36.66       166.03        13.64        11.18 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       15.35        25.58        33.04         4.01        60.66        24.30 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5C1 TCGA-FD-A6TA 
       46.78        27.35         3.62        26.73        58.92        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 
       18.81         6.15        12.69        12.36         4.31        31.07 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       70.32        21.40        10.92        32.98        19.82        20.28 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-KQ-A41Q 
       27.35         8.58        19.07         9.01         3.45        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       14.24         1.84        86.83        97.45        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9T0 TCGA-XF-AAMH TCGA-XF-AAML 
        3.22        15.98        14.93        26.27        11.31         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       71.57        91.73        86.30        13.64        30.28        94.29 
TCGA-ZF-AA4T TCGA-2F-A9KP TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 
       19.69        11.97        17.16        34.98         0.62        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       10.22        47.80        17.42         2.66         6.74         6.58 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       12.16        17.88        19.50         5.06        14.96         8.25 
TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A8HY 
       12.79        12.59        12.13        12.16        12.62        11.34 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 
       29.79         1.84        66.41        18.41       112.44        17.95 
TCGA-DK-A2I2 TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC 
        7.79         8.15        15.02        19.00        15.35        43.59 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       22.16         0.56        26.96        24.03        13.68        12.95 
TCGA-FD-A3B5 TCGA-FD-A3SP TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A6TF 
        8.94        25.74        20.91         5.36         7.10         2.27 
TCGA-FT-A3EE TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A3OP 
        3.25        20.12        66.02        29.36         0.49         2.10 
TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI 
       18.97         4.73         7.00        14.27         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41S TCGA-MV-A51V TCGA-PQ-A6FI 
       11.70         1.81        11.80         1.15        13.48        12.23 
TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HC 
       38.99        76.01        69.34         3.02       112.83         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT 
        1.87        17.88        48.62         5.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RM 
        8.32        56.48        11.97        28.41        13.41        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H 
       20.22        59.38        67.20        35.41         8.52        29.49 
TCGA-GU-AATO 
       10.65 

$`AMP PEAK 32(17Q12) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        16.77        33.83        26.14        14.89 
TCGA-BT-A3PJ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E 
       25.94        18.58        12.92         4.90        18.48        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ 
       19.00        16.70       130.88        46.68         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30        23.21         9.67        64.18        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W 
       15.68        50.70        38.24        52.01       165.73        13.64 
TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SM 
       56.15        20.32         0.92         1.22        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       29.16        19.79        12.85        15.58        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TG TCGA-FD-A6TI 
        5.69         8.25        18.08         6.28         3.06         9.67 
TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3WC 
       17.23        11.08        33.01        17.62        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC 
       24.92        32.78        22.72        25.02         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-UY-A9PH 
       27.68        52.73        50.56        35.97        33.14        51.32 
TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
      125.49        34.45         4.21        12.76        11.90        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 
       54.90        98.99        44.32        30.94        61.45        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R 
        3.88         9.63        21.11         3.48        88.87        34.06 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       57.90        12.23        24.13        94.88       104.65         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       44.94        16.83        27.62        50.04        51.16        66.54 
TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20V 
        2.50        40.08         7.33        13.15        19.04         5.06 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S 
        1.94        23.01        12.56        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-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-DK-A1A3 
       12.10        11.34        11.87        13.08         5.19        21.86 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       16.14        17.62        15.62       142.78         4.80        13.58 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 
       20.81        10.55       163.30        13.58        18.81        12.03 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       38.83        29.72         5.36         2.24        16.70         0.66 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.24         4.24        24.66        14.07        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
        8.09        32.02        16.77        12.62        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N 
        5.52        22.98        14.96        19.33        27.45         2.70 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF 
       13.35        10.85        12.66        10.65         8.94        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C 
       48.00        15.95        26.93        59.31         7.23         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 
       20.71        15.81        15.91        14.07         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
       26.70         3.12        20.98         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-K4-A5RH TCGA-K4-A5RJ 
       20.05        15.78        21.34        19.10         9.07        17.72 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       15.42        16.27        44.38        15.32        15.58        21.07 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P 
       16.67        16.54        17.62        37.05        22.68        78.25 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       35.24        29.56        17.82         6.21         3.85        45.04 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
       92.98         6.77        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RF 
       22.36        25.41        31.20        35.84        21.86        64.08 
TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       58.72         2.89         8.61        60.16        56.35        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5N 
       54.21         5.52 

  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                        0.49                         0.66 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                      166.03                       165.73 
  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE 
                      15.980                       17.735 
[1] "0.5 - 166.0 (16.0)" "0.7 - 165.7 (17.7)"
[1] "hr=" "1.2"
D32V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 32(17Q12) MUTATED         0       48        54       62
  AMP PEAK 32(17Q12) WILD-TYPE       2       81        86       73
D32V3, multiclass
           clus
vv          AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  STAGE I                            0                            2
  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 32(17Q12) MUTATED         51  75  30
  AMP PEAK 32(17Q12) WILD-TYPE       72 120  28
D32V4, multiclass
          clus
vv         AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  T0+T1+T2                         51                           72
  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 32(17Q12) MUTATED    91  18  40   2
  AMP PEAK 32(17Q12) WILD-TYPE 145  29  35   6
D32V5, multiclass
    clus
vv   AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  N0                         91                          145
  N1                         18                           29
  N2                         40                           35
  N3                          2                            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"
D32V6, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED    71   4
  AMP PEAK 32(17Q12) WILD-TYPE 121   7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED     71    4
  AMP PEAK 32(17Q12) WILD-TYPE  121    7
   clus
vv  AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  0                         71                          121
  1                          4                            7
[1] 2 2
[1] FALSE
D32V7, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED    42 123
  AMP PEAK 32(17Q12) WILD-TYPE  65 178
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED     42  123
  AMP PEAK 32(17Q12) WILD-TYPE   65  178
        clus
vv       AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  FEMALE                         42                           65
  MALE                          123                          178
[1] 2 2
[1] FALSE
D32V8, binary
                              cls
clus                             0   1
  AMP PEAK 32(17Q12) MUTATED   154   5
  AMP PEAK 32(17Q12) WILD-TYPE 210  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED    154    5
  AMP PEAK 32(17Q12) WILD-TYPE  210   15
     clus
vv    AMP PEAK 32(17Q12) MUTATED AMP PEAK 32(17Q12) WILD-TYPE
  NO                         154                          210
  YES                          5                           15
[1] 2 2
[1] FALSE
D32V9, continuous
D32V10, continuous
D32V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 32(17Q12) MUTATED      14                         9   134
  AMP PEAK 32(17Q12) WILD-TYPE    29                        13   193
D32V12, multiclass
                           clus
vv                          AMP PEAK 32(17Q12) MUTATED
  ASIAN                                             14
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            134
                           clus
vv                          AMP PEAK 32(17Q12) WILD-TYPE
  ASIAN                                               29
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              193
[1] 3 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(17Q12) MUTATED     6 144
  AMP PEAK 32(17Q12) WILD-TYPE   3 225
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 32(17Q12) MUTATED      6  144
  AMP PEAK 32(17Q12) WILD-TYPE    3  225
                        clus
vv                       AMP PEAK 32(17Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        144
                        clus
vv                       AMP PEAK 32(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          225
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(17Q23.3) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 33(17Q23.3) MUTATED   102  89
  AMP PEAK 33(17Q23.3) WILD-TYPE 125  89
  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE 
                           191                            214 
  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE 
                            89                             89 
$`AMP PEAK 33(17Q23.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
       16.27        16.77        15.12        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-DK-A2I6 
        8.35        20.48        28.70         8.98        12.92        87.32 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 
       17.72        50.27        66.05        17.98        64.18        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 
       36.66       165.73       166.03        13.64        13.64        11.18 
TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SQ 
       25.58        33.04         4.01        60.66        24.30        46.78 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TE 
        3.62        26.73        58.92        62.86        18.81        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
        3.06         4.31         9.67        31.07        17.23        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       17.62        70.32        21.40        10.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU 
       20.28        27.35         8.58        19.07         9.01         3.45 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HF 
       46.98        14.24         1.84        86.83        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 
       15.35         3.22        14.93        21.04        26.27         2.24 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        13.74        10.82        11.31         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       91.73        86.30        13.64        30.28        94.29         3.48 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-2F-A9KR TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.06        19.69       104.65         0.62        41.75        51.16 
TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       47.80        17.42        40.08         2.66         6.74         6.58 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       12.16        17.88        19.50         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        8.25        17.16        12.79        12.56        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A8HY TCGA-CU-A3YL TCGA-CU-A5W6 
       12.13        12.16        12.62        11.34        29.79         1.84 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I2 
       66.41        18.41       112.44        16.14        17.95         7.79 
TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
        8.15        10.55        15.02        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME 
       43.59        22.16         0.56        26.96         4.24        24.03 
TCGA-E7-A7PW TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SP TCGA-FD-A43U TCGA-FD-A5BV 
       13.68        16.77         8.94        25.74        20.91         5.36 
TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EJ 
       27.45         7.10         2.27        10.65         3.25        48.00 
TCGA-G2-A2EO TCGA-G2-AA3F TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42R 
       59.31        29.36        26.70         2.10         2.20        18.97 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.00        14.27        21.34         8.48        19.40        38.60 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB 
       12.16        21.24         9.07        11.70         1.81        15.42 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI TCGA-SY-A9G5 
       11.80         1.15        15.32        13.48        12.23        38.99 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PD 
       37.05        22.68        76.01        69.34         3.02        17.82 
TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SU 
        6.21         6.58         1.87        17.88        48.62         5.98 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
      110.60         2.96         8.32         6.77        56.48        11.97 
TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4V 
       31.20        28.41        13.41        64.08        20.22        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-GU-AATO 
       67.20        35.41         8.52        29.49        10.65 

$`AMP PEAK 33(17Q23.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO 
      108.95        33.83        25.94         9.96        18.58         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       15.12        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
      130.88        46.68         8.22        21.30        23.21         9.67 
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-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SL 
       56.15        20.32        15.35         0.92         1.22        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y 
       17.98        29.16        19.79        12.85        27.35        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P 
       53.88        10.78         5.69         8.25        18.08         6.28 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
        6.15        12.69        33.01        19.13        17.75        24.92 
TCGA-GU-A763 TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       32.78        22.72        25.02         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HE 
       52.73        50.56        35.97        33.14        51.32       125.49 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T2 
       15.98        34.45         4.21        12.76        11.90        18.90 
TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       66.64        54.90        98.99        44.32        30.94        61.45 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA53 
       18.58         3.88         9.63        21.11        88.87        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N 
       12.23        24.13        11.97        94.88         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-5N-A9KI TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A2LB 
       10.22         2.50         7.33        13.15        19.04        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         1.94        23.01 
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-A9FF TCGA-CF-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3IK 
        5.19        21.86        17.62        15.62       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-E5-A4U1 
       13.58        20.81       163.30        13.58        18.81        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 
       29.72         5.36         2.24        16.70         0.66        26.24 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        14.07        12.95        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43N 
       32.02        12.62        22.52        27.98         5.52        22.98 
TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
       14.96        19.33         2.70        13.35        10.85        12.66 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE 
        8.94        61.94        15.95        26.93         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       66.02         6.94        20.71        15.81        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
        0.49         8.94        13.91         3.12        20.98        11.31 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QI 
        7.63        20.05        15.78         4.73        19.10        36.49 
TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A5RJ TCGA-K4-A83P TCGA-KQ-A41R TCGA-LT-A5Z6 
        1.51        64.01        17.72        16.27        44.38        15.58 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78P TCGA-UY-A8OD 
       21.07        16.67        16.54        17.62        78.25       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A9SH TCGA-XF-A9SI 
       35.24        29.56         3.85        45.04        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAN4 
       66.41        23.64        28.24        16.27        92.98        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 
       75.39        18.84         0.66        22.36        25.41        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W 
       21.86        58.72        47.84         2.89         8.61        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        19.40        54.21         5.52 

  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE 
                          0.56                           0.49 
  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE 
                        166.03                         163.30 
  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE 
                         16.77                          18.53 
[1] "0.6 - 166.0 (16.8)" "0.5 - 163.3 (18.5)"
[1] "hr=" "1.2"
D33V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 33(17Q23.3) MUTATED         1       50        66       76
  AMP PEAK 33(17Q23.3) WILD-TYPE       1       79        74       59
D33V3, multiclass
           clus
vv          AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(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 33(17Q23.3) MUTATED         53  94  32
  AMP PEAK 33(17Q23.3) WILD-TYPE       70 101  26
D33V4, multiclass
          clus
vv         AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(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 33(17Q23.3) MUTATED    99  25  46   4
  AMP PEAK 33(17Q23.3) WILD-TYPE 137  22  29   4
D33V5, multiclass
    clus
vv   AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE
  N0                           99                            137
  N1                           25                             22
  N2                           46                             29
  N3                            4                              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"
D33V6, binary
                                cls
clus                               0   1
  AMP PEAK 33(17Q23.3) MUTATED    86   5
  AMP PEAK 33(17Q23.3) WILD-TYPE 106   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(17Q23.3) MUTATED     86    5
  AMP PEAK 33(17Q23.3) WILD-TYPE  106    6
   clus
vv  AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE
  0                           86                            106
  1                            5                              6
[1] 2 2
[1] FALSE
D33V7, binary
                                cls
clus                               0   1
  AMP PEAK 33(17Q23.3) MUTATED    55 139
  AMP PEAK 33(17Q23.3) WILD-TYPE  52 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(17Q23.3) MUTATED     55  139
  AMP PEAK 33(17Q23.3) WILD-TYPE   52  162
        clus
vv       AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE
  FEMALE                           55                             52
  MALE                            139                            162
[1] 2 2
[1] FALSE
D33V8, binary
                                cls
clus                               0   1
  AMP PEAK 33(17Q23.3) MUTATED   173  10
  AMP PEAK 33(17Q23.3) WILD-TYPE 191  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(17Q23.3) MUTATED    173   10
  AMP PEAK 33(17Q23.3) WILD-TYPE  191   10
     clus
vv    AMP PEAK 33(17Q23.3) MUTATED AMP PEAK 33(17Q23.3) WILD-TYPE
  NO                           173                            191
  YES                           10                             10
[1] 2 2
[1] FALSE
D33V9, continuous
D33V10, continuous
D33V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 33(17Q23.3) MUTATED      18                         8   159
  AMP PEAK 33(17Q23.3) WILD-TYPE    25                        14   168
D33V12, multiclass
                           clus
vv                          AMP PEAK 33(17Q23.3) MUTATED
  ASIAN                                               18
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              159
                           clus
vv                          AMP PEAK 33(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"
D33V13, binary
                                cls
clus                               0   1
  AMP PEAK 33(17Q23.3) MUTATED     6 172
  AMP PEAK 33(17Q23.3) WILD-TYPE   3 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 33(17Q23.3) MUTATED      6  172
  AMP PEAK 33(17Q23.3) WILD-TYPE    3  197
                        clus
vv                       AMP PEAK 33(17Q23.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          172
                        clus
vv                       AMP PEAK 33(17Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            197
[1] 2 2
[1] FALSE

Clustering(34) Variable = AMP PEAK 34(19Q12) MUTATION ANALYSIS
D34V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 34(19Q12) MUTATED    97  66
  AMP PEAK 34(19Q12) WILD-TYPE 130 112
  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE 
                         163                          242 
  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE 
                          66                          112 
$`AMP PEAK 34(19Q12) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD 
       16.27        16.77        15.12        26.14         8.35        20.48 
TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 
       28.70        12.92        18.48        16.70        46.68        87.32 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6S 
       66.05        64.18        67.36        15.68        38.24       166.03 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A3SL 
       13.64        11.18        15.35         0.92        24.30        23.41 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BY TCGA-FD-A5C0 
       19.79        12.85        27.35         3.62         8.25        18.08 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.28        18.81         3.06         4.31        31.07        17.23 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3JZ 
       17.62        70.32        19.13        24.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-KQ-A41O 
       20.28        19.07         9.01        25.02         2.76        50.56 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HF 
       35.97        46.98        14.24         1.84        51.32        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9SY 
       15.35         3.22        15.98        14.93        12.76        21.04 
TCGA-XF-A9T3 TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 
        2.24        71.57        98.99        44.32        86.30        18.58 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-4Z-AA80 
        9.63        13.64        21.11        88.87        19.69         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13J 
       41.75        51.16        47.80         2.50        17.42         2.66 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
        6.74        19.04        12.16         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       16.18        36.43         1.94        23.01        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3YL 
       12.59        12.13        12.62        12.00        11.34        29.79 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IL 
       21.86        66.41        18.41       112.44       142.78        13.58 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ 
       15.02        19.00        12.03        43.59        38.83        22.16 
TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B3 
        0.56         4.24        24.03        13.68        12.95        32.02 
TCGA-FD-A3B8 TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A6TK TCGA-FT-A3EE 
       12.62        22.98        20.91        27.45        10.85         3.25 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RC 
       61.94        59.31        20.12        66.02        29.36        15.91 
TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ 
       14.07        13.91        26.70        18.97         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE 
       14.27        21.34         8.48        19.40        38.60        12.16 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-MV-A51V TCGA-SY-A9G5 
        9.07        17.72        15.42        11.80        13.48        38.99 
TCGA-UY-A78L TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HC 
       37.05        69.34         3.02        35.24        29.56         6.58 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       79.66         5.98        28.24         6.77        56.48        75.39 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       64.08        20.22        59.38        56.35        19.40         8.52 
TCGA-ZF-AA58 
       54.21 

$`AMP PEAK 34(19Q12) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A3PJ TCGA-BT-A3PK 
      108.95        33.83        12.39        14.89        25.94         9.96 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 
        8.98        18.58         4.90        15.12        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       19.00       130.88         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 
       23.21         9.67        17.98        53.29        76.60        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       36.66        52.01       165.73        13.64        56.15        20.32 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SM 
       25.58         1.22        33.04         4.01        60.66        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       29.16        46.78        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
        5.69        58.92        62.86         6.15        12.69        12.36 
TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GU-A42P 
        9.67        11.08        33.01        21.40        17.75        10.92 
TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-A4AC 
       32.78        27.35         8.58        22.72         3.45         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       27.68        52.73        33.14        86.83        97.45       125.49 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 
       34.45         4.21        11.90        26.27        18.90        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       91.73        30.94        61.45         3.88        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
        3.48        34.06        57.90        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A0C8 
       34.98        27.62        50.04        66.54        10.22        40.08 
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        7.33         6.58        13.15        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-CF-A27C TCGA-CF-A3MH 
       14.96         4.67        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-A9FM TCGA-CU-A3QU 
       13.12        12.10        11.34        11.87        13.08         5.19 
TCGA-CU-A5W6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
        1.84        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
        4.80         8.15        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       18.81        15.35        29.72         5.36         2.24        16.70 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
        0.66        26.96        26.24        24.66        14.07        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37         8.09        16.77         8.94        22.52        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N 
        5.52        25.74        14.96        19.33         5.36         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35         2.27        12.66        10.65         8.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 
       48.00        15.95        26.93         7.23         6.94        20.71 
TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.81         0.49         8.94         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JX 
        2.20        11.31         7.63        20.05        15.78        19.10 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ 
       36.49         1.51        64.01        21.24        11.70         1.81 
TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       16.27        44.38         1.15        15.32        15.58        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O 
       12.23        16.67        16.54        17.62        22.68        76.01 
TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       78.25       112.83        17.82         6.21         3.85        45.04 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
        1.87        17.88        48.62        64.80        66.41        23.64 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 
       16.27        92.98       110.60         2.96         8.32        27.06 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM 
       35.84        21.86        28.41        13.41        58.72        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
        2.89         8.61        60.16        67.20        35.41        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE 
                        0.56                         0.49 
  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE 
                      166.03                       165.73 
  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE 
                      18.810                       16.735 
[1] "0.6 - 166.0 (18.8)" "0.5 - 165.7 (16.7)"
[1] "hr=" "1.2"
D34V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 34(19Q12) MUTATED         0       43        57       63
  AMP PEAK 34(19Q12) WILD-TYPE       2       86        83       72
D34V3, multiclass
           clus
vv          AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE
  STAGE I                            0                            2
  STAGE II                          43                           86
  STAGE III                         57                           83
  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 34(19Q12) MUTATED         41  85  26
  AMP PEAK 34(19Q12) WILD-TYPE       82 110  32
D34V4, multiclass
          clus
vv         AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE
  T0+T1+T2                         41                           82
  T3                               85                          110
  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
  AMP PEAK 34(19Q12) MUTATED    85  22  38   3
  AMP PEAK 34(19Q12) WILD-TYPE 151  25  37   5
D34V5, multiclass
    clus
vv   AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE
  N0                         85                          151
  N1                         22                           25
  N2                         38                           37
  N3                          3                            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
  AMP PEAK 34(19Q12) MUTATED    77   5
  AMP PEAK 34(19Q12) WILD-TYPE 115   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 34(19Q12) MUTATED     77    5
  AMP PEAK 34(19Q12) WILD-TYPE  115    6
   clus
vv  AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE
  0                         77                          115
  1                          5                            6
[1] 2 2
[1] FALSE
D34V7, binary
                              cls
clus                             0   1
  AMP PEAK 34(19Q12) MUTATED    39 125
  AMP PEAK 34(19Q12) WILD-TYPE  68 176
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 34(19Q12) MUTATED     39  125
  AMP PEAK 34(19Q12) WILD-TYPE   68  176
        clus
vv       AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE
  FEMALE                         39                           68
  MALE                          125                          176
[1] 2 2
[1] FALSE
D34V8, binary
                              cls
clus                             0   1
  AMP PEAK 34(19Q12) MUTATED   146   5
  AMP PEAK 34(19Q12) WILD-TYPE 218  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 34(19Q12) MUTATED    146    5
  AMP PEAK 34(19Q12) WILD-TYPE  218   15
     clus
vv    AMP PEAK 34(19Q12) MUTATED AMP PEAK 34(19Q12) WILD-TYPE
  NO                         146                          218
  YES                          5                           15
[1] 2 2
[1] FALSE
D34V9, continuous
D34V10, continuous
D34V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 34(19Q12) MUTATED      16                         7   132
  AMP PEAK 34(19Q12) WILD-TYPE    27                        15   195
D34V12, multiclass
                           clus
vv                          AMP PEAK 34(19Q12) MUTATED
  ASIAN                                             16
  BLACK OR AFRICAN AMERICAN                          7
  WHITE                                            132
                           clus
vv                          AMP PEAK 34(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"
D34V13, binary
                              cls
clus                             0   1
  AMP PEAK 34(19Q12) MUTATED     3 145
  AMP PEAK 34(19Q12) WILD-TYPE   6 224
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 34(19Q12) MUTATED      3  145
  AMP PEAK 34(19Q12) WILD-TYPE    6  224
                        clus
vv                       AMP PEAK 34(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        145
                        clus
vv                       AMP PEAK 34(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          224
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 35(19Q13.43) MUTATION ANALYSIS
D35V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 35(19Q13.43) MUTATED    90  64
  AMP PEAK 35(19Q13.43) WILD-TYPE 137 114
  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE 
                            154                             251 
  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE 
                             64                             114 
$`AMP PEAK 35(19Q13.43) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.27        16.77        15.12        26.14        20.48        25.94 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A1AC 
       28.70         8.98        15.12        18.48        16.70       130.88 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L 
        9.67        17.98        64.18        67.36        15.68        38.24 
TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
      166.03        13.64        11.18        15.35        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BT 
        1.22        23.41        12.85         3.62        15.58        10.78 
TCGA-FD-A5BY TCGA-FD-A6TB TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GC-A3YS 
        8.25        18.81         4.31        31.07        17.23        24.92 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A4AB 
       32.98        19.82        20.28        19.07         9.01         2.76 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK 
       50.56        46.98         1.84        97.12        15.35        15.98 
TCGA-XF-A9T3 TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN7 
        2.24        71.57        98.99        44.32        86.30        18.58 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
        9.63        21.11        30.28        88.87        34.06        19.69 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13J 
        0.62        41.75        51.16        47.80        17.42         2.66 
TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42E 
        6.74        19.04         5.06         8.25        16.18        36.43 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG 
        1.94        23.01        12.79        12.56        12.59        12.13 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 
       12.62        12.00        11.34        29.79        21.86        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       18.41       112.44       142.78         4.80        13.58         8.15 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A5KE 
       15.02        19.00        12.03        43.59        22.16         0.56 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B5 
        4.24        24.03        12.95         8.09        32.02         8.94 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FT-A3EE 
       22.98        20.91        27.45         2.27        10.85         3.25 
TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-GC-A3RC TCGA-GC-A3RD 
       61.94        59.31        20.12        66.02        15.91        14.07 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A764 
       13.91        26.70         3.12        20.98        18.97        20.05 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ 
        7.00        14.27        21.34         8.48        36.49        19.40 
TCGA-HQ-A2OE TCGA-K4-A6MB TCGA-K4-AAQO TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       38.60        15.42        11.80        16.54        17.62        37.05 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A8HB 
       69.34         3.02        35.24        29.56        17.82        45.04 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN0 
       79.66         5.98        23.64       110.60         6.77        56.48 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R7 TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 
       75.39        18.84        21.86        20.22        59.38        56.35 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-GU-AATO 
       19.40         8.52        54.21        10.65 

$`AMP PEAK 35(19Q13.43) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PK 
      108.95        33.83        12.39        14.89         8.35         9.96 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58        12.92         4.90        13.58         2.14        19.00 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B5 TCGA-DK-A6B6 
       23.21        66.05        53.29        76.60        50.70        36.66 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA77 TCGA-FD-A3B6 
       52.01       165.73        13.64        56.15        20.32        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        4.01        60.66        24.30        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A5C0 
       19.79        27.35        26.73        53.88         5.69        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       58.92         6.28        62.86         6.15        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        3.06         9.67        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QK 
       21.40        19.13        17.75        10.92        32.78        27.35 
TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R 
        8.58        22.72        25.02         3.45         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       52.73        35.97        14.24        33.14        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       97.45       125.49         3.22        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 
       12.76        11.90        21.04        26.27        18.90        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YF-AA3M TCGA-ZF-A9RC 
       91.73        30.94        61.45         3.88        13.64        94.29 
TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
        3.48        57.90        12.23        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
      104.65         8.35        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A0C8 
       27.62        50.04        66.54        10.22         2.50        40.08 
TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        7.33         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F 
        5.06        14.96        17.16         4.67        17.56        28.41 
TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       13.97        13.08        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF 
       12.10        12.26        13.12        12.10        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       13.08         5.19         1.84        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
       17.95         7.79        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       18.81        15.35        38.83        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW 
       16.70         0.66        26.96        26.24        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.07        15.32        14.37        16.77        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV 
       27.98         5.52        25.74        14.96        19.33         5.36 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        2.70         7.10        13.35        12.66        10.65         8.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F 
       48.00        15.95        26.93         7.23         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 
       20.71        15.81         0.49         8.94         2.10         2.20 
TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-H4-A2HO 
       11.31         7.63        15.78         4.73        19.10         1.51 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       64.01        12.16        21.24         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        16.27        44.38         1.15        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78M 
       21.07        13.48        12.23        16.67        38.99        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC 
       76.01        78.25       112.83         6.21         3.85         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SZ 
        1.87        17.88        48.62        64.80        66.41        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 TCGA-YC-A9TC 
       16.27        92.98         2.96         8.32        27.06         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
       11.97        22.36        25.41        31.20        35.84        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U 
       13.41        64.08        58.72        47.84         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       60.16        67.20        35.41        29.49         5.52 

  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE 
                           0.56                            0.49 
  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE 
                         166.03                          165.73 
  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE 
                         18.825                          16.770 
[1] "0.6 - 166.0 (18.8)" "0.5 - 165.7 (16.8)"
[1] "hr=" "1.2"
D35V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 35(19Q13.43) MUTATED         0       41        52       61
  AMP PEAK 35(19Q13.43) WILD-TYPE       2       88        88       74
D35V3, multiclass
           clus
vv          AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE
  STAGE I                               0                               2
  STAGE II                             41                              88
  STAGE III                            52                              88
  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 35(19Q13.43) MUTATED         36  75  28
  AMP PEAK 35(19Q13.43) WILD-TYPE       87 120  30
D35V4, multiclass
          clus
vv         AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE
  T0+T1+T2                            36                              87
  T3                                  75                             120
  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 35(19Q13.43) MUTATED    78  24  33   4
  AMP PEAK 35(19Q13.43) WILD-TYPE 158  23  42   4
D35V5, multiclass
    clus
vv   AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE
  N0                            78                             158
  N1                            24                              23
  N2                            33                              42
  N3                             4                               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"
D35V6, binary
                                 cls
clus                                0   1
  AMP PEAK 35(19Q13.43) MUTATED    70   5
  AMP PEAK 35(19Q13.43) WILD-TYPE 122   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(19Q13.43) MUTATED     70    5
  AMP PEAK 35(19Q13.43) WILD-TYPE  122    6
   clus
vv  AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE
  0                            70                             122
  1                             5                               6
[1] 2 2
[1] FALSE
D35V7, binary
                                 cls
clus                                0   1
  AMP PEAK 35(19Q13.43) MUTATED    43 112
  AMP PEAK 35(19Q13.43) WILD-TYPE  64 189
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(19Q13.43) MUTATED     43  112
  AMP PEAK 35(19Q13.43) WILD-TYPE   64  189
        clus
vv       AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE
  FEMALE                            43                              64
  MALE                             112                             189
[1] 2 2
[1] FALSE
D35V8, binary
                                 cls
clus                                0   1
  AMP PEAK 35(19Q13.43) MUTATED   136   4
  AMP PEAK 35(19Q13.43) WILD-TYPE 228  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(19Q13.43) MUTATED    136    4
  AMP PEAK 35(19Q13.43) WILD-TYPE  228   16
     clus
vv    AMP PEAK 35(19Q13.43) MUTATED AMP PEAK 35(19Q13.43) WILD-TYPE
  NO                            136                             228
  YES                             4                              16
[1] 2 2
[1] FALSE
D35V9, continuous
D35V10, continuous
D35V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 35(19Q13.43) MUTATED      13                         8   126
  AMP PEAK 35(19Q13.43) WILD-TYPE    30                        14   201
D35V12, multiclass
                           clus
vv                          AMP PEAK 35(19Q13.43) MUTATED
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               126
                           clus
vv                          AMP PEAK 35(19Q13.43) WILD-TYPE
  ASIAN                                                  30
  BLACK OR AFRICAN AMERICAN                              14
  WHITE                                                 201
[1] 3 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
  AMP PEAK 35(19Q13.43) MUTATED     3 135
  AMP PEAK 35(19Q13.43) WILD-TYPE   6 234
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(19Q13.43) MUTATED      3  135
  AMP PEAK 35(19Q13.43) WILD-TYPE    6  234
                        clus
vv                       AMP PEAK 35(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           135
                        clus
vv                       AMP PEAK 35(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             234
[1] 2 2
[1] FALSE

Clustering(36) Variable = AMP PEAK 36(20Q11.21) MUTATION ANALYSIS
D36V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 36(20Q11.21) MUTATED   143 118
  AMP PEAK 36(20Q11.21) WILD-TYPE  84  60
  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE 
                            261                             144 
  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE 
                            118                              60 
$`AMP PEAK 36(20Q11.21) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD 
      108.95        16.27        26.14        14.89         8.35        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        9.96        28.70         8.98        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       18.48         2.14       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       17.72        50.27        23.21         9.67        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 
       52.01       165.73       166.03        13.64        13.64        56.15 
TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       11.18        15.35        25.58         1.22        33.04         4.01 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        24.30        23.41        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BT TCGA-FD-A5C0 TCGA-FD-A5C1 
       27.35         3.62        26.73        10.78        18.08        58.92 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
       18.81         6.15        12.69        12.36         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       31.07        11.08        17.62        70.32        21.40        19.13 
TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       24.92        32.98        19.82        20.28         8.58        19.07 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       25.02         3.45         9.14        50.56        35.97        46.98 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF 
        1.84        33.14        86.83        51.32        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV 
       15.35         3.22        15.98        34.45        14.93        12.76 
TCGA-XF-A9SY TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML 
       21.04         2.24        66.64         2.10        10.82         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-YF-AA3M 
       71.57        91.73        98.99        44.32        30.94        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P 
       21.11        30.28        94.29        88.87        19.69        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7W 
       24.13        11.97       104.65        44.94        34.98        27.62 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
        2.50        17.42        40.08         2.66         6.74         6.58 
TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X 
       19.04        17.88        19.50         5.06         5.06         8.25 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS 
       36.43        28.41         1.94        23.01        12.79        12.56 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47X 
       12.59        12.13        12.16        10.95        12.66        12.62 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
       11.34        11.34         1.84        66.41        18.41       112.44 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 
       10.55        15.02        19.00        15.35        43.59        38.83 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H 
       22.16         0.56         4.24        24.03        13.68        12.95 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BZ 
        8.09        32.02        22.52        25.74        22.98        27.45 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-FT-A3EE 
        7.10        13.35         2.27        10.85        10.65         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3F 
       61.94        48.00        15.95        59.31        66.02        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       20.71        15.81        15.91        14.07         0.49         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91        26.70         2.10        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       18.97        20.05        15.78         7.00        14.27        21.34 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       19.10         8.48        36.49        19.40        38.60        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-AAQO 
       12.16        21.24         9.07        11.70         1.81        11.80 
TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 
        1.15        15.58        13.48        12.23        16.67        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC 
       17.62        37.05        22.68        76.01        69.34         3.02 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HH 
       35.24        29.56         6.21         3.85        45.04         1.87 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAMT TCGA-XF-AAMX 
       79.66         5.98        23.64        16.27         2.96         6.77 
TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       18.84        22.36        25.41        31.20        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       13.41        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 
       59.38        67.20        56.35        35.41        19.40        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

$`AMP PEAK 36(20Q11.21) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A3PJ TCGA-CF-A9FL 
       16.77        15.12        33.83        12.39        25.94        18.58 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IT TCGA-DK-A6AW TCGA-DK-A6B0 
       13.58        19.00        16.70        21.30        53.29        76.60 
TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A43Y TCGA-FD-A5BS 
       20.32         0.92        17.98        29.16        15.58        53.88 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FJ-A3ZF 
        5.69         8.25         6.28        62.86         3.06        17.23 
TCGA-G2-A2ES TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A6ZA 
       33.01        17.75        10.92        32.78        27.35        22.72 
TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-R3-A69X TCGA-XF-A8HE 
        9.01         2.76        27.68        52.73        14.24       125.49 
TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAMH 
        4.21        11.90        26.27        18.90        13.74        11.31 
TCGA-XF-AAMJ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       54.90        61.45        86.30        18.58         3.88         9.63 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7O 
        3.48        34.06        57.90        94.88         8.35        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20U 
       17.16        50.04         7.33        13.15        12.16        14.96 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-CF-A27C TCGA-CF-A3MH 
       17.16        16.18         4.67        17.56        13.97        13.08 
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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AE 
       11.87        13.08         5.19        29.79        21.86        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
       17.62        15.62        20.81       163.30        13.58        18.81 
TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       12.03        29.72         5.36         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P 
       26.96        26.24        24.66        14.07        15.32        14.37 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43S 
       16.77         8.94        12.62        27.98         5.52        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FJ-A3Z9 TCGA-FJ-A871 
       20.91        19.33         5.36         2.70        12.66         8.94 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GD-A3OQ TCGA-GU-A762 
       26.93         7.23        20.12         6.94         3.12         7.63 
TCGA-GU-A767 TCGA-H4-A2HO TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R 
        4.73         1.51        17.72        15.42        16.27        44.38 
TCGA-LC-A66R TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A8OD TCGA-UY-A9PD 
       15.32        21.07        16.54        78.25       112.83        17.82 
TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SZ 
        6.58        17.88        48.62        64.80        66.41        28.24 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 
       92.98       110.60         8.32        56.48        27.06        75.39 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R5 TCGA-ZF-A9RF TCGA-ZF-AA4W TCGA-ZF-AA56 
        0.66        11.97        35.84        64.08        60.16         8.52 

  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE 
                           0.49                            0.66 
  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE 
                         166.03                          163.30 
  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE 
                          18.84                           16.70 
[1] "0.5 - 166.0 (18.8)" "0.7 - 163.3 (16.7)"
[1] "hr=" "1"  
D36V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 36(20Q11.21) MUTATED         1       80        86       95
  AMP PEAK 36(20Q11.21) WILD-TYPE       1       49        54       40
D36V3, multiclass
           clus
vv          AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE
  STAGE I                               1                               1
  STAGE II                             80                              49
  STAGE III                            86                              54
  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
  AMP PEAK 36(20Q11.21) MUTATED         77 125  39
  AMP PEAK 36(20Q11.21) WILD-TYPE       46  70  19
D36V4, multiclass
          clus
vv         AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE
  T0+T1+T2                            77                              46
  T3                                 125                              70
  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 36(20Q11.21) MUTATED   139  32  54   8
  AMP PEAK 36(20Q11.21) WILD-TYPE  97  15  21   0
D36V5, multiclass
    clus
vv   AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE
  N0                           139                              97
  N1                            32                              15
  N2                            54                              21
  N3                             8                               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"
D36V6, binary
                                 cls
clus                                0   1
  AMP PEAK 36(20Q11.21) MUTATED   120   8
  AMP PEAK 36(20Q11.21) WILD-TYPE  72   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(20Q11.21) MUTATED    120    8
  AMP PEAK 36(20Q11.21) WILD-TYPE   72    3
   clus
vv  AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE
  0                           120                              72
  1                             8                               3
[1] 2 2
[1] FALSE
D36V7, binary
                                 cls
clus                                0   1
  AMP PEAK 36(20Q11.21) MUTATED    74 189
  AMP PEAK 36(20Q11.21) WILD-TYPE  33 112
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(20Q11.21) MUTATED     74  189
  AMP PEAK 36(20Q11.21) WILD-TYPE   33  112
        clus
vv       AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE
  FEMALE                            74                              33
  MALE                             189                             112
[1] 2 2
[1] FALSE
D36V8, binary
                                 cls
clus                                0   1
  AMP PEAK 36(20Q11.21) MUTATED   234  11
  AMP PEAK 36(20Q11.21) WILD-TYPE 130   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(20Q11.21) MUTATED    234   11
  AMP PEAK 36(20Q11.21) WILD-TYPE  130    9
     clus
vv    AMP PEAK 36(20Q11.21) MUTATED AMP PEAK 36(20Q11.21) WILD-TYPE
  NO                            234                             130
  YES                            11                               9
[1] 2 2
[1] FALSE
D36V9, continuous
D36V10, continuous
D36V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 36(20Q11.21) MUTATED      19                        12   219
  AMP PEAK 36(20Q11.21) WILD-TYPE    24                        10   108
D36V12, multiclass
                           clus
vv                          AMP PEAK 36(20Q11.21) MUTATED
  ASIAN                                                19
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               219
                           clus
vv                          AMP PEAK 36(20Q11.21) WILD-TYPE
  ASIAN                                                  24
  BLACK OR AFRICAN AMERICAN                              10
  WHITE                                                 108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                                 cls
clus                                0   1
  AMP PEAK 36(20Q11.21) MUTATED     4 236
  AMP PEAK 36(20Q11.21) WILD-TYPE   5 133
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 36(20Q11.21) MUTATED      4  236
  AMP PEAK 36(20Q11.21) WILD-TYPE    5  133
                        clus
vv                       AMP PEAK 36(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           236
                        clus
vv                       AMP PEAK 36(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             133
[1] 2 2
[1] FALSE

Clustering(37) Variable = AMP PEAK 37(22Q12.2) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 37(22Q12.2) MUTATED    50  37
  AMP PEAK 37(22Q12.2) WILD-TYPE 177 141
  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE 
                            87                            318 
  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE 
                            37                            141 
$`AMP PEAK 37(22Q12.2) MUTATED`
TCGA-BT-A20W TCGA-BT-A3PJ TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU 
        8.35        25.94        87.32         8.22        50.27        23.21 
TCGA-DK-AA6L TCGA-DK-AA6S TCGA-DK-AA77 TCGA-E7-A541 TCGA-FD-A3B6 TCGA-FD-A3B7 
       38.24       166.03        20.32        25.58        33.04         4.01 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BT TCGA-G2-A2ES TCGA-G2-AA3D 
       23.41        29.16        27.35        10.78        33.01        70.32 
TCGA-GC-A3BM TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-KQ-A41P 
       21.40        19.82        27.35         8.58        19.07        35.97 
TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       46.98         1.84        33.14        34.45        14.93         4.21 
TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       26.27         2.10         7.63        71.57        91.73        98.99 
TCGA-ZF-A9R4 TCGA-ZF-AA4R TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7S 
       30.28        34.06       104.65         8.35        44.94        34.98 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A2LB TCGA-C4-A0F6 
       10.22        47.80        17.42        40.08        16.18        23.01 
TCGA-CF-A3MF TCGA-CF-A8HY TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A3WX 
       12.59        11.34        66.41        18.41       112.44        10.55 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A85H TCGA-FD-A5BV 
       15.02        19.00        22.16         0.56        12.95         5.36 
TCGA-FD-A62O TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A3RD 
        7.10        61.94        59.31        66.02        20.71        14.07 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3QH 
        0.49        26.70        20.05         4.73        14.27         8.48 
TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-UY-A78L TCGA-UY-A78O 
       36.49        38.60        44.38        15.58        37.05        76.01 
TCGA-UY-A8OD TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-AAMG TCGA-XF-AAMW 
      112.83         6.21        48.62        79.66       110.60         8.32 
TCGA-XF-AAMX TCGA-ZF-A9R0 TCGA-ZF-A9RF 
        6.77        22.36        64.08 

$`AMP PEAK 37(22Q12.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       26.14        14.89        20.48         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IQ 
        2.14        19.00        16.70       130.88        46.68        17.72 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       21.30         9.67        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M 
       76.60        67.36        15.68        50.70        36.66        52.01 
TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ 
      165.73        13.64        13.64        56.15        11.18        15.35 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SQ 
        0.92         1.22        60.66        24.30        17.98        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS 
       19.79        12.85         3.62        15.58        26.73        53.88 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
        5.69         8.25        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3RB 
        9.67        31.07        17.23        11.08        17.62        19.13 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF 
       17.75        24.92        10.92        32.78        32.98        20.28 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-R3-A69X TCGA-UY-A78N TCGA-UY-A9PH 
       27.68        52.73        50.56        14.24        86.83        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.45       125.49        97.12        15.35         3.22        15.98 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       12.76        11.90        21.04        18.90         2.24        66.64 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMZ TCGA-XF-AAN1 
       13.74        10.82        11.31        54.90        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       61.45        86.30        18.58         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 
       21.11        94.29         3.48        88.87        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7O TCGA-4Z-AA7R 
       12.23        24.13        11.97        94.88        16.83        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-5N-A9KI TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
        2.50         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG 
       28.41         1.94        12.79        12.56        13.97        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-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-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.87        13.08         5.19        29.79         1.84        21.86 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q 
        4.80        13.58         8.15        20.81       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        15.35        12.03        43.59        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        5.36         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
        4.24        24.03        24.66        13.68        14.07        15.32 
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-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF 
       20.91        19.33        27.45         2.70        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ 
       10.85        12.66        10.65         8.94         3.25        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F 
       15.95        26.93         7.23        20.12         6.94        29.36 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.81        15.91         8.94        13.91         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 
       20.98         2.20        11.31        18.97         7.63        15.78 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        7.00        21.34        19.10         1.51        19.40        64.01 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT 
       15.42        16.27        11.80         1.15        15.32        21.07 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K 
       13.48        12.23        16.67        16.54        38.99        17.62 
TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB 
       22.68        78.25        69.34         3.02        35.24        29.56 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI 
       17.82         3.85        45.04         6.58         1.87        17.88 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        66.41         5.98        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       92.98         2.96        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
        0.66        11.97        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       28.41        13.41        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       19.40         8.52        54.21        29.49         5.52        10.65 

  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE 
                          0.49                           0.62 
  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE 
                        166.03                         165.73 
  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE 
                        23.410                         16.605 
[1] "0.5 - 166.0 (23.4)" "0.6 - 165.7 (16.6)"
[1] "hr=" "1.4"
D37V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 37(22Q12.2) MUTATED         1       30        34       21
  AMP PEAK 37(22Q12.2) WILD-TYPE       1       99       106      114
D37V3, multiclass
           clus
vv          AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(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 37(22Q12.2) MUTATED         29  41  10
  AMP PEAK 37(22Q12.2) WILD-TYPE       94 154  48
D37V4, multiclass
          clus
vv         AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(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 37(22Q12.2) MUTATED    58   8  11   2
  AMP PEAK 37(22Q12.2) WILD-TYPE 178  39  64   6
D37V5, multiclass
    clus
vv   AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE
  N0                           58                            178
  N1                            8                             39
  N2                           11                             64
  N3                            2                              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"
D37V6, binary
                                cls
clus                               0   1
  AMP PEAK 37(22Q12.2) MUTATED    41   2
  AMP PEAK 37(22Q12.2) WILD-TYPE 151   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(22Q12.2) MUTATED     41    2
  AMP PEAK 37(22Q12.2) WILD-TYPE  151    9
   clus
vv  AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE
  0                           41                            151
  1                            2                              9
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                               0   1
  AMP PEAK 37(22Q12.2) MUTATED    22  65
  AMP PEAK 37(22Q12.2) WILD-TYPE  85 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(22Q12.2) MUTATED     22   65
  AMP PEAK 37(22Q12.2) WILD-TYPE   85  236
        clus
vv       AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE
  FEMALE                           22                             85
  MALE                             65                            236
[1] 2 2
[1] FALSE
D37V8, binary
                                cls
clus                               0   1
  AMP PEAK 37(22Q12.2) MUTATED    79   4
  AMP PEAK 37(22Q12.2) WILD-TYPE 285  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(22Q12.2) MUTATED     79    4
  AMP PEAK 37(22Q12.2) WILD-TYPE  285   16
     clus
vv    AMP PEAK 37(22Q12.2) MUTATED AMP PEAK 37(22Q12.2) WILD-TYPE
  NO                            79                            285
  YES                            4                             16
[1] 2 2
[1] FALSE
D37V9, continuous
D37V10, continuous
D37V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 37(22Q12.2) MUTATED       6                         7    70
  AMP PEAK 37(22Q12.2) WILD-TYPE    37                        15   257
D37V12, multiclass
                           clus
vv                          AMP PEAK 37(22Q12.2) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               70
                           clus
vv                          AMP PEAK 37(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"
D37V13, binary
                                cls
clus                               0   1
  AMP PEAK 37(22Q12.2) MUTATED     3  75
  AMP PEAK 37(22Q12.2) WILD-TYPE   6 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(22Q12.2) MUTATED      3   75
  AMP PEAK 37(22Q12.2) WILD-TYPE    6  294
                        clus
vv                       AMP PEAK 37(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       AMP PEAK 37(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            294
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    48  42
  DEL PEAK  1(1P36.11) WILD-TYPE 179 136
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            90                            315 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            42                            136 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK 
       16.77        15.12        14.89         8.35        20.48         9.96 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A6B6 TCGA-DK-AA74 
       15.12        18.48        17.72        21.30        36.66        56.15 
TCGA-FD-A43Y TCGA-FD-A5C1 TCGA-FD-A6TE TCGA-FD-A6TG TCGA-G2-AA3D TCGA-GU-A763 
       15.58        58.92        12.36         3.06        70.32        32.78 
TCGA-GU-AATP TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AC TCGA-KQ-A41P TCGA-KQ-A41Q 
       32.98        22.72        25.02         9.14        35.97        46.98 
TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SV 
       97.12        15.35         3.22        15.98         4.21        12.76 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-ZF-A9R4 TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-2F-A9KO 
       30.94        61.45        30.28        88.87        57.90        24.13 
TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-BT-A0S7 
        8.35        17.16        34.98         0.62        10.22         6.58 
TCGA-BT-A20J TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MI 
       19.04        17.56        36.43        12.79        12.56        12.16 
TCGA-CF-A47X TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A3WX 
       12.62         1.84        18.41        16.14         7.79        10.55 
TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-FD-A3B5 
       13.58        19.00        15.35        12.03        43.59         8.94 
TCGA-FD-A3SO TCGA-FD-A5BU TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-AA3F TCGA-GU-A764 
        5.52        19.33        10.65        26.93        29.36        20.05 
TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3QI TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RJ 
       15.78        14.27        36.49        64.01        21.24        17.72 
TCGA-K4-A6MB TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78M 
       15.42        44.38        15.58        13.48        12.23        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-XF-A9SU 
       76.01        69.34       112.83        29.56        17.82         5.98 
TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN5 TCGA-ZF-A9R3 TCGA-ZF-AA54 
       23.64       110.60         6.77        75.39        31.20        19.40 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A3PJ 
      108.95        16.27        33.83        12.39        26.14        25.94 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A72E 
       28.70         8.98        18.58        12.92         4.90        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        2.14        19.00        16.70       130.88        46.68        87.32 
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-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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       38.24        52.01       165.73       166.03        13.64        13.64 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X 
       29.16        46.78        19.79        12.85        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 
       26.73        53.88        10.78         5.69         8.25        18.08 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TH 
        6.28        62.86        18.81         6.15        12.69         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        9.67        31.07        17.23        11.08        33.01        17.62 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JZ 
       21.40        19.13        17.75        24.92        10.92        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU 
       20.28        27.35         8.58        19.07         9.01         3.45 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-R3-A69X TCGA-S5-A6DX 
        2.76        27.68        52.73        50.56        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SM 
       33.14        86.83        51.32        97.45       125.49        34.45 
TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       14.93        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
       66.64         2.10        13.74        10.82        11.31        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 
        7.63        71.57        91.73        98.99        44.32        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       18.58         3.88         9.63        13.64        21.11        94.29 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KQ 
        3.48        34.06        19.69        12.23        11.97        94.88 
TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 
      104.65        44.94        16.83        27.62        50.04        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       51.16        66.54        47.80         2.50        17.42        40.08 
TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33         2.66         6.74        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA 
       19.50         5.06        14.96         5.06         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C 
       16.18         4.67        28.41         1.94        23.01        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.59        12.13        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-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
       11.34        11.87        13.08         5.19        29.79        21.86 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 
       66.41       112.44        17.62        15.62        17.95       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P 
        4.80        13.58         8.15        20.81       163.30        15.02 
TCGA-DK-AA6T TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       18.81        38.83        29.72         5.36        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-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 
       24.03        24.66        13.68        14.07        12.95        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-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV 
       27.98        25.74        22.98        14.96        20.91         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66         8.94         3.25        61.94        48.00        15.95 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 
       59.31         7.23        20.12        66.02         6.94        20.71 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
       15.81        15.91        14.07         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       26.70         2.10         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
       18.97         7.63         4.73         7.00        21.34        19.10 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RH 
        8.48         1.51        19.40        38.60        12.16         9.07 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R 
       11.70         1.81        16.27        11.80         1.15        15.32 
TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        16.67        16.54        38.99        17.62        37.05 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
       78.25         3.02        35.24         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
        6.58         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW 
       66.41        28.24        16.27        92.98         2.96         8.32 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 
       56.48        27.06        18.84         0.66        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       25.41        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 
       60.16        67.20        56.35        35.41         8.52        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       29.49         5.52        10.65 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.62                           0.49 
  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 
                         17.77                          17.62 
[1] "0.6 - 112.8 (17.8)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1"  
D38V2, 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
D38V3, 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
D38V4, 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 183  32  64   4
D38V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           53                            183
  N1                           15                             32
  N2                           11                             64
  N3                            4                              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"
D38V6, 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
D38V7, 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
D38V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    85   3
  DEL PEAK  1(1P36.11) WILD-TYPE 279  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     85    3
  DEL PEAK  1(1P36.11) WILD-TYPE  279   17
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                            85                            279
  YES                            3                             17
[1] 2 2
[1] FALSE
D38V9, continuous
D38V10, continuous
D38V11, 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
D38V12, 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"
D38V13, 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(39) Variable = DEL PEAK  2(1Q32.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1Q32.1) MUTATED    38  34
  DEL PEAK  2(1Q32.1) WILD-TYPE 189 144
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           72                           333 
  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                           34                           144 
$`DEL PEAK  2(1Q32.1) MUTATED`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ 
       16.77        15.12        26.14        14.89         8.35        25.94 
TCGA-BT-A3PK TCGA-CU-A0YO TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IS 
        9.96         4.90        46.68        87.32        17.72        50.27 
TCGA-DK-A3X1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-FD-A3SL TCGA-FD-A3SR TCGA-FD-A5C0 
       66.05        15.68        36.66        23.41        19.79        18.08 
TCGA-FD-A62P TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-G2-A3VY TCGA-G2-AA3D 
        6.28        12.36         4.31        31.07        17.62        70.32 
TCGA-GV-A3JZ TCGA-GV-A40E TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-S5-A6DX TCGA-XF-A8HF 
       19.82         8.58        22.72         3.45         1.84        97.12 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMQ TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 
        2.10        10.82        71.57        44.32        61.45        18.58 
TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-2F-A9KO TCGA-4Z-AA80 
       13.64        30.28        94.29        88.87        24.13         0.62 
TCGA-CF-A1HS TCGA-CU-A3YL TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-AA76 TCGA-E7-A4IJ 
       12.56        29.79         4.80         8.15        12.03        22.16 
TCGA-E7-A4XJ TCGA-E7-A85H TCGA-FD-A62S TCGA-G2-A2EK TCGA-G2-A3IE TCGA-GC-A3RC 
        2.24        12.95        13.35        15.95        20.12        15.91 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JW TCGA-GV-A3QH TCGA-K4-AAQO TCGA-LT-A5Z6 
       20.05        15.78        21.34         8.48        11.80        15.58 
TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HH 
       13.48        17.62        76.01         6.21         6.58         1.87 
TCGA-XF-AAMG TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9RF TCGA-ZF-AA5H 
      110.60         6.77        11.97        31.20        64.08        29.49 

$`DEL PEAK  2(1Q32.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A42C 
      108.95        16.27        33.83        12.39        20.48        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
        8.98        18.58        12.92        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A3IT 
        2.14        19.00        16.70       130.88         8.22        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       67.36        50.70        38.24        52.01       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ 
       13.64        13.64        56.15        11.18        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       25.58         0.92         1.22        33.04         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P 
       24.30        17.98        29.16        46.78        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        8.25        58.92        62.86        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM 
        3.06         9.67        17.23        11.08        33.01        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP 
       19.13        17.75        24.92        10.92        32.78        32.98 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB 
       20.28        27.35        19.07         9.01        25.02         2.76 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
        9.14        27.68        52.73        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE 
       14.24        33.14        86.83        51.32        97.45       125.49 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       15.35         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       12.76        11.90        21.04        26.27        18.90         2.24 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR 
       66.64        13.74        11.31        54.90         7.63        91.73 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 
       98.99        30.94        86.30         3.88         9.63        21.11 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KP 
        3.48        34.06        19.69        57.90        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       94.88       104.65         8.35        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        27.62        50.04        41.75        51.16        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         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-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
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-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-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.87        13.08         5.19         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX 
       17.95         7.79       142.78        13.58        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X 
      163.30        15.02        13.58        18.81        19.00        15.35 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A519 TCGA-E7-A5KE 
       43.59        38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 
       13.68        14.07        15.32        14.37         8.09        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       16.77         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70         7.10         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL 
       10.65         8.94         3.25        61.94        48.00        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 
       59.31         7.23        66.02         6.94        29.36        20.71 
TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 
       15.81        14.07         0.49         8.94        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI 
        7.63         4.73         7.00        14.27        19.10        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
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-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN 
       44.38         1.15        15.32        21.07        12.23        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB 
       16.54        38.99        37.05        22.68        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        35.24        29.56        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
       45.04        17.88        48.62        64.80        79.66        66.41 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
        5.98        23.64        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32        56.48        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       22.36        25.41        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       58.72        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21         5.52        10.65 

  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE 
                         0.62                          0.49 
  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 
                       17.195                        17.750 
[1] "0.6 - 110.6 (17.2)" "0.5 - 166.0 (17.8)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1Q32.1) MUTATED         0       29        18       25
  DEL PEAK  2(1Q32.1) WILD-TYPE       2      100       122      110
D39V3, multiclass
           clus
vv          DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  STAGE I                             0                             2
  STAGE II                           29                           100
  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         22  31   9
  DEL PEAK  2(1Q32.1) WILD-TYPE      101 164  49
D39V4, multiclass
          clus
vv         DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  T0+T1+T2                          22                           101
  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    33   5  19   1
  DEL PEAK  2(1Q32.1) WILD-TYPE 203  42  56   7
D39V5, multiclass
    clus
vv   DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  N0                          33                           203
  N1                           5                            42
  N2                          19                            56
  N3                           1                             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"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    30   2
  DEL PEAK  2(1Q32.1) WILD-TYPE 162   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     30    2
  DEL PEAK  2(1Q32.1) WILD-TYPE  162    9
   clus
vv  DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  0                          30                           162
  1                           2                             9
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    14  58
  DEL PEAK  2(1Q32.1) WILD-TYPE  93 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     14   58
  DEL PEAK  2(1Q32.1) WILD-TYPE   93  243
        clus
vv       DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          14                            93
  MALE                            58                           243
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1Q32.1) MUTATED    65   1
  DEL PEAK  2(1Q32.1) WILD-TYPE 299  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1Q32.1) MUTATED     65    1
  DEL PEAK  2(1Q32.1) WILD-TYPE  299   19
     clus
vv    DEL PEAK  2(1Q32.1) MUTATED DEL PEAK  2(1Q32.1) WILD-TYPE
  NO                           65                           299
  YES                           1                            19
[1] 2 2
[1] FALSE
D39V9, continuous
D39V10, continuous
D39V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q32.1) MUTATED       6                         2    61
  DEL PEAK  2(1Q32.1) WILD-TYPE    37                        20   266
D39V12, multiclass
                           clus
vv                          DEL PEAK  2(1Q32.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              61
                           clus
vv                          DEL PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                37
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               266
[1] 3 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  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(40) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    72  62
  DEL PEAK  3(2Q22.1) WILD-TYPE 155 116
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          134                           271 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           62                           116 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-C4-A0EZ 
       16.27        15.12        14.89         8.35        25.94         8.98 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A3X2 
       12.92        18.48        46.68        50.27         9.67        17.98 
TCGA-DK-A6AV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA77 TCGA-E7-A541 
       64.18        67.36        36.66       165.73        20.32        25.58 
TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A6TE 
        0.92        24.30        19.79        26.73        18.08        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-GU-A763 
        3.06         4.31        17.23        11.08        17.62        32.78 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41P TCGA-UY-A78N 
       19.82        27.35         3.45         9.14        35.97        86.83 
TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T0 
       15.35        15.98        14.93         4.21        12.76        26.27 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAN2 TCGA-YF-AA3M TCGA-ZF-A9R2 
       66.64        13.74        10.82        61.45        13.64        21.11 
TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       34.06        57.90        24.13        94.88       104.65         8.35 
TCGA-4Z-AA7S TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BT-A20P TCGA-BT-A20V 
       34.98        47.80         2.50         7.33        17.88         5.06 
TCGA-BT-A2LA TCGA-BT-A3PH TCGA-C4-A0F6 TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47X 
       17.16         4.67        23.01        12.59        12.16        12.62 
TCGA-CF-A7I0 TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A3IK 
       12.10         5.19        21.86        18.41        17.95         4.80 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-E5-A4U1 TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q 
       15.02        19.00        38.83        13.68        14.37         8.09 
TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TF 
        8.94        27.98         5.36        27.45         2.70         2.27 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3OO 
       61.94        48.00        26.93        66.02         6.94        15.81 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GD-A6C6 
       14.07         0.49         8.94         2.10        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A5RJ 
       11.31         4.73        14.27        21.34        12.16        17.72 
TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81        11.80        44.38         1.15        15.58        13.48 
TCGA-S5-AA26 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PD TCGA-XF-A8HC 
       16.54        22.68        76.01        69.34        17.82         6.58 
TCGA-XF-A8HH TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN5 TCGA-YC-A9TC 
        1.87       110.60         2.96         6.77        75.39         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG 
       11.97        22.36        31.20        28.41        64.08        58.72 
TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA56 
       47.84        20.22         8.61        67.20        19.40         8.52 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A2LD 
      108.95        16.77        33.83        12.39        26.14        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
        9.96        28.70        18.58         4.90        15.12        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN 
        2.14        19.00        16.70       130.88        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 
       17.72        21.30        23.21        66.05        53.29        76.60 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W 
       15.68        50.70        38.24        52.01       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B6 
       13.64        56.15        11.18        15.35         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        4.01        60.66        23.41        17.98        29.16        46.78 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT 
       12.85        27.35         3.62        15.58        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        5.69         8.25        58.92         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-G2-AA3D 
        6.15        12.69         9.67        31.07        33.01        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP 
       21.40        19.13        17.75        24.92        10.92        32.98 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       20.28         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X 
        2.76        27.68        52.73        50.56        46.98        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF 
        1.84        33.14        51.32        97.45       125.49        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
        3.22        34.45        11.90        21.04        18.90         2.24 
TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        44.32        30.94        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T 
        9.63        30.28        94.29         3.48        88.87        19.69 
TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W 
       12.23        11.97        44.94        16.83        17.16        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       50.04         0.62        41.75        51.16        66.54        10.22 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42        40.08         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       19.04        12.16        19.50         5.06        14.96         8.25 
TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
       16.18        17.56        36.43        28.41         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       12.56        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-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 
       11.34        11.87        13.08        29.79         1.84        66.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 
      112.44        16.14        17.62        15.62         7.79       142.78 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
       13.58         8.15        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       18.81        15.35        12.03        43.59        29.72         5.36 
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-A7XN TCGA-E7-A85H 
       26.24         4.24        24.03        24.66        14.07        12.95 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO 
       15.32        32.02        16.77        12.62        22.52         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62O 
       25.74        22.98        14.96        20.91        19.33         7.10 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3I6 
       15.95        59.31         7.23        20.12        29.36        20.71 
TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GU-A762 
       15.91        13.91        26.70         3.12        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
       20.05        15.78         7.00        19.10         8.48        36.49 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH 
        1.51        19.40        38.60        64.01        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI 
       11.70        15.42        16.27        15.32        21.07        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC 
       16.67        38.99        17.62        37.05        78.25         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
      112.83        35.24        29.56         6.21         3.85        45.04 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
       17.88        48.62        64.80        79.66        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN0 
       23.64        28.24        16.27        92.98         8.32        56.48 
TCGA-XF-AAN4 TCGA-YC-A89H TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
       27.06        18.84        25.41        35.84        21.86        13.41 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA58 
        2.89        59.38        60.16        56.35        35.41        54.21 
TCGA-ZF-AA5N 
        5.52 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.49                          0.56 
  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 
                        16.85                         17.88 
[1] "0.5 - 165.7 (16.9)" "0.6 - 166.0 (17.9)"
[1] "hr=" "1.2"
D40V2, 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
D40V3, 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
D40V4, 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    69  14  28   3
  DEL PEAK  3(2Q22.1) WILD-TYPE 167  33  47   5
D40V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                          69                           167
  N1                          14                            33
  N2                          28                            47
  N3                           3                             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"
D40V6, 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
D40V7, 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
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED   115   7
  DEL PEAK  3(2Q22.1) WILD-TYPE 249  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED    115    7
  DEL PEAK  3(2Q22.1) WILD-TYPE  249   13
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                          115                           249
  YES                           7                            13
[1] 2 2
[1] FALSE
D40V9, continuous
D40V10, continuous
D40V11, 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
D40V12, 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"
D40V13, 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(41) Variable = DEL PEAK  4(2Q34) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2Q34) MUTATED    98  76
  DEL PEAK  4(2Q34) WILD-TYPE 129 102
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                        174                         231 
  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                         76                         102 
$`DEL PEAK  4(2Q34) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
      108.95        16.27        15.12        26.14        14.89         8.35 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AC 
       28.70         8.98        12.92        18.48         2.14       130.88 
TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV 
       46.68        50.27        21.30         9.67        17.98        64.18 
TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA77 
       53.29        67.36        50.70        36.66       165.73        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SN 
       15.35        25.58         0.92         1.22        24.30        29.16 
TCGA-FD-A3SR TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TD TCGA-FD-A6TE 
       19.79        26.73         8.25        18.08        12.69        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D 
        3.06         4.31        17.23        11.08        17.62        70.32 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3QK TCGA-GV-A40G 
       19.13        17.75        24.92        10.92        27.35        19.07 
TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O 
       22.72        25.02         3.45         9.14        27.68        50.56 
TCGA-KQ-A41P TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       35.97        86.83        51.32        15.35         3.22        15.98 
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-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMZ TCGA-XF-AAN2 
       26.27         2.24        13.74        10.82        44.32        61.45 
TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 
       18.58        21.11        94.29         3.48        34.06        57.90 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7S 
       24.13        11.97        94.88         8.35        17.16        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13J 
        0.62        10.22        47.80         2.50        17.42         2.66 
TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42E TCGA-CF-A1HS 
       19.04         5.06        17.16         4.67        36.43        12.56 
TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A9FF TCGA-CU-A3QU 
       12.59        12.16        12.62        12.10        11.87         5.19 
TCGA-CU-A3YL TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       29.79        17.95         7.79         4.80        13.58         8.15 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A7PW 
       15.02        19.00        12.03        29.72        22.16        13.68 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A5BV 
       14.37         8.09        16.77         8.94        22.52         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TF TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
       27.45         2.70         2.27        61.94        15.95        26.93 
TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GU-A767 
       66.02        15.81        14.07         0.49         2.10         4.73 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A5NE 
       14.27        21.34         8.48        36.49        38.60        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-KQ-A41R 
       21.24         9.07        17.72         1.81        11.80        44.38 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 
        1.15        15.32        15.58        13.48        16.67        16.54 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       17.62        22.68        69.34        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-AAMG 
        6.21         3.85         1.87         5.98        23.64       110.60 
TCGA-XF-AAMT TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
        2.96        11.97        22.36        31.20        28.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA5H TCGA-GU-AATO 
       58.72        47.84        59.38        67.20        29.49        10.65 

$`DEL PEAK  4(2Q34) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       16.77        33.83        12.39        20.48        25.94         9.96 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB 
       18.58         4.90        15.12        13.58        19.00        16.70 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A6B0 
       87.32         8.22        17.72        23.21        66.05        76.60 
TCGA-DK-A6B2 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       15.68        38.24        52.01       166.03        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL 
       56.15        11.18        33.04         4.01        60.66        23.41 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y 
       17.98        46.78        12.85        27.35         3.62        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       53.88        10.78         5.69        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-GC-A3BM 
       18.81         6.15         9.67        31.07        33.01        21.40 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-HQ-A5ND 
       32.78        32.98        19.82        20.28         8.58         9.01 
TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
        2.76        52.73        46.98        14.24         1.84        33.14 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 
       97.45       125.49        97.12        18.90        66.64         2.10 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       11.31        54.90         7.63        71.57        91.73        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 
       30.94        86.30         3.88         9.63        13.64        30.28 
TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O 
       88.87        19.69        12.23       104.65        44.94        16.83 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-BL-A0C8 
       27.62        50.04        41.75        51.16        66.54        40.08 
TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        7.33         6.74         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-A42B 
       19.50         5.06        14.96         8.25        16.18        17.56 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MG 
       28.41         1.94        23.01        12.79        13.97        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-A8HX TCGA-CF-A8HY TCGA-CF-A9FM TCGA-CU-A5W6 
       13.12        12.00        11.34        11.34        13.08         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
       15.62       142.78        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       18.81        15.35        43.59        38.83         5.36         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-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 
       24.03        24.66        14.07        12.95        15.32        32.02 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       12.62        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
       20.91        19.33         7.10        13.35        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3IB 
       10.65         8.94         3.25        48.00        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A6I1 
       20.12         6.94        29.36        20.71        15.91         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91        26.70         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JX 
       18.97         7.63        20.05        15.78         7.00        19.10 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P 
        1.51        19.40        64.01        11.70        15.42        16.27 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       21.07        12.23        38.99        37.05        76.01        78.25 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SG 
        3.02       112.83        45.04         6.58        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       64.80        79.66        66.41        28.24        16.27        92.98 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
        8.32         6.77        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RN 
        0.66        25.41        35.84        21.86        13.41        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 
        2.89         8.61        60.16        56.35        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
        8.52        54.21         5.52 

  DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE 
                       0.49                        0.56 
  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 
                     17.195                      17.980 
[1] "0.5 - 165.7 (17.2)" "0.6 - 166.0 (18.0)"
[1] "hr=" "1.1"
D41V2, 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
D41V3, 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
D41V4, 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 144  29  33   4
D41V5, multiclass
    clus
vv   DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  N0                        92                         144
  N1                        18                          29
  N2                        42                          33
  N3                         4                           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"
D41V6, 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
D41V7, 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
D41V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2Q34) MUTATED   154   7
  DEL PEAK  4(2Q34) WILD-TYPE 210  13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2Q34) MUTATED    154    7
  DEL PEAK  4(2Q34) WILD-TYPE  210   13
     clus
vv    DEL PEAK  4(2Q34) MUTATED DEL PEAK  4(2Q34) WILD-TYPE
  NO                        154                         210
  YES                         7                          13
[1] 2 2
[1] FALSE
D41V9, continuous
D41V10, continuous
D41V11, 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
D41V12, 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"
D41V13, 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(42) Variable = DEL PEAK  5(2Q37.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.1) MUTATED   118  89
  DEL PEAK  5(2Q37.1) WILD-TYPE 109  89
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          207                           198 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                           89                            89 
$`DEL PEAK  5(2Q37.1) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
      108.95        16.27        15.12        26.14        14.89         8.35 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 
       28.70         8.98        12.92        15.12        18.48         2.14 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
      130.88        46.68        50.27        21.30        23.21         9.67 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B1 TCGA-DK-A6B5 TCGA-DK-A6B6 
       17.98        64.18        53.29        67.36        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ 
       38.24       165.73       166.03        13.64        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SR 
       25.58         0.92         1.22        24.30        29.16        19.79 
TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TC 
       12.85         3.62        26.73         8.25        18.08         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.69        12.36         3.06         4.31        17.23        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       17.62        70.32        19.13        17.75        24.92        10.92 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       32.98        20.28        27.35        19.07        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P 
       25.02         3.45         9.14        27.68        50.56        35.97 
TCGA-S5-A6DX TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
        1.84        86.83        51.32        15.35         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       14.93         4.21        12.76        11.90        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 
        2.24        13.74        10.82        30.94        61.45        18.58 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 
       13.64        21.11        94.29         3.48        34.06        57.90 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7S 
       24.13        11.97        94.88         8.35        17.16        34.98 
TCGA-4Z-AA80 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BT-A20J 
        0.62        10.22        47.80         2.50         2.66        19.04 
TCGA-BT-A20Q TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
       19.50         5.06         8.25        17.16         4.67        17.56 
TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MI 
       36.43        12.79        12.56        12.59        12.13        12.16 
TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A3QU TCGA-CU-A3YL 
       12.62        12.10        11.34        11.87         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1AD TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.84       112.44        15.62        17.95         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
        8.15        15.02        19.00        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q 
       29.72        22.16         0.56        13.68        14.37         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       16.77         8.94        22.52         5.36        27.45         2.70 
TCGA-FD-A6TF TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-AA3B TCGA-G2-AA3F 
        2.27        61.94        15.95        26.93        66.02        29.36 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A3OP TCGA-GU-A762 
       15.81        15.91        14.07         0.49         2.10         7.63 
TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73        14.27        21.34        19.10         8.48        36.49 
TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ 
       38.60        12.16        21.24         9.07        17.72         1.81 
TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 
       15.42        11.80        44.38         1.15        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M 
       13.48        16.67        16.54        38.99        17.62        22.68 
TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       76.01        69.34        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SX TCGA-XF-AAMG 
        3.85        45.04         6.58         1.87        23.64       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R9 
        2.96         8.32        11.97        22.36        31.20        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        58.72        47.84        20.22         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA5H TCGA-GU-AATO 
       67.20        29.49        10.65 

$`DEL PEAK  5(2Q37.1) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       16.77        33.83        12.39        20.48        25.94         9.96 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 
       18.58         4.90        13.58        19.00        16.70        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3X1 TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-AA6M 
        8.22        17.72        66.05        76.60        15.68        52.01 
TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       13.64        56.15        11.18        33.04         4.01        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BS 
       23.41        17.98        46.78        27.35        15.58        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
       10.78         5.69        58.92         6.28        62.86        18.81 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GU-A763 TCGA-GV-A3JZ 
        9.67        31.07        33.01        21.40        32.78        19.82 
TCGA-GV-A40E TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 
        8.58         2.76        52.73        46.98        14.24        33.14 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SM TCGA-XF-A9T2 TCGA-XF-A9T5 
       97.45       125.49        97.12        34.45        18.90        66.64 
TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        11.31        54.90         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 
       98.99        44.32        86.30         3.88         9.63        30.28 
TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O 
       88.87        19.69        12.23       104.65        44.94        16.83 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KM 
       27.62        50.04        41.75        51.16        66.54        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       40.08         7.33         6.74         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A42F TCGA-C4-A0F0 
       17.88         5.06        14.96        16.18        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       23.01        13.97        13.08        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FM 
       12.10        12.26        13.12        12.00        11.34        13.08 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I2 
       21.86        66.41        18.41        16.14        17.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
      142.78        20.81        10.55       163.30        13.58        18.81 
TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 
       43.59         5.36         2.24        16.70         0.66        26.96 
TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
       26.24         4.24        24.03        24.66        14.07        12.95 
TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
       15.32        32.02        12.62        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62O TCGA-FD-A62S 
       22.98        14.96        20.91        19.33         7.10        13.35 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ 
       10.85        12.66        10.65         8.94         3.25        48.00 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A6I1 
       59.31         7.23        20.12         6.94        20.71         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       13.91        26.70         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ TCGA-H4-A2HO TCGA-H4-A2HQ 
       18.97        20.05        15.78         7.00         1.51        19.40 
TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A83P TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-UY-A78L 
       64.01        11.70        16.27        21.07        12.23        37.05 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
       78.25         3.02       112.83        17.88        48.62        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       79.66        66.41         5.98        28.24        16.27        92.98 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        6.77        56.48        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R1 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-AA4N TCGA-ZF-AA4W 
       25.41        35.84        21.86        13.41         2.89        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       56.35        35.41        19.40         8.52        54.21         5.52 

  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         0.49                          0.66 
  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 
                        16.67                         18.81 
[1] "0.5 - 166.0 (16.7)" "0.7 - 163.3 (18.8)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(2Q37.1) MUTATED         0       65        64       77
  DEL PEAK  5(2Q37.1) WILD-TYPE       2       64        76       58
D42V3, multiclass
           clus
vv          DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  STAGE I                             0                             2
  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         61 98 32
  DEL PEAK  5(2Q37.1) WILD-TYPE       62 97 26
D42V4, multiclass
          clus
vv         DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  T0+T1+T2                          61                            62
  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 126  25  25   4
D42V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  N0                         110                           126
  N1                          22                            25
  N2                          50                            25
  N3                           4                             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"
D42V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.1) MUTATED   96  5
  DEL PEAK  5(2Q37.1) WILD-TYPE 96  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     96    5
  DEL PEAK  5(2Q37.1) WILD-TYPE   96    6
   clus
vv  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  0                          96                            96
  1                           5                             6
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED    46 161
  DEL PEAK  5(2Q37.1) WILD-TYPE  61 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     46  161
  DEL PEAK  5(2Q37.1) WILD-TYPE   61  140
        clus
vv       DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  FEMALE                          46                            61
  MALE                           161                           140
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED   186   8
  DEL PEAK  5(2Q37.1) WILD-TYPE 178  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED    186    8
  DEL PEAK  5(2Q37.1) WILD-TYPE  178   12
     clus
vv    DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  NO                          186                           178
  YES                           8                            12
[1] 2 2
[1] FALSE
D42V9, continuous
D42V10, continuous
D42V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.1) MUTATED      18                         9   169
  DEL PEAK  5(2Q37.1) WILD-TYPE    25                        13   158
D42V12, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.1) MUTATED
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             169
                           clus
vv                          DEL PEAK  5(2Q37.1) WILD-TYPE
  ASIAN                                                25
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               158
[1] 3 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  5(2Q37.1) MUTATED     7 184
  DEL PEAK  5(2Q37.1) WILD-TYPE   2 185
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      7  184
  DEL PEAK  5(2Q37.1) WILD-TYPE    2  185
                        clus
vv                       DEL PEAK  5(2Q37.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         184
                        clus
vv                       DEL PEAK  5(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           185
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    59  57
  DEL PEAK  6(3P14.2) WILD-TYPE 168 121
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                          116                           289 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           57                           121 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN 
       16.77        14.89         8.35        28.70         8.98        12.92 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3X1 
       15.12        18.48        16.70        17.72        50.27        66.05 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 
       50.70        38.24       165.73        13.64        11.18        20.32 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A43Y 
       25.58         1.22        33.04        24.30        29.16        15.58 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TG TCGA-G2-A2ES TCGA-G2-A3VY 
        8.25        58.92         6.28         3.06        33.01        17.62 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       19.13        17.75        24.92        22.72         9.01        25.02 
TCGA-K4-A4AC TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-XF-A8HD TCGA-XF-A9SK TCGA-XF-A9T0 
        9.14        35.97        46.98        97.45        15.98        26.27 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMQ TCGA-XF-AAN3 TCGA-YF-AA3M 
       66.64         2.10        13.74        71.57        86.30        13.64 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW 
        3.48        34.06        57.90        24.13       104.65         8.35 
TCGA-4Z-AA7W TCGA-4Z-AA82 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42B TCGA-BT-A42E 
       27.62        51.16         5.06         8.25        17.56        36.43 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A2I2 TCGA-DK-A3IM 
        1.94        12.56        29.79        66.41         7.79         8.15 
TCGA-DK-A3WX TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 
       10.55        13.58        43.59        12.95         8.09        16.77 
TCGA-FD-A3N5 TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3ZE 
       22.52        22.98         5.36        27.45         2.27        10.65 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F 
       61.94        48.00         7.23        20.12        66.02        29.36 
TCGA-GC-A3I6 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW 
       20.71         2.20        11.31         4.73         7.00        21.34 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB TCGA-PQ-A6FI 
       19.40        38.60        21.24        11.70        15.42        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-A8HI TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT 
      112.83        29.56        17.88         5.98       110.60         2.96 
TCGA-XF-AAMW TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4W 
        8.32        28.41        13.41        64.08        58.72        60.16 
TCGA-ZF-AA56 TCGA-ZF-AA5H 
        8.52        29.49 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A72E 
       20.48        25.94         9.96        18.58         4.90        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
        2.14        19.00       130.88        46.68        87.32         8.22 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       21.30        23.21         9.67        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6S 
       76.60        67.36        15.68        36.66        52.01       166.03 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3NA 
       13.64        56.15        15.35         0.92         4.01        60.66 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        17.98        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 
        3.62        26.73        53.88        10.78         5.69        18.08 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
       62.86        18.81         6.15        12.69        12.36         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-AA3D TCGA-GC-A3BM 
        9.67        31.07        17.23        11.08        70.32        21.40 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       10.92        32.78        32.98        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-GV-A40G TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N 
        8.58        19.07         3.45         2.76        27.68        52.73 
TCGA-KQ-A41O TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       50.56        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP 
      125.49        97.12        15.35         3.22        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 
        4.21        12.76        11.90        21.04        18.90         2.24 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMY 
       10.82        11.31        54.90         7.63        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       44.32        30.94        61.45        18.58         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA5P 
       21.11        30.28        94.29        88.87        19.69        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
       11.97        94.88        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04         0.62        41.75        66.54        10.22        47.80 
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-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42F 
        5.06        14.96        17.16        16.18         4.67        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-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 
       11.87        13.08         5.19         1.84        21.86        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 
      112.44        16.14        17.62        15.62        17.95       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T 
        4.80        13.58        20.81       163.30        15.02        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        38.83        29.72         5.36 
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-A7PW TCGA-E7-A7XN 
       26.24         4.24        24.03        24.66        13.68        14.07 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.32        14.37        32.02         8.94        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N 
        5.52        25.74        14.96        20.91        19.33         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE 
        7.10        13.35        10.85        12.66         8.94         3.25 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RC 
       15.95        26.93        59.31         6.94        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        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        3.12        20.98        18.97         7.63        20.05        15.78 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF 
       14.27        19.10         8.48        36.49         1.51        64.01 
TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO 
       12.16         9.07        17.72         1.81        16.27        11.80 
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-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A9PA TCGA-UY-A9PD 
       16.54        17.62        37.05        22.68        35.24        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG 
        6.21         3.85        45.04         6.58         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41        23.64        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       92.98         6.77        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
        0.66        11.97        22.36        25.41        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       21.86        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5N 
       67.20        56.35        35.41        19.40        54.21         5.52 
TCGA-GU-AATO 
       10.65 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         1.22                          0.49 
  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 
                       19.265                        17.160 
[1] "1.2 - 165.7 (19.3)" "0.5 - 166.0 (17.2)"
[1] "hr=" "1.1"
D43V2, 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
D43V3, 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
D43V4, 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 172  26  59   2
D43V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  N0                          64                           172
  N1                          21                            26
  N2                          16                            59
  N3                           6                             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"
D43V6, 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
D43V7, 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
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED   108   5
  DEL PEAK  6(3P14.2) WILD-TYPE 256  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED    108    5
  DEL PEAK  6(3P14.2) WILD-TYPE  256   15
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NO                          108                           256
  YES                           5                            15
[1] 2 2
[1] FALSE
D43V9, continuous
D43V10, continuous
D43V11, 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
D43V12, 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"
D43V13, 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(44) Variable = DEL PEAK  7(4Q22.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(4Q22.1) MUTATED    81  80
  DEL PEAK  7(4Q22.1) WILD-TYPE 146  98
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                          161                           244 
  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                           80                            98 
$`DEL PEAK  7(4Q22.1) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C TCGA-CU-A0YN 
      108.95        16.77        20.48        25.94        28.70        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
        4.90        15.12        46.68        87.32         8.22        17.72 
TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 
       21.30        17.98        64.18        15.68        50.70        36.66 
TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
       38.24       165.73        13.64        15.35        25.58         0.92 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43Y TCGA-FD-A5BR 
       33.04         4.01        24.30        23.41        15.58        26.73 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH 
        8.25        58.92         6.28         6.15         3.06         4.31 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB 
       31.07        17.23        33.01        70.32        21.40        19.13 
TCGA-GU-AATP TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O 
       32.98        22.72        25.02         9.14        27.68        50.56 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HF 
       46.98        14.24        33.14        86.83        51.32        97.12 
TCGA-XF-A8HG TCGA-XF-A9SK TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMJ 
       15.35        15.98        26.27        66.64        13.74        54.90 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M 
       98.99        44.32        61.45        86.30        18.58        13.64 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-2F-A9KW TCGA-4Z-AA7R 
       30.28        94.29         3.48        88.87         8.35        17.16 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BT-A20R 
        0.62        51.16        10.22         2.50         7.33         5.06 
TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F 
       14.96         5.06        16.18         4.67        17.56        28.41 
TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47V 
        1.94        12.79        12.56        12.13        12.16        12.46 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK 
       21.86        18.41       112.44        17.95         7.79         4.80 
TCGA-DK-A3IM TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A6MD 
        8.15        13.58        43.59        38.83        29.72         4.24 
TCGA-FD-A3B3 TCGA-FD-A3SO TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
       32.02         5.52         2.70         7.10        13.35        10.85 
TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-GC-A3OO TCGA-GC-A4ZW 
       61.94        26.93        59.31         7.23        15.81         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
        8.94        13.91        26.70         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GV-A3JV TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WV 
       20.05        14.27         8.48        19.40        64.01        21.24 
TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41S 
        9.07        11.70        17.72         1.81        15.42         1.15 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O 
       12.23        16.67        38.99        17.62        22.68        76.01 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF 
       69.34       112.83        35.24        29.56         6.21         3.85 
TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW 
        6.58        48.62        23.64       110.60         2.96         8.32 
TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG 
       56.48        22.36        21.86        13.41        64.08        58.72 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 
       20.22         2.89         8.61        67.20        19.40 

$`DEL PEAK  7(4Q22.1) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
       16.27        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-CU-A72E 
        8.35         9.96         8.98        18.58        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IS TCGA-DK-A3IU 
        2.14        19.00        16.70       130.88        50.27        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6M 
        9.67        66.05        53.29        76.60        67.36        52.01 
TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DV 
      166.03        13.64        56.15        11.18        20.32         1.22 
TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       60.66        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 
       27.35         3.62        53.88        10.78         5.69        18.08 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FT-A61P 
       62.86        18.81        12.69        12.36         9.67        11.08 
TCGA-G2-A3VY TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       17.62        17.75        24.92        10.92        32.78        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU 
       20.28        27.35         8.58        19.07         9.01         3.45 
TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41P TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HE 
        2.76        52.73        35.97         1.84        97.45       125.49 
TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
        3.22        34.45        14.93         4.21        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH 
       21.04        18.90         2.24         2.10        10.82        11.31 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 TCGA-XF-AAN8 TCGA-YC-A8S6 
        7.63        71.57        91.73        30.94         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       21.11        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       11.97        94.88       104.65        44.94        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA87 TCGA-5N-A9KM 
       27.62        50.04        41.75        66.54        47.80        17.42 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         2.66         6.74         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42E 
       12.16        17.88        19.50         8.25        17.16        36.43 
TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T 
       23.01        13.97        12.59        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-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I4 
        1.84        66.41        16.14        17.62        15.62       142.78 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T 
       13.58        20.81        10.55       163.30        15.02        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       19.00        15.35        12.03         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME 
       16.70         0.56         0.66        26.96        26.24        24.03 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        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-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       27.45         2.27        12.66        10.65         8.94         3.25 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       48.00        15.95        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       20.71        15.91        14.07         2.10         3.12        20.98 
TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX 
       18.97        15.78         4.73         7.00        21.34        19.10 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A83P TCGA-K4-AAQO 
       36.49         1.51        38.60        12.16        16.27        11.80 
TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 
       44.38        15.32        15.58        21.07        13.48        16.54 
TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HH 
       37.05        78.25         3.02        17.82        45.04         1.87 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ 
       17.88        64.80        79.66        66.41         5.98        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       16.27        92.98         6.77        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
        0.66        11.97        25.41        31.20        35.84        28.41 
TCGA-ZF-A9RM TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 
       47.84        59.38        60.16        56.35        35.41         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE 
                         0.49                          0.56 
  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 
                        17.95                         17.29 
[1] "0.5 - 165.7 (17.9)" "0.6 - 166.0 (17.3)"
[1] "hr=" "1.2"
D44V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(4Q22.1) MUTATED         0       45        55       61
  DEL PEAK  7(4Q22.1) WILD-TYPE       2       84        85       74
D44V3, 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                          55                            85
  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  84  20
  DEL PEAK  7(4Q22.1) WILD-TYPE       79 111  38
D44V4, multiclass
          clus
vv         DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  T0+T1+T2                          44                            79
  T3                                84                           111
  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   1
  DEL PEAK  7(4Q22.1) WILD-TYPE 153  23  42   7
D44V5, multiclass
    clus
vv   DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  N0                          83                           153
  N1                          24                            23
  N2                          33                            42
  N3                           1                             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"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    70   2
  DEL PEAK  7(4Q22.1) WILD-TYPE 122   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     70    2
  DEL PEAK  7(4Q22.1) WILD-TYPE  122    9
   clus
vv  DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  0                          70                           122
  1                           2                             9
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED    44 117
  DEL PEAK  7(4Q22.1) WILD-TYPE  63 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED     44  117
  DEL PEAK  7(4Q22.1) WILD-TYPE   63  184
        clus
vv       DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  FEMALE                          44                            63
  MALE                           117                           184
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(4Q22.1) MUTATED   141   6
  DEL PEAK  7(4Q22.1) WILD-TYPE 223  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q22.1) MUTATED    141    6
  DEL PEAK  7(4Q22.1) WILD-TYPE  223   14
     clus
vv    DEL PEAK  7(4Q22.1) MUTATED DEL PEAK  7(4Q22.1) WILD-TYPE
  NO                          141                           223
  YES                           6                            14
[1] 2 2
[1] FALSE
D44V9, continuous
D44V10, continuous
D44V11, 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
D44V12, 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"
D44V13, 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(45) Variable = DEL PEAK  8(4Q34.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4Q34.2) MUTATED    97  80
  DEL PEAK  8(4Q34.2) WILD-TYPE 130  98
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                          177                           228 
  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                           80                            98 
$`DEL PEAK  8(4Q34.2) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
      108.95        16.77        15.12        26.14        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A2HX 
       20.48        28.70        12.92         4.90        15.12        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 
       87.32         8.22        21.30        64.18        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 
       36.66        38.24       165.73       166.03        13.64        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 
       20.32        15.35        25.58         0.92        33.04         4.01 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C1 
       23.41        29.16        15.58        26.73         8.25        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
        4.31        31.07        17.23        17.62        70.32        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-AATP TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS 
       19.13        17.75        32.98        19.07        22.72        25.02 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 
        9.14        27.68        50.56        46.98        14.24        33.14 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9ST 
       86.83        51.32        97.12        15.35         3.22         4.21 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMY 
       21.04        26.27        66.64        10.82        54.90        98.99 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       61.45        86.30        18.58        13.64        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA80 TCGA-4Z-AA82 
        3.48        19.69         8.35        17.16         0.62        51.16 
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A13J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB 
       10.22         2.50         2.66         5.06         5.06        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR 
        4.67        17.56        36.43        28.41         1.94        12.79 
TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47S TCGA-DK-A1A3 TCGA-DK-A1A7 
       12.56        12.13        12.16        10.95        21.86        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IM 
      112.44        16.14        17.95         7.79         4.80         8.15 
TCGA-DK-AA6Q TCGA-E5-A2PC TCGA-E7-A85H TCGA-FD-A3B3 TCGA-FD-A3SO TCGA-FD-A43N 
       13.58        43.59        12.95        32.02         5.52        22.98 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EF 
        2.70         7.10        13.35         2.27        10.85        61.94 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO 
       26.93         7.23        20.12        66.02        29.36        15.81 
TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 
       15.91        13.91        26.70         2.20        11.31         7.63 
TCGA-GU-A764 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE 
       20.05        14.27        21.34         8.48        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       64.01        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A6MB TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 
       15.42         1.15        15.58        13.48        16.67        38.99 
TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD 
       17.62        22.68        76.01        78.25        69.34       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       35.24        29.56         6.21         3.85        45.04         6.58 
TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 
       23.64       110.60         2.96         8.32         6.77        56.48 
TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4U 
       22.36        21.86        13.41        58.72         2.89         8.61 
TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA5H 
       67.20        19.40        29.49 

$`DEL PEAK  8(4Q34.2) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ 
       16.27        33.83        12.39        25.94         9.96         8.98 
TCGA-CF-A9FL TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB 
       18.58        18.48        13.58         2.14        19.00        16.70 
TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
      130.88        17.72        50.27        23.21         9.67        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6M TCGA-DK-AA71 
       17.98        53.29        76.60        67.36        52.01        13.64 
TCGA-DK-AA74 TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SQ 
       56.15         1.22        60.66        24.30        17.98        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT 
       19.79        12.85        27.35         3.62        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES 
        5.69        18.08        18.81         9.67        11.08        33.01 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK 
       24.92        10.92        32.78        19.82        20.28        27.35 
TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41P 
        8.58         9.01         3.45         2.76        52.73        35.97 
TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
        1.84        97.45       125.49        15.98        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-A9T8 
       12.76        11.90        18.90         2.24         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN1 
       11.31         7.63        71.57        91.73        44.32        30.94 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 
        3.88         9.63        21.11        88.87        34.06        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N 
       12.23        24.13        11.97        94.88       104.65        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-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 
       47.80        17.42        40.08         7.33         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
       13.15        19.04        12.16        17.88        19.50        14.96 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH 
        8.25        17.16        23.01        13.97        12.59        13.08 
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-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AF TCGA-DK-A1AG 
        5.19        29.79         1.84        66.41        17.62        15.62 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
      142.78        13.58        20.81        10.55       163.30        15.02 
TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 
       18.81        19.00        15.35        12.03        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        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-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 
       14.07        15.32        14.37         8.09        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U 
       12.62        22.52        27.98        25.74        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       19.33         5.36        27.45        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-AA3C TCGA-GC-A3I6 
        3.25        48.00        15.95        59.31         6.94        20.71 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07         0.49         8.94         2.10         3.12        20.98 
TCGA-GU-A42R TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JX TCGA-GV-A3QI 
       18.97        15.78         4.73         7.00        19.10        36.49 
TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R 
        1.51        12.16        16.27        11.80        44.38        15.32 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78L TCGA-UY-A8OC TCGA-UY-A9PD 
       21.07        12.23        16.54        37.05         3.02        17.82 
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-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAN4 TCGA-XF-AAN5 
        5.98        28.24        16.27        92.98        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       18.84         0.66        11.97        25.41        31.20        35.84 
TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA4W 
       28.41        64.08        47.84        20.22        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        35.41         8.52        54.21         5.52        10.65 

  DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE 
                         0.62                          0.49 
  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 
                        17.72                         17.52 
[1] "0.6 - 166.0 (17.7)" "0.5 - 163.3 (17.5)"
[1] "hr=" "1"  
D45V2, 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
D45V3, 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
D45V4, 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 145  23  34   7
D45V5, multiclass
    clus
vv   DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  N0                          91                           145
  N1                          24                            23
  N2                          41                            34
  N3                           1                             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"
D45V6, 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
D45V7, 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
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q34.2) MUTATED   157   8
  DEL PEAK  8(4Q34.2) WILD-TYPE 207  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q34.2) MUTATED    157    8
  DEL PEAK  8(4Q34.2) WILD-TYPE  207   12
     clus
vv    DEL PEAK  8(4Q34.2) MUTATED DEL PEAK  8(4Q34.2) WILD-TYPE
  NO                          157                           207
  YES                           8                            12
[1] 2 2
[1] FALSE
D45V9, continuous
D45V10, continuous
D45V11, 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
D45V12, 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"
D45V13, 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(46) Variable = DEL PEAK  9(5Q12.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(5Q12.1) MUTATED   104  96
  DEL PEAK  9(5Q12.1) WILD-TYPE 123  82
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                          200                           205 
  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                           96                            82 
$`DEL PEAK  9(5Q12.1) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
      108.95        16.77        15.12        26.14        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-DK-A1A5 TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ 
       20.48        25.94         2.14        87.32         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 
       50.27        21.30        23.21         9.67        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S 
       64.18        15.68        50.70        38.24       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       13.64        11.18        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A3SS 
       33.04        24.30        23.41        17.98        19.79        12.85 
TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG 
       26.73         8.25        18.08        18.81         6.15         3.06 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-A42P 
       31.07        17.23        11.08        17.62        24.92        10.92 
TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND 
       32.98        20.28         8.58        19.07        22.72         9.01 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P 
        3.45         2.76         9.14        27.68        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       46.98        14.24        97.12        15.35         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9T3 TCGA-XF-AAMJ TCGA-XF-AAML 
       34.45        14.93        12.76         2.24        54.90         7.63 
TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       44.32        13.64        88.87        34.06        19.69        57.90 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W 
       24.13        11.97         8.35        16.83        17.16        27.62 
TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 
       10.22         2.50        17.42        40.08         7.33         6.58 
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH 
       19.04         5.06         5.06        17.16        16.18         4.67 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG 
       17.56        36.43        23.01        12.79        12.56        12.13 
TCGA-CF-A3MH TCGA-CF-A8HY TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 
       13.08        11.34         5.19        18.41       112.44        17.95 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-AA6P 
      142.78         4.80        13.58         8.15        10.55        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 
       13.58        19.00        15.35        43.59        38.83        29.72 
TCGA-E7-A4IJ TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 
       22.16         4.24        24.03        13.68         8.09         8.94 
TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       22.52        25.74        20.91         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EF 
        7.10        13.35         2.27        10.85        10.65        61.94 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A4ZW 
       26.93         7.23        66.02        29.36        15.81         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A762 
        8.94        13.91        26.70         2.10         2.20         7.63 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        21.34        19.10         8.48        36.49 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RI 
       19.40        38.60        64.01        12.16        21.24        11.70 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-MV-A51V TCGA-PQ-A6FN 
        1.81        15.42        11.80        44.38        13.48        16.67 
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-A8HC TCGA-XF-A9SX 
       29.56        17.82         6.21         3.85         6.58        23.64 
TCGA-XF-A9SZ TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R0 
       28.24         2.96         6.77        56.48        11.97        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-A9RN 
       25.41        31.20        21.86        28.41        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 
        2.89        59.38        67.20        56.35        35.41         8.52 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

$`DEL PEAK  9(5Q12.1) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       16.27        33.83        12.39         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A6AW TCGA-DK-A6B0 
       19.00        16.70       130.88        46.68        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       67.36        36.66        52.01        13.64        56.15        20.32 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X 
        4.01        60.66        29.16        46.78        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P 
       15.58        53.88        10.78         5.69        58.92         6.28 
TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-G2-A2ES 
       62.86        12.69        12.36         4.31         9.67        33.01 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A763 TCGA-GV-A3JZ 
       70.32        21.40        19.13        17.75        32.78        19.82 
TCGA-GV-A3QK TCGA-K4-A3WS TCGA-KQ-A41N TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       27.35        25.02        52.73         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY 
       51.32        97.45       125.49         4.21        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       26.27        18.90        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       11.31        71.57        91.73        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30        18.58         3.88         9.63        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA5P TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N 
       94.29         3.48        12.23        94.88       104.65        44.94 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 
       34.98        50.04         0.62        41.75        51.16        66.54 
TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
       47.80         2.66         6.74        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A27C 
       19.50        14.96         8.25        28.41         1.94        13.97 
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-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-A9FF TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 
       11.87        13.08        29.79         1.84        21.86        66.41 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WY 
       16.14        17.62        15.62         7.79        20.81       163.30 
TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       18.81        12.03         5.36         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A85H 
        0.66        26.96        26.24        24.66        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.32        14.37        32.02        16.77        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU TCGA-FJ-A3Z9 TCGA-FJ-A871 
        5.52        22.98        14.96        19.33        12.66         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3C 
        3.25        48.00        15.95        59.31        20.12         6.94 
TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q 
       20.71        15.91        14.07         3.12        20.98        11.31 
TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HO TCGA-K4-A5RH 
       18.97        20.05        15.78        14.27         1.51         9.07 
TCGA-K4-A5RJ TCGA-K4-A83P TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       17.72        16.27         1.15        15.32        15.58        21.07 
TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       12.23        16.54        76.01        78.25         3.02        35.24 
TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI 
       45.04         1.87        17.88        48.62        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW 
       66.41         5.98        16.27        92.98       110.60         8.32 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R5 TCGA-ZF-A9RD 
       27.06        75.39        18.84         0.66        35.84        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA58 
       64.08        58.72         8.61        60.16        19.40        54.21 
TCGA-ZF-AA5N 
        5.52 

  DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE 
                         0.49                          0.56 
  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 
                        17.59                         17.75 
[1] "0.5 - 166.0 (17.6)" "0.6 - 163.3 (17.8)"
[1] "hr=" "1.3"
D46V2, 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
D46V3, 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
D46V4, 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    97  28  46   6
  DEL PEAK  9(5Q12.1) WILD-TYPE 139  19  29   2
D46V5, multiclass
    clus
vv   DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  N0                          97                           139
  N1                          28                            19
  N2                          46                            29
  N3                           6                             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"
D46V6, 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
D46V7, 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
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(5Q12.1) MUTATED   180   8
  DEL PEAK  9(5Q12.1) WILD-TYPE 184  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q12.1) MUTATED    180    8
  DEL PEAK  9(5Q12.1) WILD-TYPE  184   12
     clus
vv    DEL PEAK  9(5Q12.1) MUTATED DEL PEAK  9(5Q12.1) WILD-TYPE
  NO                          180                           184
  YES                           8                            12
[1] 2 2
[1] FALSE
D46V9, continuous
D46V10, continuous
D46V11, 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
D46V12, 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"
D46V13, 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(47) Variable = DEL PEAK 10(6P25.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(6P25.3) MUTATED    58  48
  DEL PEAK 10(6P25.3) WILD-TYPE 169 130
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                          106                           299 
  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                           48                           130 
$`DEL PEAK 10(6P25.3) MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A2LD TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AB TCGA-DK-A1AC 
       16.77        20.48        15.12        13.58        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
       46.68        21.30        66.05        17.98        67.36        36.66 
TCGA-DK-AA6R TCGA-DK-AA71 TCGA-E5-A4TZ TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
      165.73        13.64        15.35        33.04         4.01        60.66 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A62P TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-GV-A3JZ 
       23.41        29.16         6.28        31.07        17.23        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41P 
       20.28        27.35         8.58         2.76        52.73        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N TCGA-XF-A8HG TCGA-XF-A9SM TCGA-XF-A9ST 
       46.98        14.24        86.83        15.35        34.45         4.21 
TCGA-XF-A9T0 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ 
       26.27        10.82        54.90         7.63        98.99        44.32 
TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-AA53 TCGA-2F-A9KW 
       86.30        13.64        21.11        94.29        57.90         8.35 
TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB 
       17.16        51.16         5.06         8.25        17.16        16.18 
TCGA-BT-A3PH TCGA-CF-A3MG TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A2I1 TCGA-DK-A2I2 
        4.67        12.13         1.84        66.41        17.95         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 
      142.78        13.58        15.02        19.00        12.03        38.83 
TCGA-E7-A4IJ TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       22.16         4.24        13.68        14.37         8.09        16.77 
TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-G2-A2EO TCGA-GC-A6I3 TCGA-GD-A3OP 
       20.91         5.36         7.10        59.31        13.91         2.10 
TCGA-GD-A3OS TCGA-GU-A764 TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OF 
       20.98        20.05         8.48        36.49        19.40        64.01 
TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V 
       11.70         1.81        44.38         1.15        15.58        13.48 
TCGA-PQ-A6FI TCGA-UY-A78K TCGA-UY-A8OD TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SZ 
       12.23        17.62       112.83         1.87        48.62        28.24 
TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-ZF-A9R0 
      110.60         8.32         6.77        56.48        75.39        22.36 
TCGA-ZF-A9R1 TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA51 
       25.41         2.89        59.38        56.35 

$`DEL PEAK 10(6P25.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ 
       14.89         8.35        25.94         9.96        28.70         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58        12.92         4.90        18.48         2.14        19.00 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV 
       87.32         8.22        17.72        50.27        23.21         9.67 
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-AA6M TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
       52.01       166.03        13.64        56.15        11.18        20.32 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SQ 
       25.58         0.92         1.22        24.30        17.98        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       19.79        12.85        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
       62.86        18.81         6.15        12.69        12.36         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31         9.67        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       32.98        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH 
        9.14        27.68        50.56         1.84        33.14        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP 
       97.45       125.49        97.12         3.22        15.98        14.93 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       12.76        11.90        21.04        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAN1 
        2.10        13.74        11.31        71.57        91.73        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RE 
       61.45        18.58         3.88         9.63        30.28         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
       88.87        34.06        19.69        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W 
       94.88       104.65        44.94        16.83        34.98        27.62 
TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       50.04         0.62        41.75        66.54        10.22        47.80 
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-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        5.06        14.96        17.56        36.43        28.41         1.94 
TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH 
       23.01        12.79        12.56        13.97        12.59        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 
       11.87        13.08         5.19        29.79        21.86        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK TCGA-DK-A3IM 
      112.44        16.14        17.62        15.62         4.80         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X 
       20.81        10.55       163.30        13.58        18.81        15.35 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       43.59        29.72         5.36         2.24        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        0.66        26.96        26.24        24.03        24.66        14.07 
TCGA-E7-A85H TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.95        15.32        32.02         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A5BU 
       27.98         5.52        25.74        22.98        14.96        19.33 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
       27.45         2.70        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       10.65         8.94         3.25        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F 
       26.93         7.23        20.12        66.02         6.94        29.36 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       20.71        15.81        15.91        14.07         0.49         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       26.70         3.12         2.20        11.31        18.97         7.63 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ 
        1.51        38.60        12.16        21.24         9.07        17.72 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN 
       15.42        16.27        11.80        15.32        21.07        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P 
       16.54        38.99        37.05        22.68        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       69.34         3.02        35.24        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
        3.85        45.04         6.58        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
       66.41         5.98        23.64        16.27        92.98         2.96 
TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       27.06        18.84         0.66        11.97        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 
       20.22         8.61        60.16        67.20        35.41        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE 
                         1.15                          0.49 
  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 
                        18.49                         17.56 
[1] "1.1 - 165.7 (18.5)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D47V2, 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
D47V3, 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
D47V4, 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 182  39  51   4
D47V5, multiclass
    clus
vv   DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  N0                          54                           182
  N1                           8                            39
  N2                          24                            51
  N3                           4                             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"
D47V6, 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
D47V7, 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
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(6P25.3) MUTATED    99   2
  DEL PEAK 10(6P25.3) WILD-TYPE 265  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.3) MUTATED     99    2
  DEL PEAK 10(6P25.3) WILD-TYPE  265   18
     clus
vv    DEL PEAK 10(6P25.3) MUTATED DEL PEAK 10(6P25.3) WILD-TYPE
  NO                           99                           265
  YES                           2                            18
[1] 2 2
[1] FALSE
D47V9, continuous
D47V10, continuous
D47V11, 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
D47V12, 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"
D47V13, 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(48) Variable = DEL PEAK 11(6Q21) MUTATION ANALYSIS
D48V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(6Q21) MUTATED   102  88
  DEL PEAK 11(6Q21) WILD-TYPE 125  90
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                        190                         215 
  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                         88                          90 
$`DEL PEAK 11(6Q21) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LD 
      108.95        16.27        16.77        26.14        14.89        20.48 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IQ 
        9.96        28.70        16.70        46.68        87.32        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-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 
       36.66        38.24       165.73       166.03        13.64        13.64 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
       15.35        25.58         1.22        24.30        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BT 
       46.78        19.79        12.85        27.35        26.73        10.78 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TC TCGA-FD-A6TE 
        8.25        18.08        58.92         6.28         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        3.06         4.31        31.07        11.08        33.01        17.62 
TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A40E 
       70.32        19.13        10.92        32.98        20.28         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41O TCGA-R3-A69X 
       19.07        22.72         2.76        52.73        50.56        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
        1.84        33.14        97.45        97.12        15.35         3.22 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 
       15.98        14.93         4.21        11.90        26.27         2.24 
TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN3 
        2.10        54.90         7.63        91.73        44.32        86.30 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO 
       13.64        21.11        34.06        19.69        57.90        24.13 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       94.88       104.65        27.62         0.62        41.75        51.16 
TCGA-4Z-AA86 TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F0 
       10.22        19.04         5.06        16.18         4.67         1.94 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU 
       12.79        13.97        12.13        12.16        12.62         5.19 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A2I1 
        1.84        21.86        66.41        18.41        16.14        17.95 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6Q 
        7.79       142.78         4.80        13.58        15.02        13.58 
TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE 
       18.81        12.03        43.59        38.83        22.16         0.56 
TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43U 
        4.24        24.03        12.95         8.09         8.94        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-G2-A2EO 
       19.33         5.36        27.45         7.10        13.35        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A4ZW 
       20.12        66.02        29.36        20.71        14.07         0.49 
TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ 
        8.94         2.10        18.97         7.63         4.73         7.00 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
       21.34        19.10         8.48        19.40        38.60        64.01 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-MV-A51V 
       21.24        11.70         1.81        44.38        15.58        13.48 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD 
       16.67        38.99        37.05        22.68        69.34       112.83 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       29.56        17.82         3.85        45.04         6.58         1.87 
TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-AAMW TCGA-XF-AAMX 
       17.88        48.62        79.66        28.24         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R7 
       56.48        75.39        11.97        22.36        25.41        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4X TCGA-ZF-AA51 
       28.41        64.08        20.22         2.89        67.20        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       35.41        19.40        54.21        29.49 

$`DEL PEAK 11(6Q21) WILD-TYPE`
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A3PJ TCGA-C4-A0EZ 
       15.12        33.83        12.39         8.35        25.94         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E 
       18.58        12.92         4.90        15.12        18.48        13.58 
TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV 
        2.14        19.00       130.88         8.22        23.21         9.67 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6M TCGA-DK-AA74 
       53.29        76.60        67.36        15.68        52.01        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA 
       11.18        20.32         0.92        33.04         4.01        60.66 
TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A6TA 
       17.98         3.62        15.58        53.88         5.69        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3WC 
       18.81        12.69         9.67        17.23        21.40        17.75 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-HQ-A5ND TCGA-K4-A3WS 
       24.92        32.78        19.82        27.35         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-UY-A78N 
        3.45         9.14        27.68        35.97        46.98        86.83 
TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T2 
       51.32       125.49        34.45        12.76        21.04        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMY 
       66.64        13.74        10.82        11.31        71.57        98.99 
TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 
       30.94        61.45        18.58         3.88         9.63        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KW 
       94.29         3.48        88.87        12.23        11.97         8.35 
TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       44.94        16.83        17.16        34.98        50.04        66.54 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42E 
        5.06        14.96         8.25        17.16        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MH TCGA-CF-A47S 
       28.41        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-A9FM TCGA-CU-A3YL 
       12.10        11.34        11.34        11.87        13.08        29.79 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      112.44        17.62        15.62         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
      163.30        19.00        15.35        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW 
       16.70         0.66        26.96        26.24        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 
       14.07        15.32        14.37        32.02        16.77        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S 
       22.52        27.98         5.52        25.74        22.98        14.96 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        2.70         2.27        10.85        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-AA3C TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ 
        6.94        15.81        15.91        13.91        26.70         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV 
       20.98         2.20        11.31        20.05        15.78        14.27 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
       36.49         1.51        12.16         9.07        17.72        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI 
       16.27        11.80         1.15        15.32        21.07        12.23 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       16.54        17.62        76.01        78.25         3.02        35.24 
TCGA-UY-A9PE TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 
        6.21        64.80        66.41         5.98        23.64        16.27 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC 
       92.98       110.60         2.96        27.06        18.84         0.66 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4U 
       31.20        35.84        13.41        58.72        47.84         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-GU-AATO 
       59.38        60.16         8.52         5.52        10.65 

  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE 
                       0.49                        0.66 
  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 
                      19.23                       15.95 
[1] "0.5 - 166.0 (19.2)" "0.7 - 163.3 (15.9)"
[1] "hr=" "1"  
D48V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q21) MUTATED         0       56        56       77
  DEL PEAK 11(6Q21) WILD-TYPE       2       73        84       58
D48V3, multiclass
           clus
vv          DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  STAGE I                           0                           2
  STAGE II                         56                          73
  STAGE III                        56                          84
  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 11(6Q21) MUTATED         55 97 24
  DEL PEAK 11(6Q21) WILD-TYPE       68 98 34
D48V4, multiclass
          clus
vv         DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  T0+T1+T2                        55                          68
  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    92  24  48   4
  DEL PEAK 11(6Q21) WILD-TYPE 144  23  27   4
D48V5, multiclass
    clus
vv   DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  N0                        92                         144
  N1                        24                          23
  N2                        48                          27
  N3                         4                           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"
D48V6, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    88   2
  DEL PEAK 11(6Q21) WILD-TYPE 104   9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     88    2
  DEL PEAK 11(6Q21) WILD-TYPE  104    9
   clus
vv  DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  0                        88                         104
  1                         2                           9
[1] 2 2
[1] FALSE
D48V7, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED    54 136
  DEL PEAK 11(6Q21) WILD-TYPE  53 165
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED     54  136
  DEL PEAK 11(6Q21) WILD-TYPE   53  165
        clus
vv       DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  FEMALE                        54                          53
  MALE                         136                         165
[1] 2 2
[1] FALSE
D48V8, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q21) MUTATED   169   8
  DEL PEAK 11(6Q21) WILD-TYPE 195  12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q21) MUTATED    169    8
  DEL PEAK 11(6Q21) WILD-TYPE  195   12
     clus
vv    DEL PEAK 11(6Q21) MUTATED DEL PEAK 11(6Q21) WILD-TYPE
  NO                        169                         195
  YES                         8                          12
[1] 2 2
[1] FALSE
D48V9, continuous
D48V10, continuous
D48V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q21) MUTATED      15                        11   153
  DEL PEAK 11(6Q21) WILD-TYPE    28                        11   174
D48V12, multiclass
                           clus
vv                          DEL PEAK 11(6Q21) MUTATED
  ASIAN                                            15
  BLACK OR AFRICAN AMERICAN                        11
  WHITE                                           153
                           clus
vv                          DEL PEAK 11(6Q21) WILD-TYPE
  ASIAN                                              28
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             174
[1] 3 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 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(49) Variable = DEL PEAK 12(6Q27) MUTATION ANALYSIS
D49V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 12(6Q27) MUTATED   100  90
  DEL PEAK 12(6Q27) WILD-TYPE 127  88
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        190                         215 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                         90                          88 
$`DEL PEAK 12(6Q27) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PK 
      108.95        16.27        16.77        26.14        20.48         9.96 
TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YR TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 
       28.70        18.58        15.12        16.70        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 
        8.22        17.72        50.27        21.30        66.05        17.98 
TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S 
       64.18        50.70        36.66        38.24       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SN 
       13.64        13.64        15.35         1.22        23.41        29.16 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BT 
       46.78        19.79        12.85        15.58        26.73        10.78 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
        8.25        18.08        58.92         6.28        62.86         6.15 
TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES 
       12.36         3.06         4.31        31.07        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       17.62        70.32        19.13        10.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB 
       20.28         8.58        19.07        22.72        25.02         2.76 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        50.56        35.97        14.24         1.84 
TCGA-SY-A9G0 TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       33.14        97.45        97.12        15.35         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 
       34.45        14.93         4.21        11.90        26.27         2.24 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M 
       54.90         7.63        91.73        44.32        86.30        13.64 
TCGA-ZF-A9R2 TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KR 
       21.11        34.06        19.69        57.90        24.13       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
        8.35        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA86 TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PH TCGA-C4-A0F0 
       10.22        19.04         5.06        16.18         4.67         1.94 
TCGA-CF-A1HR TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CU-A3QU TCGA-CU-A5W6 
       12.79        12.13        12.16        12.62         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       21.86        66.41       112.44        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
        4.80        13.58        15.02        13.58        18.81        19.00 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD TCGA-E7-A6ME 
       12.03        43.59        22.16         0.56         4.24        24.03 
TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O 
       12.95         8.94        19.33         5.36        27.45         7.10 
TCGA-FD-A62S TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD 
       13.35        59.31        20.12        29.36        20.71        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A762 
        0.49         8.94        26.70         2.10        18.97         7.63 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        21.34        19.10         8.48        36.49 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-KQ-A41R 
       19.40        38.60        64.01        11.70         1.81        44.38 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       15.58        13.48        16.67        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE 
       22.68        69.34       112.83        29.56        17.82         6.21 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
        3.85        45.04         6.58         1.87        17.88        48.62 
TCGA-XF-A9SI TCGA-XF-A9SZ TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 
       79.66        28.24         8.32         6.77        56.48        75.39 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-AA4N 
       11.97        22.36        25.41        21.86        28.41         2.89 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       67.20        35.41        19.40        29.49 

$`DEL PEAK 12(6Q27) WILD-TYPE`
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PJ 
       15.12        33.83        12.39        14.89         8.35        25.94 
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
        8.98        12.92         4.90        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 
       19.00       130.88        23.21         9.67        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6M TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 
       67.36        15.68        52.01        56.15        11.18        20.32 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ 
       25.58         0.92        33.04         4.01        60.66        24.30 
TCGA-FD-A3SM TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BX TCGA-FD-A6TB 
       17.98        27.35         3.62        53.88         5.69        18.81 
TCGA-FD-A6TD TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GC-A3YS 
       12.69         9.67        17.23        21.40        17.75        24.92 
TCGA-GU-A763 TCGA-GV-A3QK TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AC TCGA-KQ-A41Q 
       32.78        27.35         9.01         3.45         9.14        46.98 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T2 
       86.83        51.32       125.49        12.76        21.04        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ 
       66.64         2.10        13.74        10.82        11.31        71.57 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       98.99        30.94        61.45        18.58         3.88         9.63 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA5P TCGA-2F-A9KP 
       30.28        94.29         3.48        88.87        12.23        11.97 
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-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       47.80         2.50        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A42B TCGA-BT-A42E 
        5.06        14.96         8.25        17.16        17.56        36.43 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MH 
       28.41        23.01        12.56        13.97        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-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3YL TCGA-DK-A1A7 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IM 
       29.79        18.41        16.14        17.62        15.62         8.15 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 
       20.81        10.55       163.30        15.35        38.83        29.72 
TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A677 TCGA-E7-A678 
        5.36         2.24        16.70         0.66        26.96        26.24 
TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        13.68        14.07        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02        16.77        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A6TF 
       25.74        22.98        14.96        20.91         2.70         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85        12.66        10.65         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3B TCGA-G2-AA3C 
       48.00        15.95        26.93         7.23        66.02         6.94 
TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       15.81        15.91        13.91         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HO TCGA-HQ-A5NE 
       11.31        20.05        15.78        14.27         1.51        12.16 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       21.24         9.07        17.72        15.42        16.27        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78O 
        1.15        15.32        21.07        12.23        16.54        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU 
       78.25         3.02        35.24        64.80        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAN4 
       23.64        16.27        92.98       110.60         2.96        27.06 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       18.84         0.66        31.20        35.84        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        47.84        20.22         8.61        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35         8.52        54.21         5.52        10.65 

  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                       0.49                        0.66 
  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 
                     19.055                      16.140 
[1] "0.5 - 166.0 (19.1)" "0.7 - 163.3 (16.1)"
[1] "hr=" "1.1"
D49V2, 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
D49V3, 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
D49V4, 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 143  24  25   3
D49V5, multiclass
    clus
vv   DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  N0                        93                         143
  N1                        23                          24
  N2                        50                          25
  N3                         5                           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"
D49V6, 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
D49V7, 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
D49V8, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED   169   7
  DEL PEAK 12(6Q27) WILD-TYPE 195  13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED    169    7
  DEL PEAK 12(6Q27) WILD-TYPE  195   13
     clus
vv    DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  NO                        169                         195
  YES                         7                          13
[1] 2 2
[1] FALSE
D49V9, continuous
D49V10, continuous
D49V11, 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
D49V12, 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"
D49V13, 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(50) Variable = DEL PEAK 13(7Q36.3) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7Q36.3) MUTATED    39  21
  DEL PEAK 13(7Q36.3) WILD-TYPE 188 157
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           60                           345 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           21                           157 
$`DEL PEAK 13(7Q36.3) MUTATED`
TCGA-BT-A20N TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-FD-A3NA TCGA-FD-A5BY TCGA-FD-A5C0 
       26.14        20.32        15.35        60.66         8.25        18.08 
TCGA-FD-A6TA TCGA-FD-A6TE TCGA-FJ-A3ZF TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-AATP 
       62.86        12.36        17.23        19.13        24.92        32.98 
TCGA-K4-A3WS TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-XF-A8HD TCGA-XF-A9SM TCGA-XF-AAML 
       25.02        52.73        46.98        97.45        34.45         7.63 
TCGA-XF-AAMZ TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-2F-A9KW TCGA-4Z-AA7R 
       44.32        13.64        94.29        88.87         8.35        17.16 
TCGA-BL-A13J TCGA-BT-A20X TCGA-CF-A1HS TCGA-CF-A47X TCGA-DK-A2I4 TCGA-DK-A3IK 
        2.66         8.25        12.56        12.62       142.78         4.80 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-E5-A4U1 TCGA-E7-A6ME TCGA-E7-A97P TCGA-FD-A3N6 
        8.15        15.02        38.83        24.03        14.37        27.98 
TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       27.45         2.27        20.71        14.07         0.49         8.94 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3QI TCGA-K4-A5RH TCGA-K4-A5RI 
        7.63        15.78         7.00        36.49         9.07        11.70 
TCGA-K4-A6MB TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-UY-A8OB 
       15.42        15.32        15.58        12.23        16.67        69.34 
TCGA-XF-AAMG TCGA-XF-AAMT TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-AA4W TCGA-GU-AATO 
      110.60         2.96        64.08        47.84        60.16        10.65 

$`DEL PEAK 13(7Q36.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
       14.89         8.35        20.48        25.94         9.96        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.98        18.58        12.92         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
       13.58         2.14        19.00        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       87.32         8.22        17.72        50.27        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ 
       25.58         0.92         1.22        33.04         4.01        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       23.41        17.98        29.16        46.78        19.79        12.85 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       27.35         3.62        15.58        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD 
        5.69        58.92         6.28        18.81         6.15        12.69 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A2ES 
        3.06         4.31         9.67        31.07        11.08        33.01 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 
       17.62        70.32        21.40        17.75        10.92        32.78 
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-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O 
        9.01         3.45         2.76         9.14        27.68        50.56 
TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH 
       35.97        14.24         1.84        33.14        86.83        51.32 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP 
      125.49        97.12        15.35         3.22        15.98        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
        2.24        66.64         2.10        13.74        10.82        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 
       54.90        71.57        91.73        98.99        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       86.30        18.58         3.88         9.63        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
        3.48        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7S 
       11.97        94.88       104.65        44.94        16.83        34.98 
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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       10.22        47.80         2.50        17.42        40.08         7.33 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A2LB 
       19.50         5.06        14.96         5.06        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         1.94        23.01 
TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI 
       12.79        13.97        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-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CF-A9FM 
       12.00        12.10        11.34        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
       13.58        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
       19.00        15.35        12.03        43.59        29.72         5.36 
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-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H 
       26.24         4.24        24.66        13.68        14.07        12.95 
TCGA-E7-A8O7 TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 
       15.32         8.09        32.02        16.77         8.94        12.62 
TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U 
       22.52         5.52        25.74        22.98        14.96        20.91 
TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
       19.33         5.36         2.70         7.10        13.35        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
       15.95        26.93        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A2C5 
        6.94        29.36        15.81        15.91        13.91        26.70 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R 
        2.10         3.12        20.98         2.20        11.31        18.97 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
       20.05         4.73        14.27        21.34        19.10         8.48 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV 
        1.51        19.40        38.60        64.01        12.16        21.24 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S 
       17.72         1.81        16.27        11.80        44.38         1.15 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        13.48        16.54        38.99        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PA 
       22.68        76.01        78.25         3.02       112.83        35.24 
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-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-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW 
        5.98        23.64        28.24        16.27        92.98         8.32 
TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        6.77        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       28.41        13.41        58.72        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       59.38        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       54.21        29.49         5.52 

  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         0.49                          0.56 
  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                        17.720 
[1] "0.5 - 142.8 (16.9)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.4"
D50V2, 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
D50V3, 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
D50V4, 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 200  43  61   8
D50V5, multiclass
    clus
vv   DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  N0                          36                           200
  N1                           4                            43
  N2                          14                            61
  N3                           0                             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"
D50V6, 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
D50V7, 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
D50V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED    56   1
  DEL PEAK 13(7Q36.3) WILD-TYPE 308  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     56    1
  DEL PEAK 13(7Q36.3) WILD-TYPE  308   19
     clus
vv    DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  NO                           56                           308
  YES                           1                            19
[1] 2 2
[1] FALSE
D50V9, continuous
D50V10, continuous
D50V11, 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
D50V12, 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"
D50V13, 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(51) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED   137 103
  DEL PEAK 14(8P23.3) WILD-TYPE  90  75
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          240                           165 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          103                            75 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK 
      108.95        16.27        16.77         8.35        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A1A5 
       28.70         8.98        12.92        15.12        18.48         2.14 
TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
      130.88        46.68        87.32         8.22        17.72        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L 
       23.21         9.67        64.18        15.68        50.70        38.24 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 
       52.01       165.73       166.03        13.64        11.18        20.32 
TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
       15.35        25.58         0.92         1.22        33.04         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43Y 
       24.30        23.41        17.98        19.79        27.35        15.58 
TCGA-FD-A5BR TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA 
       26.73         5.69         8.25        18.08         6.28        62.86 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        6.15        12.69        12.36         4.31        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS 
       11.08        17.62        70.32        19.13        17.75        24.92 
TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       10.92        32.98        19.82         8.58        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N 
       52.73        35.97        46.98        14.24        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       51.32        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 
        4.21        12.76        11.90        26.27         2.24        66.64 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN7 
       54.90         7.63        71.57        98.99        61.45        18.58 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW 
       57.90        12.23        24.13        11.97       104.65         8.35 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       16.83        17.16        27.62         0.62        41.75        51.16 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J 
       10.22        47.80         2.50        40.08         2.66        19.04 
TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS 
        5.06        16.18        36.43        28.41         1.94        12.56 
TCGA-CF-A27C TCGA-CF-A47S TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A3QU TCGA-DK-A1A3 
       13.97        10.95        11.34        11.87         5.19        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       18.41       112.44        17.95       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 
        8.15        15.02        19.00        12.03        38.83        29.72 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A97P 
       22.16         0.56        26.96         4.24        13.68        14.37 
TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.09        16.77         8.94        22.52         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TF 
       22.98        19.33        27.45         2.70        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A3IE 
       10.85        12.66        10.65        61.94        15.95        20.12 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 
        6.94        29.36        15.91        14.07         0.49        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 
       26.70         2.10         3.12        20.98         2.20         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HQ 
       20.05        15.78         4.73        19.10         8.48        19.40 
TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB 
       64.01        12.16        21.24        17.72         1.81        15.42 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
       16.27        11.80        44.38        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       13.48        16.67        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-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG 
        6.21         3.85        45.04         6.58         1.87        48.62 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
       79.66         5.98       110.60         2.96         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9RD 
       56.48        75.39        18.84        22.36        25.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X 
       64.08        20.22         8.61        59.38        60.16        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       56.35        35.41         8.52        54.21        29.49        10.65 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LD 
       15.12        33.83        12.39        26.14        14.89        20.48 
TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IS 
       18.58         4.90        13.58        19.00        16.70        50.27 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 
       66.05        17.98        53.29        76.60        67.36        36.66 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-FD-A3NA TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS 
       13.64        56.15        60.66        29.16        46.78        12.85 
TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5C1 TCGA-FD-A6TB TCGA-FD-A6TG 
        3.62        53.88        10.78        58.92        18.81         3.06 
TCGA-FD-A6TI TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK 
        9.67        33.01        21.40        32.78        20.28        27.35 
TCGA-KQ-A41O TCGA-S5-A6DX TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SY 
       50.56         1.84        97.45       125.49        97.12        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR 
       18.90         2.10        13.74        10.82        11.31        91.73 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M 
       44.32        30.94        86.30         3.88         9.63        13.64 
TCGA-ZF-A9R2 TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 
       21.11        94.88        44.94        34.98        50.04        66.54 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O 
       17.42         7.33         6.74         6.58        13.15        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA 
       17.88        19.50         5.06        14.96         8.25        17.16 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A3MF TCGA-CF-A3MG 
        4.67        17.56        23.01        12.79        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       13.08        12.16        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-A9FM 
       12.26        13.12        12.00        12.10        11.34        13.08 
TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       29.79         1.84        66.41        16.14        17.62        15.62 
TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        7.79        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       15.35        43.59         5.36         2.24        16.70         0.66 
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-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV 
       32.02        12.62        27.98        14.96        20.91         5.36 
TCGA-FD-A62O TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO 
        7.10         8.94         3.25        48.00        26.93        59.31 
TCGA-G2-A3IB TCGA-G2-AA3B TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GU-A42Q 
        7.23        66.02        20.71        15.81         8.94        11.31 
TCGA-GU-A42R TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QI TCGA-H4-A2HO 
       18.97         7.00        14.27        21.34        36.49         1.51 
TCGA-HQ-A2OE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-S5-AA26 
       38.60         9.07        11.70         1.15        12.23        16.54 
TCGA-UY-A78P TCGA-UY-A9PA TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SX 
       78.25        35.24        17.88        64.80        66.41        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L 
       28.24        16.27        92.98        27.06         0.66        11.97 
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                          0.66 
  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 
                       17.735                        17.420 
[1] "0.5 - 166.0 (17.7)" "0.7 - 163.3 (17.4)"
[1] "hr=" "1.1"
D51V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(8P23.3) MUTATED         1       75        74       92
  DEL PEAK 14(8P23.3) WILD-TYPE       1       54        66       43
D51V3, multiclass
           clus
vv          DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  STAGE I                             1                             1
  STAGE II                           75                            54
  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         72 112  37
  DEL PEAK 14(8P23.3) WILD-TYPE       51  83  21
D51V4, multiclass
          clus
vv         DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  T0+T1+T2                          72                            51
  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   127  35  48   6
  DEL PEAK 14(8P23.3) WILD-TYPE 109  12  27   2
D51V5, multiclass
    clus
vv   DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  N0                         127                           109
  N1                          35                            12
  N2                          48                            27
  N3                           6                             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"
D51V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED   105   8
  DEL PEAK 14(8P23.3) WILD-TYPE  87   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED    105    8
  DEL PEAK 14(8P23.3) WILD-TYPE   87    3
   clus
vv  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  0                         105                            87
  1                           8                             3
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED    61 182
  DEL PEAK 14(8P23.3) WILD-TYPE  46 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     61  182
  DEL PEAK 14(8P23.3) WILD-TYPE   46  119
        clus
vv       DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  FEMALE                          61                            46
  MALE                           182                           119
[1] 2 2
[1] FALSE
D51V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED   216   9
  DEL PEAK 14(8P23.3) WILD-TYPE 148  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED    216    9
  DEL PEAK 14(8P23.3) WILD-TYPE  148   11
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  NO                          216                           148
  YES                           9                            11
[1] 2 2
[1] FALSE
D51V9, continuous
D51V10, continuous
D51V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.3) MUTATED      18                        18   198
  DEL PEAK 14(8P23.3) WILD-TYPE    25                         4   129
D51V12, multiclass
                           clus
vv                          DEL PEAK 14(8P23.3) MUTATED
  ASIAN                                              18
  BLACK OR AFRICAN AMERICAN                          18
  WHITE                                             198
                           clus
vv                          DEL PEAK 14(8P23.3) WILD-TYPE
  ASIAN                                                25
  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"
D51V13, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     5 220
  DEL PEAK 14(8P23.3) WILD-TYPE   4 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      5  220
  DEL PEAK 14(8P23.3) WILD-TYPE    4  149
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         220
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           149
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 15(8P21.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P21.3) MUTATED   146 104
  DEL PEAK 15(8P21.3) WILD-TYPE  81  74
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          250                           155 
  DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE 
                          104                            74 
$`DEL PEAK 15(8P21.3) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20W 
      108.95        16.27        16.77        15.12        33.83         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN 
       20.48        25.94         9.96        28.70         8.98        12.92 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       18.48         2.14       130.88        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6B2 
       17.72        21.30        23.21         9.67        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       50.70        38.24        52.01       165.73       166.03        13.64 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV 
       11.18        20.32        15.35        25.58         0.92         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR 
       29.16        19.79        12.85        27.35        15.58        26.73 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC 
        5.69         8.25        18.08         6.28        62.86         6.15 
TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P 
       12.69        12.36         4.31        31.07        17.23        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P 
       17.62        70.32        19.13        17.75        24.92        10.92 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       32.98        19.82        20.28         8.58        19.07        22.72 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
        9.01        25.02         3.45         2.76         9.14        27.68 
TCGA-KQ-A41N TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       52.73        35.97        46.98        14.24         1.84        33.14 
TCGA-UY-A9PH TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP 
       51.32        15.35         3.22        15.98        34.45        14.93 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T0 TCGA-XF-A9T3 TCGA-XF-A9T5 
        4.21        12.76        11.90        26.27         2.24        66.64 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-ZF-A9R4 
       54.90         7.63        71.57        98.99        61.45        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
        3.48        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7R TCGA-4Z-AA7W 
       24.13        11.97       104.65         8.35        17.16        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
        0.62        41.75        51.16        10.22        47.80         2.50 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A42E 
       40.08         2.66        19.04         5.06        16.18        36.43 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47S 
       28.41         1.94        12.56        13.97        12.16        10.95 
TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
       11.34        11.34        11.87         5.19        29.79        21.86 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       18.41       112.44        17.95       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 
        8.15        15.02        19.00        12.03        38.83        29.72 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A85H 
       22.16         0.56        26.96         4.24        13.68        12.95 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO 
       14.37         8.09        16.77         8.94        22.52         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62S 
       25.74        22.98        19.33        27.45         2.70        13.35 
TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EK 
        2.27        10.85        12.66        10.65        61.94        15.95 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12        66.02         6.94        29.36        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42R 
        0.49        13.91        26.70         2.10         3.12        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX 
        7.63        20.05        15.78         4.73        21.34        19.10 
TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH 
        8.48        19.40        64.01        12.16        21.24         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       17.72         1.81        15.42        16.27        11.80        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN 
       15.32        15.58        21.07        13.48        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A8OB 
       38.99        17.62        37.05        22.68        76.01        69.34 
TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF 
        3.02       112.83        29.56        17.82         6.21         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-AAMG 
       45.04         6.58         1.87        48.62        79.66       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN5 TCGA-YC-A89H 
        2.96         8.32         6.77        56.48        75.39        18.84 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RN 
       22.36        25.41        21.86        13.41        64.08        20.22 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        8.61        59.38        60.16        67.20        56.35        35.41 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
        8.52        54.21        29.49        10.65 

$`DEL PEAK 15(8P21.3) WILD-TYPE`
TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR 
       12.39        26.14        14.89        18.58         4.90        15.12 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A3X2 
       13.58        19.00        16.70        50.27        66.05        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA71 TCGA-DK-AA74 
       53.29        76.60        67.36        36.66        13.64        56.15 
TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5C1 TCGA-FD-A6TB 
       46.78         3.62        53.88        10.78        58.92        18.81 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GU-A763 TCGA-GV-A3QK 
        3.06         9.67        33.01        21.40        32.78        27.35 
TCGA-KQ-A41O TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SY 
       50.56        86.83        97.45       125.49        97.12        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR 
       18.90         2.10        13.74        10.82        11.31        91.73 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       44.32        30.94        86.30        18.58         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7O 
       13.64        21.11        94.29        94.88        44.94        16.83 
TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA83 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       34.98        50.04        66.54        17.42         7.33         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
        6.58        13.15        12.16        17.88        19.50         5.06 
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-A9FM TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       13.08         1.84        66.41        16.14        17.62        15.62 
TCGA-DK-A2I2 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        7.79        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       15.35        43.59         5.36         2.24        16.70         0.66 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 
       26.24        24.03        24.66        14.07        15.32        32.02 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O 
       12.62        27.98        14.96        20.91         5.36         7.10 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
        8.94         3.25        48.00        26.93        59.31         7.23 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       20.71        15.81         8.94        20.98         2.20        11.31 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A5RI 
        7.00        14.27        36.49         1.51        38.60        11.70 
TCGA-KQ-A41S TCGA-S5-AA26 TCGA-UY-A78P TCGA-UY-A9PA TCGA-XF-A8HI TCGA-XF-A9SH 
        1.15        16.54        78.25        35.24        17.88        64.80 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAN4 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
       27.06         0.66        11.97        31.20        35.84        28.41 
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                          0.66 
  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 
                       17.785                        17.160 
[1] "0.5 - 166.0 (17.8)" "0.7 - 163.3 (17.2)"
[1] "hr=" "1.1"
D52V2, 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
D52V3, 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
D52V4, 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   133  33  51   7
  DEL PEAK 15(8P21.3) WILD-TYPE 103  14  24   1
D52V5, multiclass
    clus
vv   DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  N0                         133                           103
  N1                          33                            14
  N2                          51                            24
  N3                           7                             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"
D52V6, 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
D52V7, 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
D52V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.3) MUTATED   224  10
  DEL PEAK 15(8P21.3) WILD-TYPE 140  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.3) MUTATED    224   10
  DEL PEAK 15(8P21.3) WILD-TYPE  140   10
     clus
vv    DEL PEAK 15(8P21.3) MUTATED DEL PEAK 15(8P21.3) WILD-TYPE
  NO                          224                           140
  YES                          10                            10
[1] 2 2
[1] FALSE
D52V9, continuous
D52V10, continuous
D52V11, 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
D52V12, 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"
D52V13, 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(53) Variable = DEL PEAK 16(9P23) MUTATION ANALYSIS
D53V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(9P23) MUTATED   103  72
  DEL PEAK 16(9P23) WILD-TYPE 124 106
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                        175                         230 
  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                         72                         106 
$`DEL PEAK 16(9P23) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PK 
      108.95        16.27        26.14        14.89         8.35         9.96 
TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA 
       28.70        18.58         4.90        18.48        13.58        19.00 
TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 
       16.70         8.22        17.72        50.27        21.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6W 
       17.98        64.18        15.68        50.70       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3SM 
       13.64        11.18        20.32        25.58         0.92        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A5BR TCGA-FD-A5C0 
       29.16        46.78        19.79        12.85        26.73        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FT-A61P 
       58.92         6.28        62.86        18.81         3.06        11.08 
TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3YS TCGA-GU-AATP TCGA-GV-A3QK TCGA-GV-A6ZA 
       17.62        70.32        24.92        32.98        27.35        22.72 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q 
       25.02         3.45         2.76        50.56        35.97        46.98 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       14.24         1.84        15.98         4.21        12.76        11.90 
TCGA-XF-A9T0 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       26.27        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-2F-A9KP 
       18.58        21.11        94.29         3.48        88.87        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7Y 
       94.88       104.65         8.35        16.83        34.98        50.04 
TCGA-4Z-AA80 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20Q 
        0.62        17.42        40.08        13.15        19.04        19.50 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C 
       17.16        16.18        36.43         1.94        12.79        13.97 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5U8 
       12.59        12.13        13.08        12.16        12.62        13.12 
TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       12.00        11.34        11.87        29.79         1.84        21.86 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3WX TCGA-DK-AA6P 
       17.62        15.62        17.95         4.80        10.55        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 
       13.58        19.00        15.35        12.03        43.59        38.83 
TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A97Q 
       29.72         0.56         0.66         4.24        13.68         8.09 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O 
       16.77         8.94        22.98         5.36        27.45         7.10 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3ZE TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A3IB 
       13.35        10.85        10.65        48.00        59.31         7.23 
TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS 
       66.02        29.36        14.07         8.94         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW 
        2.20        11.31         7.63         4.73         7.00        21.34 
TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH 
        8.48        19.40        38.60        64.01        21.24         9.07 
TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT 
       11.70        15.42        11.80        44.38         1.15        21.07 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A8OB TCGA-UY-A8OD 
       12.23        16.67        16.54        38.99        69.34       112.83 
TCGA-UY-A9PE TCGA-XF-A8HI TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAMX TCGA-YF-AA3L 
        6.21        17.88         5.98        16.27         6.77        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-AA4U TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       25.41        28.41         8.61        56.35        19.40         8.52 
TCGA-GU-AATO 
       10.65 

$`DEL PEAK 16(9P23) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ 
       16.77        15.12        33.83        12.39        20.48        25.94 
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A2HX 
        8.98        12.92        15.12         2.14       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 
       87.32        23.21         9.67        53.29        76.60        67.36 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E5-A4TZ 
       36.66        38.24        52.01       165.73        56.15        15.35 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35         3.62        15.58        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI 
        8.25         6.15        12.69        12.36         4.31         9.67 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC 
       31.07        17.23        33.01        21.40        19.13        17.75 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G 
       10.92        32.78        19.82        20.28         8.58        19.07 
TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-SY-A9G0 TCGA-UY-A78N 
        9.01         9.14        27.68        52.73        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ 
       51.32        97.45       125.49        97.12        15.35         3.22 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       34.45        14.93        21.04        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.10        13.74        10.82        11.31        54.90         7.63 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 
       61.45        86.30         3.88         9.63        13.64        30.28 
TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-4Z-AA7N 
       34.06        19.69        57.90        12.23        24.13        44.94 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 
       17.16        27.62        41.75        51.16        66.54        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 
       47.80         2.50         7.33         2.66         6.74         6.58 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88         5.06        14.96         5.06         8.25 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HS TCGA-CF-A47S 
        4.67        17.56        28.41        23.01        12.56        10.95 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A7I0 TCGA-CF-A8HX 
       12.66        12.46        12.10        12.26        12.10        11.34 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE 
       13.08         5.19        66.41        18.41       112.44        16.14 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WY 
        7.79       142.78        13.58         8.15        20.81       163.30 
TCGA-DK-AA6T TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A677 
       18.81         5.36        22.16         2.24        16.70        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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       14.37        32.02        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N TCGA-FD-A6TF 
       25.74        14.96        20.91        19.33         2.70         2.27 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EL 
       12.66         8.94         3.25        61.94        15.95        26.93 
TCGA-G2-A3IE TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW 
       20.12         6.94        20.71        15.81        15.91         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A42R TCGA-GU-A764 TCGA-GU-A766 
       13.91        26.70         2.10        18.97        20.05        15.78 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A5RJ 
       14.27        19.10        36.49         1.51        12.16        17.72 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K 
        1.81        16.27        15.32        15.58        13.48        17.62 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PA 
       37.05        22.68        76.01        78.25         3.02        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       29.56        17.82         3.85        45.04         6.58         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ 
       48.62        64.80        79.66        66.41        23.64        28.24 
TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 
       92.98       110.60         2.96         8.32        56.48        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 
       75.39        18.84         0.66        22.36        31.20        35.84 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN 
       21.86        13.41        64.08        58.72        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 
        2.89        59.38        60.16        67.20        35.41        54.21 
TCGA-ZF-AA5H TCGA-ZF-AA5N 
       29.49         5.52 

  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE 
                       0.56                        0.49 
  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 
                     16.700                      18.825 
[1] "0.6 - 166.0 (16.7)" "0.5 - 165.7 (18.8)"
[1] "hr=" "1"  
D53V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(9P23) MUTATED         1       56        65       54
  DEL PEAK 16(9P23) WILD-TYPE       1       73        75       81
D53V3, 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                         54                          81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1+T2  T3  T4
  DEL PEAK 16(9P23) MUTATED         52  86  25
  DEL PEAK 16(9P23) WILD-TYPE       71 109  33
D53V4, multiclass
          clus
vv         DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  T0+T1+T2                        52                          71
  T3                              86                         109
  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 16(9P23) MUTATED   108  18  32   4
  DEL PEAK 16(9P23) WILD-TYPE 128  29  43   4
D53V5, multiclass
    clus
vv   DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  N0                       108                         128
  N1                        18                          29
  N2                        32                          43
  N3                         4                           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"
D53V6, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    86   5
  DEL PEAK 16(9P23) WILD-TYPE 106   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     86    5
  DEL PEAK 16(9P23) WILD-TYPE  106    6
   clus
vv  DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  0                        86                         106
  1                         5                           6
[1] 2 2
[1] FALSE
D53V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED    48 129
  DEL PEAK 16(9P23) WILD-TYPE  59 172
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED     48  129
  DEL PEAK 16(9P23) WILD-TYPE   59  172
        clus
vv       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  FEMALE                        48                          59
  MALE                         129                         172
[1] 2 2
[1] FALSE
D53V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED   159  10
  DEL PEAK 16(9P23) WILD-TYPE 205  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED    159   10
  DEL PEAK 16(9P23) WILD-TYPE  205   10
     clus
vv    DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  NO                        159                         205
  YES                        10                          10
[1] 2 2
[1] FALSE
D53V9, continuous
D53V10, continuous
D53V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P23) MUTATED      18                        10   140
  DEL PEAK 16(9P23) WILD-TYPE    25                        12   187
D53V12, multiclass
                           clus
vv                          DEL PEAK 16(9P23) MUTATED
  ASIAN                                            18
  BLACK OR AFRICAN AMERICAN                        10
  WHITE                                           140
                           clus
vv                          DEL PEAK 16(9P23) WILD-TYPE
  ASIAN                                              25
  BLACK OR AFRICAN AMERICAN                          12
  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"
D53V13, binary
                             cls
clus                            0   1
  DEL PEAK 16(9P23) MUTATED     4 161
  DEL PEAK 16(9P23) WILD-TYPE   5 208
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(9P23) MUTATED      4  161
  DEL PEAK 16(9P23) WILD-TYPE    5  208
                        clus
vv                       DEL PEAK 16(9P23) MUTATED DEL PEAK 16(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           5
  NOT HISPANIC OR LATINO                       161                         208
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 17(9P21.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9P21.3) MUTATED   132 105
  DEL PEAK 17(9P21.3) WILD-TYPE  95  73
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          237                           168 
  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                          105                            73 
$`DEL PEAK 17(9P21.3) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        33.83        12.39        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ 
        8.35         9.96        28.70        18.58         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A3IQ 
       13.58         2.14        19.00        16.70         8.22        17.72 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B2 
       50.27        21.30        66.05        17.98        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 
       50.70       166.03        13.64        13.64        11.18        20.32 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3NA TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
       25.58         0.92        60.66        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BX 
       19.79        12.85         3.62        15.58        26.73         5.69 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD 
       18.08        58.92         6.28        62.86        18.81        12.69 
TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM 
        3.06        31.07        11.08        17.62        70.32        21.40 
TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E 
       24.92        32.78        32.98        20.28        27.35         8.58 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A9PH 
       50.56        35.97        46.98        14.24         1.84        51.32 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
      125.49        97.12        15.98         4.21        12.76        11.90 
TCGA-XF-A9T0 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY 
       26.27        66.64        13.74        71.57        91.73        98.99 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       44.32        30.94        86.30        18.58        21.11        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ 
        3.48        88.87        57.90        24.13        11.97        94.88 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y 
      104.65         8.35        16.83        34.98        27.62        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
        0.62        51.16        17.42        40.08         7.33         2.66 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U 
        6.58        13.15        19.04        17.88        19.50        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
        5.06         8.25        16.18        17.56        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-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.34        11.87        29.79         1.84        21.86 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3WW 
       16.14        17.62        15.62        17.95         4.80        20.81 
TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 
       10.55        15.02        13.58        19.00        15.35        12.03 
TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A677 
       43.59        38.83        29.72         0.56         0.66        26.96 
TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
        4.24        13.68        12.95        15.32        14.37         8.09 
TCGA-FD-A3B5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BU 
        8.94        27.98        25.74        22.98        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3ZE 
        5.36        27.45         7.10        13.35        10.85        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B 
        8.94        61.94        59.31         7.23        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ 
        6.94        29.36        14.07         8.94        13.91         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 
       20.98         2.20        11.31        18.97         7.63         4.73 
TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF 
        7.00        21.34         8.48        19.40        38.60        64.01 
TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41R 
       21.24         9.07        11.70        15.42        11.80        44.38 
TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
        1.15        21.07        12.23        16.67        16.54        38.99 
TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PD 
       22.68        78.25        69.34         3.02       112.83        17.82 
TCGA-UY-A9PE TCGA-XF-A8HI TCGA-XF-A9SU TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX 
        6.21        17.88         5.98         2.96         8.32         6.77 
TCGA-XF-AAN5 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
       21.86        28.41        20.22         8.61        60.16        56.35 
TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-GU-AATO 
       19.40         8.52        10.65 

$`DEL PEAK 17(9P21.3) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-C4-A0EZ TCGA-CU-A0YN 
       16.77        15.12        20.48        25.94         8.98        12.92 
TCGA-CU-A0YR TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IU TCGA-DK-A3IV 
       15.12       130.88        46.68        87.32        23.21         9.67 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       53.29        76.60        67.36        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 
      165.73        56.15        15.35         1.22        33.04         4.01 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY 
       24.30        23.41        27.35        53.88        10.78         8.25 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES 
        6.15        12.36         4.31         9.67        17.23        33.01 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A40G TCGA-K4-A54R 
       19.13        17.75        10.92        19.82        19.07        27.68 
TCGA-KQ-A41N TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HG TCGA-XF-A9SJ 
       52.73        33.14        86.83        97.45        15.35         3.22 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T6 
       34.45        14.93        21.04        18.90         2.24         2.10 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN8 
       10.82        11.31        54.90         7.63        61.45         3.88 
TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA5P 
        9.63        13.64        30.28        34.06        19.69        12.23 
TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 
       44.94        17.16        41.75        66.54        10.22        47.80 
TCGA-5N-A9KI TCGA-BL-A3JM TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A3PH 
        2.50         6.74        12.16         5.06        17.16         4.67 
TCGA-BT-A42F TCGA-CF-A1HS TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y 
       28.41        12.56        10.95        12.46        12.10        12.26 
TCGA-CF-A9FM TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I2 
       13.08         5.19        66.41        18.41       112.44         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WY TCGA-DK-AA6T TCGA-E7-A3Y1 
      142.78        13.58         8.15       163.30        18.81         5.36 
TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF 
       22.16         2.24        16.70        26.24        24.03        24.66 
TCGA-E7-A7XN TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SO 
       14.07        32.02        16.77        12.62        22.52         5.52 
TCGA-FD-A43S TCGA-FD-A62N TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ 
       14.96         2.70         2.27        12.66         3.25        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW 
       15.95        26.93        20.71        15.81        15.91         0.49 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV TCGA-GV-A3JX 
       26.70         2.10        20.05        15.78        14.27        19.10 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P 
       36.49         1.51        12.16        17.72         1.81        16.27 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       15.32        15.58        13.48        17.62        37.05        76.01 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH 
       35.24        29.56         3.85        45.04         6.58         1.87 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ 
       48.62        64.80        79.66        66.41        23.64        28.24 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A89H 
       16.27        92.98       110.60        56.48        27.06        18.84 
TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       35.84        13.41        64.08        58.72        47.84         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       59.38        67.20        35.41        54.21        29.49         5.52 

  DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE 
                         0.56                          0.49 
  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 
                        17.42                         18.61 
[1] "0.6 - 166.0 (17.4)" "0.5 - 165.7 (18.6)"
[1] "hr=" "1.1"
D54V2, 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
D54V3, 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
D54V4, 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  94  21  33   4
D54V5, multiclass
    clus
vv   DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  N0                         142                            94
  N1                          26                            21
  N2                          42                            33
  N3                           4                             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"
D54V6, 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
D54V7, 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
D54V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(9P21.3) MUTATED   215  13
  DEL PEAK 17(9P21.3) WILD-TYPE 149   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9P21.3) MUTATED    215   13
  DEL PEAK 17(9P21.3) WILD-TYPE  149    7
     clus
vv    DEL PEAK 17(9P21.3) MUTATED DEL PEAK 17(9P21.3) WILD-TYPE
  NO                          215                           149
  YES                          13                             7
[1] 2 2
[1] FALSE
D54V9, continuous
D54V10, continuous
D54V11, 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
D54V12, 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"
D54V13, 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(55) Variable = DEL PEAK 18(9Q22.33) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(9Q22.33) MUTATED   104  73
  DEL PEAK 18(9Q22.33) WILD-TYPE 123 105
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                           177                            228 
  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                            73                            105 
$`DEL PEAK 18(9Q22.33) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A2LD 
      108.95        16.27        33.83        26.14        14.89        20.48 
TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       28.70        18.58         4.90        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV 
       19.00        17.72        50.27        21.30        17.98        64.18 
TCGA-DK-A6B5 TCGA-DK-AA6W TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU 
       50.70        13.64        11.18        20.32        25.58         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR 
        1.22        33.04         4.01        17.98        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5C0 TCGA-FD-A5C1 
       12.85         3.62        15.58        26.73        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-FT-A61P 
        6.28        62.86        18.81         3.06        31.07        11.08 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QK TCGA-GV-A40G 
       17.62        21.40        32.78        32.98        27.35        19.07 
TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P 
       22.72         3.45         2.76        27.68        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A8HG 
       46.98        14.24         1.84        33.14        97.12        15.35 
TCGA-XF-A9SK TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-AAMQ TCGA-XF-AAMR 
       15.98         4.21        12.76        26.27        71.57        91.73 
TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC 
       44.32        30.94        18.58        13.64        21.11        94.29 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR 
        3.48        88.87        24.13        11.97        94.88       104.65 
TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 
        8.35        16.83        17.16        34.98        50.04         0.62 
TCGA-4Z-AA83 TCGA-5N-A9KM TCGA-BT-A0S7 TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A2LB 
       66.54        17.42         6.58        17.88        19.50        16.18 
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-A47S TCGA-CF-A47V TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HX TCGA-CF-A8HY 
       10.95        12.46        12.62        13.12        11.34        11.34 
TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A6 TCGA-DK-A1AD 
       11.87        13.08         5.19         1.84        66.41       112.44 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3WX TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X 
       17.62        15.62        10.55        15.02        19.00        15.35 
TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A519 TCGA-E7-A5KE 
       12.03        43.59        38.83        29.72        16.70         0.56 
TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43N 
        0.66         4.24        13.68         8.09         8.94        22.98 
TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A62O TCGA-FD-A6TF TCGA-G2-A2EK TCGA-G2-A2EL 
       19.33        27.45         7.10         2.27        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RD TCGA-GC-A4ZW 
       59.31        20.12        66.02        29.36        14.07         0.49 
TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A767 TCGA-GV-A3JV 
        8.94        26.70         2.10         2.20         4.73        14.27 
TCGA-GV-A3JW TCGA-GV-A3QH TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI 
       21.34         8.48        38.60        64.01        21.24        11.70 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       11.80         1.15        21.07        16.67        16.54        38.99 
TCGA-UY-A78O TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SU 
       76.01        17.82         3.85        17.88        64.80         5.98 
TCGA-XF-AAMW TCGA-XF-AAN5 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        8.32        75.39        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA51 
       21.86        28.41        64.08        20.22         8.61        56.35 
TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-GU-AATO 
       19.40        54.21        10.65 

$`DEL PEAK 18(9Q22.33) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK 
       16.77        15.12        12.39         8.35        25.94         9.96 
TCGA-C4-A0EZ TCGA-CU-A0YN TCGA-CU-A0YR TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX 
        8.98        12.92        15.12        16.70       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AW 
       87.32         8.22        23.21         9.67        66.05        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       76.60        67.36        15.68        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-E5-A4TZ TCGA-FD-A3NA 
      165.73       166.03        13.64        56.15        15.35        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A43P TCGA-FD-A5BS TCGA-FD-A5BT 
       24.30        23.41        29.16        27.35        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TH 
        5.69         8.25         6.15        12.69        12.36         4.31 
TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
        9.67        17.23        33.01        70.32        19.13        17.75 
TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-HQ-A5ND 
       24.92        10.92        19.82        20.28         8.58         9.01 
TCGA-K4-A3WS TCGA-K4-A4AC TCGA-KQ-A41N TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       25.02         9.14        52.73        86.83        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9SW TCGA-XF-A9SY 
      125.49         3.22        34.45        14.93        11.90        21.04 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF 
       18.90         2.24        66.64         2.10        13.74        10.82 
TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAN2 TCGA-XF-AAN3 
       11.31        54.90         7.63        98.99        61.45        86.30 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
        3.88         9.63        30.28        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-4Z-AA7N TCGA-4Z-AA7W TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA86 
       12.23        44.94        27.62        41.75        51.16        10.22 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       47.80         2.50        40.08         7.33         2.66         6.74 
TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V 
       13.15        19.04        12.16         5.06        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
        8.25        17.16         4.67        17.56        36.43        28.41 
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-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AE 
       12.00        12.10        29.79        21.86        18.41        16.14 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       17.95         7.79       142.78         4.80        13.58         8.15 
TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       20.81       163.30        13.58        18.81         5.36        22.16 
TCGA-E7-A4XJ TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7XN 
        2.24        26.96        26.24        24.03        24.66        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-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U 
       22.52        27.98         5.52        25.74        14.96        20.91 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
        5.36         2.70        13.35        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-G2-AA3C 
        8.94         3.25        61.94        48.00         7.23         6.94 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS 
       20.71        15.81        15.91        13.91         3.12        20.98 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-AATQ 
       11.31        18.97         7.63        20.05        15.78         7.00 
TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A5RH 
       19.10        36.49         1.51        19.40        12.16         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R 
       17.72         1.81        15.42        16.27        44.38        15.32 
TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       15.58        13.48        12.23        17.62        37.05        22.68 
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        35.24        29.56 
TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI 
        6.21        45.04         6.58         1.87        48.62        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       66.41        23.64        28.24        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-YC-A89H TCGA-YC-A9TC 
        2.96         6.77        56.48        27.06        18.84         0.66 
TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V 
       35.84        13.41        58.72        47.84         2.89        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       60.16        67.20        35.41         8.52        29.49         5.52 

  DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE 
                          0.49                           0.66 
  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 
                        17.880                         16.965 
[1] "0.5 - 112.4 (17.9)" "0.7 - 166.0 (17.0)"
[1] "hr=" "1.1"
D55V2, 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
D55V3, 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
D55V4, 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 130  30  43   4
D55V5, multiclass
    clus
vv   DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  N0                          106                            130
  N1                           17                             30
  N2                           32                             43
  N3                            4                              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"
D55V6, 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
D55V7, 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
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(9Q22.33) MUTATED   160  10
  DEL PEAK 18(9Q22.33) WILD-TYPE 204  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(9Q22.33) MUTATED    160   10
  DEL PEAK 18(9Q22.33) WILD-TYPE  204   10
     clus
vv    DEL PEAK 18(9Q22.33) MUTATED DEL PEAK 18(9Q22.33) WILD-TYPE
  NO                           160                            204
  YES                           10                             10
[1] 2 2
[1] FALSE
D55V9, continuous
D55V10, continuous
D55V11, 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
D55V12, 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"
D55V13, 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(56) Variable = DEL PEAK 19(10P11.21) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 19(10P11.21) MUTATED    38  36
  DEL PEAK 19(10P11.21) WILD-TYPE 189 142
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             74                             331 
  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                             36                             142 
$`DEL PEAK 19(10P11.21) MUTATED`
TCGA-4Z-AA7Q TCGA-BT-A42C TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-DK-A2HX TCGA-DK-A3IS 
       16.77        28.70        15.12        18.48        46.68        50.27 
TCGA-DK-A3IT TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ 
       21.30        38.24        52.01        13.64        11.18        15.35 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y 
       25.58         1.22         4.01        19.79        12.85        15.58 
TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-AA3D TCGA-GC-A3BM 
        8.25        12.69        31.07        17.23        70.32        21.40 
TCGA-GC-A3WC TCGA-GV-A40G TCGA-K4-A3WU TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-XF-A8HE 
       17.75        19.07         3.45        50.56        46.98       125.49 
TCGA-XF-A9SV TCGA-XF-AAMF TCGA-ZF-A9RE TCGA-2F-A9KR TCGA-BT-A20J TCGA-BT-A20U 
       12.76        10.82         3.48       104.65        19.04        14.96 
TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A27C TCGA-CF-A8HY TCGA-CU-A5W6 TCGA-DK-A2I2 
       17.16         1.94        13.97        11.34         1.84         7.79 
TCGA-DK-A3IK TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
        4.80        15.02        19.00        15.35        12.03        43.59 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FJ-A3ZE TCGA-G2-A2EL TCGA-G2-A3IB 
       16.77         8.94        22.52        10.65        26.93         7.23 
TCGA-GC-A3RC TCGA-GC-A6I3 TCGA-H4-A2HQ TCGA-K4-A5RH TCGA-K4-A5RI TCGA-MV-A51V 
       15.91        13.91        19.40         9.07        11.70        13.48 
TCGA-PQ-A6FI TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG 
       12.23        29.56         6.21         6.58         1.87        48.62 
TCGA-XF-A9SI TCGA-XF-AAMX TCGA-ZF-A9R1 TCGA-ZF-A9RD TCGA-ZF-A9RM TCGA-ZF-AA4N 
       79.66         6.77        25.41        13.41        47.84         2.89 
TCGA-ZF-AA4W TCGA-ZF-AA56 
       60.16         8.52 

$`DEL PEAK 19(10P11.21) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        15.12        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ 
       14.89         8.35        20.48        25.94         9.96         8.98 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       18.58        12.92         4.90        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU 
       16.70       130.88        87.32         8.22        17.72        23.21 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
        9.67        66.05        17.98        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S 
       67.36        15.68        50.70        36.66       165.73       166.03 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3NA 
       13.64        56.15        20.32         0.92        33.04        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43P 
       24.30        23.41        17.98        29.16        46.78        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 
        3.62        26.73        53.88        10.78         5.69        18.08 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE 
       58.92         6.28        62.86        18.81         6.15        12.36 
TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY 
        3.06         4.31         9.67        11.08        33.01        17.62 
TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       19.13        24.92        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       20.28        27.35         8.58        22.72         9.01        25.02 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X 
        2.76         9.14        27.68        52.73        35.97        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF 
        1.84        33.14        86.83        51.32        97.45        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST 
       15.35         3.22        15.98        34.45        14.93         4.21 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       11.90        21.04        26.27        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
        2.10        13.74        11.31        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29        88.87        34.06        19.69        57.90        12.23 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       24.13        11.97        94.88         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       17.16        34.98        27.62        50.04         0.62        41.75 
TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       51.16        66.54        10.22        47.80         2.50        17.42 
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A20X 
       12.16        17.88        19.50         5.06         5.06         8.25 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 
       16.18         4.67        17.56        36.43        28.41        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-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD 
        5.19        29.79        21.86        66.41        18.41       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IL 
       16.14        17.62        15.62        17.95       142.78        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
        8.15        20.81        10.55       163.30        13.58        18.81 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        13.68        14.07        12.95        15.32        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.09        32.02        12.62        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        8.94         3.25        61.94        48.00        15.95        59.31 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       20.12        66.02         6.94        29.36        20.71        15.81 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07         0.49         8.94        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 
       20.98         2.20        11.31        18.97         7.63        20.05 
TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
       15.78         4.73         7.00        14.27        21.34        19.10 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
        8.48        36.49         1.51        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO 
       21.24        17.72         1.81        15.42        16.27        11.80 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN 
       44.38         1.15        15.32        15.58        21.07        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O 
       16.54        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-A9PD 
       78.25        69.34         3.02       112.83        35.24        17.82 
TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SU 
        3.85        45.04        17.88        64.80        66.41         5.98 
TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT 
       23.64        28.24        16.27        92.98       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
       11.97        22.36        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       64.08        58.72        20.22         8.61        59.38        67.20 
TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N 
       56.35        35.41        19.40        54.21        29.49         5.52 
TCGA-GU-AATO 
       10.65 

  DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE 
                           1.22                            0.49 
  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                           17.98 
[1] "1.2 - 125.5 (15.3)" "0.5 - 166.0 (18.0)"
[1] "hr=" "1.3"
D56V2, 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
D56V3, 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
D56V4, 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 190  41  62   4
D56V5, multiclass
    clus
vv   DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  N0                            46                             190
  N1                             6                              41
  N2                            13                              62
  N3                             4                               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"
D56V6, 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
D56V7, 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
D56V8, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10P11.21) MUTATED    67   4
  DEL PEAK 19(10P11.21) WILD-TYPE 297  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10P11.21) MUTATED     67    4
  DEL PEAK 19(10P11.21) WILD-TYPE  297   16
     clus
vv    DEL PEAK 19(10P11.21) MUTATED DEL PEAK 19(10P11.21) WILD-TYPE
  NO                             67                             297
  YES                             4                              16
[1] 2 2
[1] FALSE
D56V9, continuous
D56V10, continuous
D56V11, 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
D56V12, 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"
D56V13, 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(57) Variable = DEL PEAK 20(10Q23.31) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 20(10Q23.31) MUTATED    86  81
  DEL PEAK 20(10Q23.31) WILD-TYPE 141  97
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                            167                             238 
  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                             81                              97 
$`DEL PEAK 20(10Q23.31) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD 
       16.27        16.77        15.12        26.14         8.35        20.48 
TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
        4.90        18.48         2.14        46.68        87.32         8.22 
TCGA-DK-A3IS TCGA-DK-A3IV TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       50.27         9.67        67.36        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E7-A541 TCGA-E7-A7DV 
      165.73       166.03        13.64        11.18        25.58         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       33.04         4.01        24.30        19.79        12.85        27.35 
TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
        8.25        58.92        62.86        12.69        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GU-A42P TCGA-GV-A3JZ 
       11.08        17.62        21.40        17.75        10.92        19.82 
TCGA-GV-A3QF TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU 
       20.28        19.07        22.72         9.01        25.02         3.45 
TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-XF-A8HD 
        9.14        27.68        50.56        35.97        46.98        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9T8 
      125.49        97.12         3.22        14.93        12.76        13.74 
TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN7 
       10.82        54.90         7.63        44.32        61.45        18.58 
TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T 
       13.64        21.11        94.29         3.48        34.06        19.69 
TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7R TCGA-4Z-AA82 TCGA-5N-A9KI 
       24.13        11.97       104.65        17.16        51.16         2.50 
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A42B 
       40.08         2.66         5.06        14.96         5.06        17.56 
TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A8HY TCGA-CU-A3QU TCGA-CU-A5W6 
        1.94        23.01        13.97        11.34         5.19         1.84 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I2 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       18.41       112.44         7.79         4.80        13.58         8.15 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
       15.02        19.00        15.35        12.03        43.59        29.72 
TCGA-E7-A4IJ TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A8O7 TCGA-FD-A3N5 TCGA-FD-A43N 
       22.16        24.03        13.68        15.32        22.52        22.98 
TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-G2-A2EK TCGA-G2-A2EL 
       20.91        27.45         2.27        10.65        15.95        26.93 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3RC 
        7.23        20.12        66.02         6.94        29.36        15.91 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GU-A764 
       14.07         0.49         8.94        13.91         2.10        20.05 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI 
        4.73         7.00        21.34        19.10         8.48        36.49 
TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       19.40        64.01         9.07        11.70        17.72         1.81 
TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
       11.80         1.15        15.32        15.58        13.48        12.23 
TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC 
       38.99        76.01        35.24        17.82         6.21         6.58 
TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-AAMT 
        1.87        48.62        79.66         5.98        23.64         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9RM TCGA-ZF-A9RN 
        8.32         6.77        11.97        22.36        47.84        20.22 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 
        2.89         8.61        67.20        56.35        35.41 

$`DEL PEAK 20(10Q23.31) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A3PJ TCGA-BT-A3PK 
      108.95        33.83        12.39        14.89        25.94         9.96 
TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A72E 
       28.70         8.98        18.58        12.92        15.12        13.58 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
       19.00        16.70       130.88        17.72        21.30        23.21 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 
       66.05        17.98        64.18        53.29        76.60        15.68 
TCGA-DK-A6B5 TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU 
       50.70        13.64        56.15        20.32        15.35         0.92 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A43X 
       60.66        23.41        17.98        29.16        46.78         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 
       15.58        26.73        53.88        10.78         5.69        18.08 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28        18.81         6.15        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A763 
        9.67        33.01        70.32        19.13        24.92        32.78 
TCGA-GU-AATP TCGA-GV-A3QK TCGA-GV-A40E TCGA-K4-A4AB TCGA-KQ-A41N TCGA-R3-A69X 
       32.98        27.35         8.58         2.76        52.73        14.24 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HG TCGA-XF-A9SK 
        1.84        33.14        86.83        51.32        15.35        15.98 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       34.45         4.21        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.24        66.64         2.10        11.31        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 
       98.99        30.94        86.30         3.88         9.63        30.28 
TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N 
       88.87        57.90        12.23        94.88         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 
       16.83        34.98        27.62        50.04         0.62        41.75 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM 
       66.54        10.22        47.80        17.42         7.33         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-BT-A42F 
        8.25        17.16        16.18         4.67        36.43        28.41 
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-A9FM 
       13.12        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       29.79        21.86        66.41        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
       17.95       142.78        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       18.81        38.83         5.36         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-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 
       12.95        14.37         8.09        32.02        16.77         8.94 
TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU 
       12.62        27.98         5.52        25.74        14.96        19.33 
TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 
        5.36         2.70         7.10        13.35        10.85        12.66 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-GC-A3I6 
        8.94         3.25        61.94        48.00        59.31        20.71 
TCGA-GC-A3OO TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A42Q 
       15.81        26.70         3.12        20.98         2.20        11.31 
TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GV-A3JV TCGA-H4-A2HO TCGA-HQ-A2OE 
       18.97         7.63        15.78        14.27         1.51        38.60 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-LT-A8JT 
       12.16        21.24        15.42        16.27        44.38        21.07 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P 
       16.67        16.54        17.62        37.05        22.68        78.25 
TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB 
       69.34         3.02       112.83        29.56         3.85        45.04 
TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       17.88        64.80        66.41        28.24        16.27        92.98 
TCGA-XF-AAMG TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
      110.60        56.48        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA54 TCGA-ZF-AA56 
       64.08        58.72        59.38        60.16        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE 
                           0.49                            0.56 
  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 
                          17.56                           17.80 
[1] "0.5 - 166.0 (17.6)" "0.6 - 163.3 (17.8)"
[1] "hr=" "1.3"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(10Q23.31) MUTATED         1       55        52       60
  DEL PEAK 20(10Q23.31) WILD-TYPE       1       74        88       75
D57V3, multiclass
           clus
vv          DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  STAGE I                               1                               1
  STAGE II                             55                              74
  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
  DEL PEAK 20(10Q23.31) MUTATED         48  80  22
  DEL PEAK 20(10Q23.31) WILD-TYPE       75 115  36
D57V4, multiclass
          clus
vv         DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  T0+T1+T2                            48                              75
  T3                                  80                             115
  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 20(10Q23.31) MUTATED    85  20  31   6
  DEL PEAK 20(10Q23.31) WILD-TYPE 151  27  44   2
D57V5, multiclass
    clus
vv   DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  N0                            85                             151
  N1                            20                              27
  N2                            31                              44
  N3                             6                               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"
D57V6, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED    71   6
  DEL PEAK 20(10Q23.31) WILD-TYPE 121   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED     71    6
  DEL PEAK 20(10Q23.31) WILD-TYPE  121    5
   clus
vv  DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  0                            71                             121
  1                             6                               5
[1] 2 2
[1] FALSE
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED    44 124
  DEL PEAK 20(10Q23.31) WILD-TYPE  63 177
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED     44  124
  DEL PEAK 20(10Q23.31) WILD-TYPE   63  177
        clus
vv       DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  FEMALE                            44                              63
  MALE                             124                             177
[1] 2 2
[1] FALSE
D57V8, binary
                                 cls
clus                                0   1
  DEL PEAK 20(10Q23.31) MUTATED   147   9
  DEL PEAK 20(10Q23.31) WILD-TYPE 217  11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED    147    9
  DEL PEAK 20(10Q23.31) WILD-TYPE  217   11
     clus
vv    DEL PEAK 20(10Q23.31) MUTATED DEL PEAK 20(10Q23.31) WILD-TYPE
  NO                            147                             217
  YES                             9                              11
[1] 2 2
[1] FALSE
D57V9, continuous
D57V10, continuous
D57V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q23.31) MUTATED      10                        10   138
  DEL PEAK 20(10Q23.31) WILD-TYPE    33                        12   189
D57V12, multiclass
                           clus
vv                          DEL PEAK 20(10Q23.31) MUTATED
  ASIAN                                                10
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               138
                           clus
vv                          DEL PEAK 20(10Q23.31) WILD-TYPE
  ASIAN                                                  33
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 189
[1] 3 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 20(10Q23.31) MUTATED     3 151
  DEL PEAK 20(10Q23.31) WILD-TYPE   6 218
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(10Q23.31) MUTATED      3  151
  DEL PEAK 20(10Q23.31) WILD-TYPE    6  218
                        clus
vv                       DEL PEAK 20(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           151
                        clus
vv                       DEL PEAK 20(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             218
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(11P15.5) MUTATED   114  95
  DEL PEAK 21(11P15.5) WILD-TYPE 113  83
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           209                            196 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            95                             83 
$`DEL PEAK 21(11P15.5) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.77        15.12        33.83        26.14        14.89 
TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YR TCGA-CU-A3KJ 
        8.35         9.96        28.70         8.98        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       13.58         2.14        16.70        46.68        87.32         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 
       17.72        50.27        21.30        17.98        64.18        50.70 
TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ 
       38.24       165.73       166.03        56.15        20.32        15.35 
TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SL 
       25.58         0.92         1.22         4.01        24.30        23.41 
TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5C0 TCGA-FD-A5C1 
       29.16        19.79        12.85        15.58        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FJ-A3Z7 
        6.28        62.86         6.15         3.06         4.31        31.07 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-AATP 
       11.08        17.62        70.32        21.40        24.92        32.98 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       20.28         8.58        19.07        22.72         9.01        25.02 
TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       52.73        50.56        46.98        14.24         1.84        33.14 
TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-A9ST 
       51.32        97.12        15.35         3.22        14.93         4.21 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ 
       12.76        11.90         2.24        66.64         2.10        54.90 
TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN7 TCGA-ZF-A9R2 
        7.63        71.57        91.73        44.32        18.58        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T 
       30.28        94.29         3.48        88.87        34.06        19.69 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7O TCGA-4Z-AA7S 
       12.23        24.13       104.65         8.35        16.83        34.98 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 
       27.62         0.62        47.80         2.50        17.42        40.08 
TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A3PH TCGA-BT-A42B 
        2.66        19.04         5.06         5.06         4.67        17.56 
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-A47X TCGA-CF-A5U8 
       12.13        13.08        12.16        10.95        12.62        13.12 
TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FF TCGA-CU-A5W6 TCGA-DK-A1A7 
       12.00        12.10        11.34        11.87         1.84        18.41 
TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
      112.44        17.62        17.95         4.80        13.58         8.15 
TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A5KE 
       15.02        19.00        12.03        38.83        29.72         0.56 
TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        0.66         4.24        24.03        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
        8.09         8.94        22.98         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A6TF TCGA-FJ-A3ZE TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B 
        7.10         2.27        10.65        59.31        20.12        66.02 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RD TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 
       29.36        20.71        14.07        26.70         2.10         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       11.31        18.97         4.73         7.00        14.27        21.34 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6MB 
       19.40        38.60        64.01        21.24        11.70        15.42 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 
       11.80        44.38         1.15        21.07        12.23        16.54 
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-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SU 
       17.82         6.21         3.85        48.62        64.80         5.98 
TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       28.24       110.60         8.32         6.77        56.48        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-A9RM 
       22.36        25.41        21.86        13.41        58.72        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       20.22         8.61        67.20        35.41        29.49 

$`DEL PEAK 21(11P15.5) WILD-TYPE`
TCGA-4Z-AA7M TCGA-BL-A5ZZ TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-CF-A9FL TCGA-CU-A0YN 
       16.27        12.39        20.48        25.94        18.58        12.92 
TCGA-CU-A0YO TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
        4.90        19.00       130.88        23.21         9.67        66.05 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M 
       53.29        76.60        67.36        15.68        36.66        52.01 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA75 TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SM 
       13.64        13.64        11.18        33.04        60.66        17.98 
TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       46.78        27.35         3.62        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI 
        5.69         8.25        18.81        12.69        12.36         9.67 
TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 
       17.23        33.01        19.13        17.75        10.92        32.78 
TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R 
       19.82        27.35         3.45         2.76         9.14        27.68 
TCGA-KQ-A41P TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SK TCGA-XF-A9SM 
       35.97        86.83        97.45       125.49        15.98        34.45 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH 
       21.04        26.27        18.90        13.74        10.82        11.31 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 
       98.99        30.94        61.45        86.30         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-AA53 TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-4Z-AA7N TCGA-4Z-AA7R 
       13.64        57.90        11.97        94.88        44.94        17.16 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A13I 
       50.04        41.75        51.16        66.54        10.22         7.33 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42E TCGA-BT-A42F 
       14.96         8.25        17.16        16.18        36.43        28.41 
TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A8HX TCGA-CF-A9FM 
       12.66        12.46        12.10        12.26        11.34        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AG 
        5.19        29.79        21.86        66.41        16.14        15.62 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q 
        7.79       142.78        20.81        10.55       163.30        13.58 
TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ 
       18.81        15.35        43.59         5.36        22.16         2.24 
TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
       16.70        26.96        26.24        24.66        14.07        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02        16.77        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62S TCGA-FD-A6TK 
       25.74        14.96        20.91        19.33        13.35        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66         8.94         3.25        61.94        48.00        15.95 
TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A4ZW 
       26.93         7.23         6.94        15.81        15.91         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A762 TCGA-GU-A764 
        8.94        13.91         3.12        20.98         7.63        20.05 
TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE 
       15.78        19.10         8.48        36.49         1.51        12.16 
TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A83P TCGA-LC-A66R TCGA-LT-A5Z6 
        9.07        17.72         1.81        16.27        15.32        15.58 
TCGA-MV-A51V TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78P TCGA-UY-A9PA 
       13.48        16.67        17.62        37.05        78.25        35.24 
TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI 
       29.56        45.04         6.58         1.87        17.88        79.66 
TCGA-XF-A9SL TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN4 
       66.41        23.64        16.27        92.98         2.96        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R9 
       75.39        18.84         0.66        31.20        35.84        28.41 
TCGA-ZF-A9RF TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 
       64.08         2.89        59.38        60.16        56.35        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21         5.52        10.65 

  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                          0.56                           0.49 
  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 
                         17.62                          17.67 
[1] "0.6 - 166.0 (17.6)" "0.5 - 163.3 (17.7)"
[1] "hr=" "1.1"
D58V2, 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
D58V3, 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
D58V4, 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 126  22  25   4
D58V5, multiclass
    clus
vv   DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  N0                          110                            126
  N1                           25                             22
  N2                           50                             25
  N3                            4                              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"
D58V6, 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
D58V7, 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
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED   184  11
  DEL PEAK 21(11P15.5) WILD-TYPE 180   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED    184   11
  DEL PEAK 21(11P15.5) WILD-TYPE  180    9
     clus
vv    DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  NO                           184                            180
  YES                           11                              9
[1] 2 2
[1] FALSE
D58V9, continuous
D58V10, continuous
D58V11, 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
D58V12, 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"
D58V13, 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(59) Variable = DEL PEAK 22(11Q23.3) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(11Q23.3) MUTATED    87  65
  DEL PEAK 22(11Q23.3) WILD-TYPE 140 113
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                           152                            253 
  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                            65                            113 
$`DEL PEAK 22(11Q23.3) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A42C TCGA-C4-A0EZ 
      108.95        33.83        26.14        14.89        28.70         8.98 
TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IN 
       12.92        18.48         2.14        16.70       130.88         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6R TCGA-DK-AA6S 
       17.72        50.27        64.18        36.66       165.73       166.03 
TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B6 
       13.64        11.18        15.35        25.58         0.92        33.04 
TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C0 
        4.01        24.30         3.62        15.58         8.25        18.08 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-AA3D 
       58.92        62.86         6.15         4.31        11.08        70.32 
TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       21.40        24.92        27.35         8.58        19.07        22.72 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-UY-A78N TCGA-XF-A8HE 
        2.76         9.14        50.56        46.98        86.83       125.49 
TCGA-XF-A8HG TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 
       15.35        34.45        12.76        11.90        66.64         2.10 
TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-ZF-A9R2 
       54.90         7.63        71.57        61.45        18.58        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       30.28        94.29        19.69        57.90        12.23        24.13 
TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
      104.65        16.83        34.98         0.62        41.75        51.16 
TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        2.50        40.08        16.18         4.67        17.56        36.43 
TCGA-BT-A42F TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A47X 
       28.41        12.56        13.97        12.59        12.13        12.62 
TCGA-CF-A5U8 TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-DK-A1A6 TCGA-DK-A1AD 
       13.12        12.10        11.34        11.34        66.41       112.44 
TCGA-DK-A3IM TCGA-DK-AA6P TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE 
        8.15        15.02        43.59        38.83        22.16         0.56 
TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        0.66         4.24        24.03        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N 
        8.09         8.94        22.98        19.33         5.36         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-G2-A3IB TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 
        7.10        13.35         7.23         0.49         8.94        26.70 
TCGA-GD-A3OP TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        2.10        11.31        18.97         4.73         7.00        14.27 
TCGA-GV-A3JW TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH 
       21.34        19.40        38.60        64.01        21.24         9.07 
TCGA-K4-A5RI TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78O 
       11.70        44.38         1.15        12.23        38.99        76.01 
TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE 
       78.25        69.34         3.02       112.83        29.56         6.21 
TCGA-XF-A9SG TCGA-XF-A9SU TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 
       48.62         5.98       110.60         2.96         8.32        56.48 
TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 
       21.86        13.41        20.22         8.61        67.20        19.40 
TCGA-ZF-AA58 TCGA-ZF-AA5H 
       54.21        29.49 

$`DEL PEAK 22(11Q23.3) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD 
       16.27        16.77        15.12        12.39         8.35        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E 
       25.94         9.96        18.58         4.90        15.12        13.58 
TCGA-DK-A1AA TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
       19.00        46.68        87.32        21.30        23.21         9.67 
TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        17.98        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 
       50.70        38.24        52.01        13.64        56.15        20.32 
TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ 
        1.22        60.66        23.41        17.98        29.16        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT 
       19.79        12.85        27.35        26.73        53.88        10.78 
TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        5.69         6.28        18.81        12.69        12.36         3.06 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3RB 
        9.67        31.07        17.23        33.01        17.62        19.13 
TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF 
       17.75        10.92        32.78        32.98        19.82        20.28 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P 
        9.01        25.02         3.45        27.68        52.73        35.97 
TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HF 
       14.24         1.84        33.14        51.32        97.45        97.12 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T0 
        3.22        15.98        14.93         4.21        21.04        26.27 
TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR 
       18.90         2.24        13.74        10.82        11.31        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 
       98.99        44.32        30.94        86.30         3.88         9.63 
TCGA-YF-AA3M TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-2F-A9KP TCGA-2F-A9KQ 
       13.64         3.48        88.87        34.06        11.97        94.88 
TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA83 
        8.35        44.94        17.16        27.62        50.04        66.54 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
       10.22        47.80        17.42         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F0 
        5.06        14.96         5.06         8.25        17.16         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-A9FM 
       12.46        12.10        12.26        12.00        11.87        13.08 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AE 
        5.19        29.79         1.84        21.86        18.41        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       17.62        15.62        17.95         7.79       142.78         4.80 
TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
       13.58        20.81        10.55       163.30        13.58        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       19.00        15.35        12.03        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
       16.70        26.96        26.24        24.66        14.07        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02        16.77        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FD-A6TK 
       25.74        14.96        20.91        27.45         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ 
       12.66        10.65         8.94         3.25        61.94        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C 
       15.95        26.93        59.31        20.12        66.02         6.94 
TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 
       29.36        20.71        15.81        15.91        14.07        13.91 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
        3.12        20.98         2.20         7.63        20.05        15.78 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A5RJ 
       19.10         8.48        36.49         1.51        12.16        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
        1.81        15.42        16.27        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L 
       21.07        13.48        16.67        16.54        17.62        37.05 
TCGA-UY-A78M TCGA-UY-A9PA TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC 
       22.68        35.24        17.82         3.85        45.04         6.58 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SX 
        1.87        17.88        64.80        79.66        66.41        23.64 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 
       28.24        16.27        92.98         6.77        27.06        75.39 
TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       18.84         0.66        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N 
       35.84        28.41        64.08        58.72        47.84         2.89 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       59.38        60.16        56.35        35.41         8.52         5.52 
TCGA-GU-AATO 
       10.65 

  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE 
                          0.49                           0.66 
  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 
                         18.28                          17.62 
[1] "0.5 - 166.0 (18.3)" "0.7 - 163.3 (17.6)"
[1] "hr=" "1.1"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(11Q23.3) MUTATED         1       51        50       50
  DEL PEAK 22(11Q23.3) WILD-TYPE       1       78        90       85
D59V3, multiclass
           clus
vv          DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  STAGE I                              1                              1
  STAGE II                            51                             78
  STAGE III                           50                             90
  STAGE IV                            50                             85
[1] 4 2
[1] 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         56  66  24
  DEL PEAK 22(11Q23.3) WILD-TYPE       67 129  34
D59V4, multiclass
          clus
vv         DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  T0+T1+T2                           56                             67
  T3                                 66                            129
  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 22(11Q23.3) MUTATED    86  20  27   1
  DEL PEAK 22(11Q23.3) WILD-TYPE 150  27  48   7
D59V5, multiclass
    clus
vv   DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  N0                           86                            150
  N1                           20                             27
  N2                           27                             48
  N3                            1                              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"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED    68   3
  DEL PEAK 22(11Q23.3) WILD-TYPE 124   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED     68    3
  DEL PEAK 22(11Q23.3) WILD-TYPE  124    8
   clus
vv  DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  0                           68                            124
  1                            3                              8
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED    43 110
  DEL PEAK 22(11Q23.3) WILD-TYPE  64 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED     43  110
  DEL PEAK 22(11Q23.3) WILD-TYPE   64  191
        clus
vv       DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  FEMALE                           43                             64
  MALE                            110                            191
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(11Q23.3) MUTATED   133  10
  DEL PEAK 22(11Q23.3) WILD-TYPE 231  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED    133   10
  DEL PEAK 22(11Q23.3) WILD-TYPE  231   10
     clus
vv    DEL PEAK 22(11Q23.3) MUTATED DEL PEAK 22(11Q23.3) WILD-TYPE
  NO                           133                            231
  YES                           10                             10
[1] 2 2
[1] FALSE
D59V9, continuous
D59V10, continuous
D59V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11Q23.3) MUTATED      19                        10   116
  DEL PEAK 22(11Q23.3) WILD-TYPE    24                        12   211
D59V12, multiclass
                           clus
vv                          DEL PEAK 22(11Q23.3) MUTATED
  ASIAN                                               19
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              116
                           clus
vv                          DEL PEAK 22(11Q23.3) WILD-TYPE
  ASIAN                                                 24
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                211
[1] 3 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 22(11Q23.3) MUTATED     4 133
  DEL PEAK 22(11Q23.3) WILD-TYPE   5 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q23.3) MUTATED      4  133
  DEL PEAK 22(11Q23.3) WILD-TYPE    5  236
                        clus
vv                       DEL PEAK 22(11Q23.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       DEL PEAK 22(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            236
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 23(11Q25) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 23(11Q25) MUTATED    80  63
  DEL PEAK 23(11Q25) WILD-TYPE 147 115
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                         143                          262 
  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                          63                          115 
$`DEL PEAK 23(11Q25) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BT-A20W TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN 
      108.95        33.83         8.35        28.70         8.98        12.92 
TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       18.48         2.14        16.70         8.22        17.72        50.27 
TCGA-DK-A6AV TCGA-DK-A6B6 TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 
       64.18        36.66       166.03        11.18        15.35        25.58 
TCGA-E7-A7DU TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY 
        0.92         4.01        24.30        15.58        26.73         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A2ES 
       18.08        58.92         6.15         4.31        11.08        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-GV-A40E 
       17.62        21.40        24.92        19.82        27.35         8.58 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41O 
       19.07        22.72         9.01         2.76         9.14        50.56 
TCGA-KQ-A41Q TCGA-UY-A78N TCGA-XF-A8HG TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SW 
       46.98        86.83        15.35        34.45        12.76        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAN2 
       66.64         2.10        54.90         7.63        71.57        61.45 
TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-ZF-AA53 
       18.58        21.11        30.28        94.29        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KR TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-4Z-AA80 
       12.23        24.13       104.65        16.83        34.98         0.62 
TCGA-4Z-AA82 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BT-A2LA TCGA-BT-A2LB 
       51.16         2.50        17.42        40.08        17.16        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
        4.67        17.56        36.43        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-DK-A1A6 TCGA-DK-A3IM TCGA-DK-AA6P TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A5KE 
       66.41         8.15        15.02        43.59        22.16         0.56 
TCGA-E7-A5KF TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P 
        0.66         4.24        24.03        13.68        12.95        14.37 
TCGA-E7-A97Q TCGA-FD-A3B5 TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O 
        8.09         8.94        22.98         5.36         2.70         7.10 
TCGA-FD-A62S TCGA-G2-A3IB TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A2C5 TCGA-GD-A3OP 
       13.35         7.23         0.49         8.94        26.70         2.10 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW 
       11.31        18.97         4.73         7.00        14.27        21.34 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       19.40        38.60        64.01        21.24         9.07        11.70 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A78P 
       44.38         1.15        12.23        38.99        76.01        78.25 
TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A9SG TCGA-XF-AAMG 
       69.34       112.83        29.56         6.21        48.62       110.60 
TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9RD TCGA-ZF-A9RN 
        2.96         8.32        56.48        22.36        13.41        20.22 
TCGA-ZF-AA4U TCGA-ZF-AA4X TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
        8.61        67.20        19.40        54.21        29.49 

$`DEL PEAK 23(11Q25) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
       16.27        16.77        15.12        12.39        26.14        14.89 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR 
       20.48        25.94         9.96        18.58         4.90        15.12 
TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IT 
       13.58        19.00       130.88        46.68        87.32        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        66.05        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R 
       67.36        15.68        50.70        38.24        52.01       165.73 
TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DV TCGA-FD-A3B6 
       13.64        13.64        56.15        20.32         1.22        33.04 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       60.66        23.41        17.98        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       12.85        27.35         3.62        53.88        10.78         5.69 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86        18.81        12.69        12.36         3.06 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
        9.67        31.07        17.23        70.32        19.13        17.75 
TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-K4-A3WS TCGA-K4-A3WU 
       10.92        32.78        32.98        20.28        25.02         3.45 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 
       27.68        52.73        35.97        14.24         1.84        33.14 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK 
       51.32        97.45       125.49        97.12         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       14.93         4.21        21.04        26.27        18.90         2.24 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ 
       13.74        10.82        11.31        91.73        98.99        44.32 
TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9RE 
       30.94        86.30         3.88         9.63        13.64         3.48 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N 
       88.87        34.06        11.97        94.88         8.35        44.94 
TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 
       17.16        27.62        50.04        41.75        66.54        10.22 
TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       47.80         7.33         2.66         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
        5.06         8.25        28.41         1.94        23.01        12.79 
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-A5UA TCGA-CF-A9FF TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       12.26        12.00        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
        1.84        21.86        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.35        12.03        38.83        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
       16.70        26.96        26.24        24.66        14.07        15.32 
TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02        16.77        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BZ TCGA-FD-A6TF 
       25.74        14.96        20.91        19.33        27.45         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85        12.66        10.65         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3B 
       48.00        15.95        26.93        59.31        20.12        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
        6.94        29.36        20.71        15.81        15.91        14.07 
TCGA-GC-A6I3 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A764 
       13.91         3.12        20.98         2.20         7.63        20.05 
TCGA-GU-A766 TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE 
       15.78        19.10         8.48        36.49         1.51        12.16 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R 
       17.72         1.81        15.42        16.27        11.80        15.32 
TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K 
       15.58        21.07        13.48        16.67        16.54        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        35.24        17.82         3.85 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       45.04         6.58         1.87        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
        6.77        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RF 
       25.41        31.20        35.84        21.86        28.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA51 
       58.72        47.84         2.89        59.38        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-GU-AATO 
       35.41         8.52         5.52        10.65 

  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE 
                        0.49                         0.66 
  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 
                      17.420                       17.785 
[1] "0.5 - 166.0 (17.4)" "0.7 - 165.7 (17.8)"
[1] "hr=" "1"  
D60V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(11Q25) MUTATED         1       48        50       44
  DEL PEAK 23(11Q25) WILD-TYPE       1       81        90       91
D60V3, multiclass
           clus
vv          DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  STAGE I                            1                            1
  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         52  62  23
  DEL PEAK 23(11Q25) WILD-TYPE       71 133  35
D60V4, multiclass
          clus
vv         DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  T0+T1+T2                         52                           71
  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 154  31  51   6
D60V5, multiclass
    clus
vv   DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  N0                         82                          154
  N1                         16                           31
  N2                         24                           51
  N3                          2                            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"
D60V6, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED    64   3
  DEL PEAK 23(11Q25) WILD-TYPE 128   8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     64    3
  DEL PEAK 23(11Q25) WILD-TYPE  128    8
   clus
vv  DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  0                         64                          128
  1                          3                            8
[1] 2 2
[1] FALSE
D60V7, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED    41 103
  DEL PEAK 23(11Q25) WILD-TYPE  66 198
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED     41  103
  DEL PEAK 23(11Q25) WILD-TYPE   66  198
        clus
vv       DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  FEMALE                         41                           66
  MALE                          103                          198
[1] 2 2
[1] FALSE
D60V8, binary
                              cls
clus                             0   1
  DEL PEAK 23(11Q25) MUTATED   125   9
  DEL PEAK 23(11Q25) WILD-TYPE 239  11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED    125    9
  DEL PEAK 23(11Q25) WILD-TYPE  239   11
     clus
vv    DEL PEAK 23(11Q25) MUTATED DEL PEAK 23(11Q25) WILD-TYPE
  NO                         125                          239
  YES                          9                           11
[1] 2 2
[1] FALSE
D60V9, continuous
D60V10, continuous
D60V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q25) MUTATED      20                         9   108
  DEL PEAK 23(11Q25) WILD-TYPE    23                        13   219
D60V12, multiclass
                           clus
vv                          DEL PEAK 23(11Q25) MUTATED
  ASIAN                                             20
  BLACK OR AFRICAN AMERICAN                          9
  WHITE                                            108
                           clus
vv                          DEL PEAK 23(11Q25) WILD-TYPE
  ASIAN                                               23
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              219
[1] 3 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 23(11Q25) MUTATED     4 127
  DEL PEAK 23(11Q25) WILD-TYPE   5 242
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(11Q25) MUTATED      4  127
  DEL PEAK 23(11Q25) WILD-TYPE    5  242
                        clus
vv                       DEL PEAK 23(11Q25) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        127
                        clus
vv                       DEL PEAK 23(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          242
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 24(12P13.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(12P13.1) MUTATED    34  33
  DEL PEAK 24(12P13.1) WILD-TYPE 193 145
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            67                            338 
  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                            33                            145 
$`DEL PEAK 24(12P13.1) MUTATED`
TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A9FL TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-DK-A3IV 
       14.89        28.70        18.58       130.88        17.72         9.67 
TCGA-DK-A6AV TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43X TCGA-FD-A5BX 
       64.18        23.41        46.78        19.79         3.62         5.69 
TCGA-FD-A5C0 TCGA-FD-A6TC TCGA-FD-A6TE TCGA-G2-AA3D TCGA-GC-A3YS TCGA-KQ-A41Q 
       18.08         6.15        12.36        70.32        24.92        46.98 
TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SP TCGA-XF-A9SV TCGA-XF-A9T3 
       33.14        97.12        15.35        14.93        12.76         2.24 
TCGA-XF-AAMF TCGA-XF-AAML TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KW TCGA-4Z-AA87 
       10.82         7.63        19.69        24.13         8.35        47.80 
TCGA-5N-A9KI TCGA-BT-A2LA TCGA-CF-A27C TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A7I0 
        2.50        17.16        13.97        12.16        12.62        12.10 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A3IL TCGA-E5-A2PC TCGA-E7-A85H TCGA-E7-A97Q 
        5.19         1.84        13.58        43.59        12.95         8.09 
TCGA-FD-A43N TCGA-G2-AA3F TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GU-A764 TCGA-GV-A3JW 
       22.98        29.36        26.70        20.98        20.05        21.34 
TCGA-K4-A6FZ TCGA-KQ-A41R TCGA-KQ-A41S TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OD 
        1.81        44.38         1.15        22.68        78.25       112.83 
TCGA-UY-A9PD TCGA-XF-A8HH TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX 
       17.82         1.87        28.24       110.60         8.32         6.77 
TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W 
       56.48        11.97        22.36        20.22         8.61        60.16 
TCGA-ZF-AA52 
       35.41 

$`DEL PEAK 24(12P13.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ 
      108.95        16.27        16.77        15.12        33.83        12.39 
TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ 
       26.14         8.35        20.48        25.94         9.96         8.98 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       12.92         4.90        15.12        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS 
       19.00        16.70        46.68        87.32         8.22        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 
       21.30        23.21        66.05        17.98        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M 
       67.36        15.68        50.70        36.66        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 
      165.73       166.03        13.64        13.64        56.15        11.18 
TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 
       20.32        15.35        25.58         0.92         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SS 
        4.01        60.66        24.30        17.98        29.16        12.85 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BY 
       27.35        15.58        26.73        53.88        10.78         8.25 
TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG 
       58.92         6.28        62.86        18.81        12.69         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        4.31         9.67        31.07        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 
       17.62        21.40        19.13        17.75        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC 
       22.72         9.01        25.02         3.45         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        50.56        35.97        14.24         1.84 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SK 
       86.83        51.32        97.45       125.49         3.22        15.98 
TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
       34.45         4.21        11.90        21.04        26.27        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ 
       66.64         2.10        13.74        11.31        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN3 
       91.73        98.99        44.32        30.94        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P 
       94.29         3.48        88.87        34.06        57.90        12.23 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R 
       11.97        94.88       104.65        44.94        16.83        17.16 
TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 
       34.98        27.62        50.04         0.62        41.75        51.16 
TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P 
        6.74         6.58        13.15        19.04        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB 
       19.50         5.06        14.96         5.06         8.25        16.18 
TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        4.67        17.56        36.43        28.41         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-A3YL TCGA-DK-A1A3 
       11.34        11.34        11.87        13.08        29.79        21.86 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       66.41        18.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95         7.79       142.78         4.80         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       10.55       163.30        15.02        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       15.35        12.03        38.83        29.72         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
        4.24        24.03        24.66        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.37        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU 
       27.98         5.52        25.74        14.96        20.91        19.33 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF 
        5.36        27.45         2.70         7.10        13.35         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EF 
       10.85        12.66        10.65         8.94         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       48.00        15.95        26.93        59.31         7.23        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       66.02         6.94        20.71        15.81        15.91        14.07 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 
        0.49         8.94        13.91         2.10         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ 
       11.31        18.97         7.63        15.78         4.73         7.00 
TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ 
       14.27        19.10         8.48        36.49         1.51        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI 
       38.60        64.01        12.16        21.24         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 
       17.72        15.42        16.27        11.80        15.32        15.58 
TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
       21.07        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       17.62        37.05        76.01        69.34         3.02        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI 
       29.56         6.21         3.85        45.04         6.58        17.88 
TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX 
       48.62        64.80        79.66        66.41         5.98        23.64 
TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       16.27        92.98         2.96        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 
        0.66        25.41        31.20        35.84        21.86        28.41 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4V 
       13.41        64.08        58.72        47.84         2.89        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       67.20        56.35        19.40         8.52        54.21        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE 
                          1.15                           0.49 
  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 
                         18.08                          17.59 
[1] "1.1 - 130.9 (18.1)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D61V2, 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
D61V3, 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
D61V4, 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 202  39  59   7
D61V5, multiclass
    clus
vv   DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  N0                           34                            202
  N1                            8                             39
  N2                           16                             59
  N3                            1                              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"
D61V6, 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
D61V7, 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
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(12P13.1) MUTATED    60   3
  DEL PEAK 24(12P13.1) WILD-TYPE 304  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(12P13.1) MUTATED     60    3
  DEL PEAK 24(12P13.1) WILD-TYPE  304   17
     clus
vv    DEL PEAK 24(12P13.1) MUTATED DEL PEAK 24(12P13.1) WILD-TYPE
  NO                            60                            304
  YES                            3                             17
[1] 2 2
[1] FALSE
D61V9, continuous
D61V10, continuous
D61V11, 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
D61V12, 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"
D61V13, 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(62) Variable = DEL PEAK 25(12Q24.33) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(12Q24.33) MUTATED    44  43
  DEL PEAK 25(12Q24.33) WILD-TYPE 183 135
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             87                             318 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             43                             135 
$`DEL PEAK 25(12Q24.33) MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20W TCGA-BT-A2LD TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR 
       15.12         8.35        20.48        18.58         4.90        15.12 
TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-AA6L TCGA-E5-A4TZ TCGA-E7-A541 
       17.72         9.67        17.98        38.24        15.35        25.58 
TCGA-E7-A7DV TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43X TCGA-FD-A62P 
        1.22        23.41        46.78        12.85         3.62         6.28 
TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3YS 
       12.36         4.31        11.08        17.62        70.32        24.92 
TCGA-GU-AATP TCGA-GV-A6ZA TCGA-K4-A4AC TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HF 
       32.98        22.72         9.14        33.14        51.32        97.12 
TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAML 
       15.35         3.22        14.93        10.82        54.90         7.63 
TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-2F-A9KR TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI 
       44.32        61.45       104.65        10.22        47.80         2.50 
TCGA-BT-A2LA TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MI 
       17.16        28.41         1.94        12.56        13.97        12.16 
TCGA-CF-A47X TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CU-A3QU TCGA-DK-A2I4 TCGA-DK-AA6P 
       12.62        12.00        12.10         5.19       142.78        15.02 
TCGA-E5-A2PC TCGA-E7-A7PW TCGA-E7-A97Q TCGA-FD-A3SO TCGA-FD-A5BZ TCGA-FD-A6TF 
       43.59        13.68         8.09         5.52        27.45         2.27 
TCGA-G2-AA3F TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GU-A766 TCGA-GU-A767 
       29.36        15.91        14.07         0.49        15.78         4.73 
TCGA-GV-A3JW TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-KQ-A41S TCGA-LC-A66R 
       21.34        12.16         9.07        17.72         1.15        15.32 
TCGA-PQ-A6FI TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PD TCGA-XF-A9SH 
       12.23        22.68        69.34       112.83        17.82        64.80 
TCGA-XF-A9SI TCGA-XF-A9SX TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-ZF-A9R0 TCGA-ZF-A9RM 
       79.66        23.64         8.32        56.48        22.36        47.84 
TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
       67.20        35.41        29.49 

$`DEL PEAK 25(12Q24.33) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
      108.95        16.27        16.77        33.83        12.39        26.14 
TCGA-BT-A20T TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CU-A0YN 
       14.89        25.94         9.96        28.70         8.98        12.92 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
       18.48        13.58         2.14        19.00        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
       46.68        87.32         8.22        50.27        21.30        23.21 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
       66.05        64.18        53.29        76.60        67.36        15.68 
TCGA-DK-A6B5 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       50.70        36.66        52.01       165.73       166.03        13.64 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3B6 
       13.64        56.15        11.18        20.32         0.92        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SR 
        4.01        60.66        24.30        17.98        29.16        19.79 
TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
       27.35        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC 
        8.25        18.08        58.92        62.86        18.81         6.15 
TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-G2-A2ES 
       12.69         3.06         9.67        31.07        17.23        33.01 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3JZ 
       21.40        19.13        17.75        10.92        32.78        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WS 
       20.28        27.35         8.58        19.07         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        3.45         2.76        27.68        52.73        50.56        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HE 
       46.98        14.24         1.84        86.83        97.45       125.49 
TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY 
       15.98        34.45         4.21        12.76        11.90        21.04 
TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       26.27        18.90         2.24        66.64         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN3 
       11.31        71.57        91.73        98.99        30.94        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 
       94.29         3.48        88.87        34.06        19.69        57.90 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N 
       12.23        24.13        11.97        94.88         8.35        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W TCGA-4Z-AA7Y TCGA-4Z-AA80 
       16.83        17.16        34.98        27.62        50.04         0.62 
TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA83 TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I 
       41.75        51.16        66.54        17.42        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         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-A2LB TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F6 TCGA-CF-A1HR 
       16.18         4.67        17.56        36.43        23.01        12.79 
TCGA-CF-A3MF TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.59        12.13        13.08        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.10        12.26        13.12        11.34        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.08        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        17.95         7.79 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       13.58        18.81        19.00        15.35        12.03        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE 
       29.72         5.36        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-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-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43N 
        8.94        12.62        22.52        27.98        25.74        22.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A62N TCGA-FD-A62O 
       14.96        20.91        19.33         5.36         2.70         7.10 
TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE 
       13.35        10.85        12.66        10.65         8.94         3.25 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
       61.94        48.00        15.95        26.93        59.31         7.23 
TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I1 
       20.12        66.02         6.94        20.71        15.81         8.94 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 
       13.91        26.70         2.10         3.12        20.98         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JV 
       11.31        18.97         7.63        20.05         7.00        14.27 
TCGA-GV-A3JX TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
       19.10         8.48        36.49         1.51        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       64.01        21.24        11.70         1.81        15.42        16.27 
TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       11.80        44.38        15.58        21.07        13.48        16.67 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P 
       16.54        38.99        17.62        37.05        76.01        78.25 
TCGA-UY-A8OC TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HB 
        3.02        35.24        29.56         6.21         3.85        45.04 
TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SL TCGA-XF-A9SU 
        6.58         1.87        17.88        48.62        66.41         5.98 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX 
       28.24        16.27        92.98       110.60         2.96         6.77 
TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9R1 
       27.06        75.39        18.84         0.66        11.97        25.41 
TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       31.20        35.84        21.86        28.41        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W 
       58.72        20.22         2.89         8.61        59.38        60.16 
TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       56.35        19.40         8.52        54.21         5.52        10.65 

  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                           0.49                            0.56 
  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 
                         15.780                          17.915 
[1] "0.5 - 142.8 (15.8)" "0.6 - 166.0 (17.9)"
[1] "hr=" "1.2"
D62V2, 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
D62V3, 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
D62V4, 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 194  35  53   5
D62V5, multiclass
    clus
vv   DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  N0                            42                             194
  N1                            12                              35
  N2                            22                              53
  N3                             3                               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"
D62V6, 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
D62V7, 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
D62V8, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED    78   6
  DEL PEAK 25(12Q24.33) WILD-TYPE 286  14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED     78    6
  DEL PEAK 25(12Q24.33) WILD-TYPE  286   14
     clus
vv    DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  NO                             78                             286
  YES                             6                              14
[1] 2 2
[1] FALSE
D62V9, continuous
D62V10, continuous
D62V11, 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
D62V12, 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"
D62V13, 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(63) Variable = DEL PEAK 26(13Q14.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(13Q14.2) MUTATED    87  69
  DEL PEAK 26(13Q14.2) WILD-TYPE 140 109
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           156                            249 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            69                            109 
$`DEL PEAK 26(13Q14.2) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A3PJ 
       16.27        16.77        15.12        26.14        14.89        25.94 
TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
        9.96        28.70         8.98       130.88        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
        8.22        17.72         9.67        17.98        67.36        36.66 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E7-A541 TCGA-E7-A7DV 
       52.01       165.73        13.64        11.18        25.58         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR 
       33.04         4.01        24.30        29.16        46.78        19.79 
TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A5BY TCGA-FD-A5C1 TCGA-FD-A6TC TCGA-FD-A6TE 
       12.85        27.35         8.25        58.92         6.15        12.36 
TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3BM TCGA-GC-A3RB 
        4.31        17.23        11.08        33.01        21.40        19.13 
TCGA-GC-A3YS TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q 
       24.92         9.01         9.14        27.68        52.73        46.98 
TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SW TCGA-XF-A9SY 
       86.83        97.45         3.22        34.45        11.90        21.04 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMZ 
        2.24        66.64        54.90         7.63        71.57        44.32 
TCGA-XF-AAN7 TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-4Z-AA7S TCGA-4Z-AA7W 
       18.58         3.48        19.69        57.90        34.98        27.62 
TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20R 
        0.62        51.16        47.80         2.66         6.74         5.06 
TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B TCGA-BT-A42E 
        5.06         8.25        17.16         4.67        17.56        36.43 
TCGA-C4-A0F0 TCGA-CF-A1HS TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A7 
        1.94        12.56         5.19         1.84        21.86        18.41 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM 
      112.44        16.14         7.79       142.78         4.80         8.15 
TCGA-DK-AA6T TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6MD 
       18.81        43.59        29.72        22.16         0.56         4.24 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 
       24.03        13.68        12.95        14.37        32.02         8.94 
TCGA-FD-A3N5 TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-G2-A2EO 
       22.52        19.33         5.36        27.45         2.70        59.31 
TCGA-G2-AA3F TCGA-GC-A3OO TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A6C6 
       29.36        15.81         8.94        13.91         2.10         2.20 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RH 
       21.34        19.10        36.49        38.60        12.16         9.07 
TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
       17.72         1.81         1.15        15.32        15.58        13.48 
TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78M TCGA-UY-A8OB 
       12.23        16.67        16.54        17.62        22.68        69.34 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HC 
      112.83        35.24        29.56        17.82         3.85         6.58 
TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       48.62        23.64       110.60         6.77        56.48        11.97 
TCGA-ZF-A9R9 TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       28.41        64.08        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H 
       60.16        67.20        56.35        19.40        54.21        29.49 

$`DEL PEAK 26(13Q14.2) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20W TCGA-BT-A2LD TCGA-CF-A9FL 
      108.95        33.83        12.39         8.35        20.48        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 
       12.92         4.90        15.12        18.48        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 
       19.00        16.70        50.27        21.30        23.21        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-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU 
      166.03        13.64        56.15        20.32        15.35         0.92 
TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       60.66        23.41        17.98         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TA 
       53.88        10.78         5.69        18.08         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-A3VY 
       18.81        12.69         3.06         9.67        31.07        17.62 
TCGA-G2-AA3D TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3JZ 
       70.32        17.75        10.92        32.78        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS 
       20.28        27.35         8.58        19.07        22.72        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
        3.45         2.76        50.56        35.97        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SK 
       33.14        51.32       125.49        97.12        15.35        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T6 
       14.93         4.21        12.76        26.27        18.90         2.10 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAN1 
       13.74        10.82        11.31        91.73        98.99        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 
       61.45        86.30         3.88         9.63        13.64        21.11 
TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KO 
       30.28        94.29        88.87        34.06        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O 
       11.97        94.88       104.65         8.35        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI 
       17.16        50.04        41.75        66.54        10.22         2.50 
TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       17.42        40.08         7.33         6.58        13.15        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A42F 
       12.16        17.88        19.50        14.96        16.18        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-A9FM TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AF TCGA-DK-A1AG 
       11.87        13.08        29.79        66.41        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P 
       17.95        13.58        20.81        10.55       163.30        15.02 
TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A3Y1 
       13.58        19.00        15.35        12.03        38.83         5.36 
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-A7XN TCGA-E7-A8O7 TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B8 TCGA-FD-A3N6 
       14.07        15.32         8.09        16.77        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A62O 
        5.52        25.74        22.98        14.96        20.91         7.10 
TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       13.35         2.27        10.85        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-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A3RD 
       20.12        66.02         6.94        20.71        15.91        14.07 
TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
        0.49        26.70         3.12        20.98        11.31        18.97 
TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV 
        7.63        20.05        15.78         4.73         7.00        14.27 
TCGA-GV-A3QH TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A5RI 
        8.48         1.51        19.40        64.01        21.24        11.70 
TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R TCGA-LT-A8JT TCGA-SY-A9G5 
       15.42        16.27        11.80        44.38        21.07        38.99 
TCGA-UY-A78L TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A9PE TCGA-XF-A8HB 
       37.05        76.01        78.25         3.02         6.21        45.04 
TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU 
        1.87        17.88        64.80        79.66        66.41         5.98 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAN4 
       28.24        16.27        92.98         2.96         8.32        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA52 
       35.84        21.86        13.41         8.61        59.38        35.41 
TCGA-ZF-AA56 TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52         5.52        10.65 

  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                          0.56                           0.49 
  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 
                        18.695                         16.700 
[1] "0.6 - 165.7 (18.7)" "0.5 - 166.0 (16.7)"
[1] "hr=" "1"  
D63V2, 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
D63V3, 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
D63V4, 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    79  20  35   3
  DEL PEAK 26(13Q14.2) WILD-TYPE 157  27  40   5
D63V5, multiclass
    clus
vv   DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  N0                           79                            157
  N1                           20                             27
  N2                           35                             40
  N3                            3                              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 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
D63V7, 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
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED   135   7
  DEL PEAK 26(13Q14.2) WILD-TYPE 229  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED    135    7
  DEL PEAK 26(13Q14.2) WILD-TYPE  229   13
     clus
vv    DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  NO                           135                            229
  YES                            7                             13
[1] 2 2
[1] FALSE
D63V9, continuous
D63V10, continuous
D63V11, 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
D63V12, 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"
D63V13, 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(64) Variable = DEL PEAK 27(14Q24.1) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(14Q24.1) MUTATED    78  58
  DEL PEAK 27(14Q24.1) WILD-TYPE 149 120
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                           136                            269 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                            58                            120 
$`DEL PEAK 27(14Q24.1) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20T TCGA-BT-A20W 
      108.95        16.27        16.77        15.12        14.89         8.35 
TCGA-BT-A3PK TCGA-CU-A0YO TCGA-CU-A0YR TCGA-DK-A1A5 TCGA-DK-A1AC TCGA-DK-A3IQ 
        9.96         4.90        15.12         2.14       130.88        17.72 
TCGA-DK-A3IS TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-AA6S TCGA-E5-A4TZ 
       50.27        66.05        64.18        50.70       166.03        15.35 
TCGA-E7-A7DU TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43Y 
        0.92        24.30        29.16        46.78        19.79        15.58 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TC TCGA-FD-A6TG 
       18.08        58.92         6.28        62.86         6.15         3.06 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31        31.07        17.23        11.08        17.62        70.32 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA 
       32.98        19.82        20.28         8.58        19.07        22.72 
TCGA-K4-A3WU TCGA-KQ-A41O TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX 
        3.45        50.56        35.97        46.98        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HF TCGA-XF-A9SK TCGA-XF-A9ST 
       33.14        86.83        51.32        97.12        15.98         4.21 
TCGA-XF-A9T0 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 
       26.27        54.90         7.63        98.99        44.32        61.45 
TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-AA4T TCGA-2F-A9KO TCGA-2F-A9KP 
       86.30        13.64        94.29        19.69        24.13        11.97 
TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA82 TCGA-4Z-AA87 
      104.65         8.35         0.62        41.75        51.16        47.80 
TCGA-5N-A9KI TCGA-BT-A20J TCGA-BT-A20V TCGA-BT-A2LB TCGA-CF-A1HR TCGA-CF-A1HS 
        2.50        19.04         5.06        16.18        12.79        12.56 
TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5U8 TCGA-CF-A8HY TCGA-CU-A3QU TCGA-CU-A5W6 
       12.16        12.62        13.12        11.34         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-AA6U TCGA-DK-AA76 
       21.86        18.41       112.44        17.95        19.00        12.03 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A6MD TCGA-E7-A6ME TCGA-E7-A85H TCGA-E7-A8O7 
       38.83        22.16         4.24        24.03        12.95        15.32 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43U TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B 
       25.74        22.98        20.91        61.94        20.12        66.02 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GD-A2C5 TCGA-GU-A42Q TCGA-GV-A3QI TCGA-H4-A2HQ 
       14.07         0.49        26.70        11.31        36.49        19.40 
TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A6MB TCGA-KQ-A41R TCGA-KQ-A41S TCGA-MV-A51V 
       38.60        64.01        15.42        44.38         1.15        13.48 
TCGA-PQ-A6FI TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A9PD 
       12.23        38.99        17.62        37.05        22.68        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG TCGA-XF-A9SX TCGA-XF-A9SZ 
        6.21         3.85         1.87        48.62        23.64        28.24 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-A9RM 
        8.32         6.77        56.48        25.41        28.41        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA51 TCGA-ZF-AA52 
       20.22         2.89        56.35        35.41 

$`DEL PEAK 27(14Q24.1) WILD-TYPE`
TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       33.83        12.39        26.14        20.48        25.94        28.70 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA 
        8.98        18.58        12.92        18.48        13.58        19.00 
TCGA-DK-A1AB TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IT TCGA-DK-A3IU 
       16.70        46.68        87.32         8.22        21.30        23.21 
TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 
        9.67        17.98        53.29        76.60        67.36        15.68 
TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA71 
       36.66        38.24        52.01       165.73        13.64        13.64 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3B6 
       56.15        11.18        20.32        25.58         1.22        33.04 
TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SS TCGA-FD-A43P 
        4.01        60.66        23.41        17.98        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
        3.62        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TI TCGA-G2-A2ES TCGA-GC-A3BM 
       18.81        12.69        12.36         9.67        33.01        21.40 
TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 TCGA-GV-A3QK 
       19.13        17.75        24.92        10.92        32.78        27.35 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
        9.01        25.02         2.76         9.14        27.68        52.73 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9SP 
       97.45       125.49        15.35         3.22        34.45        14.93 
TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 
       12.76        11.90        21.04        18.90         2.24        66.64 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        13.74        10.82        11.31        71.57        91.73 
TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       30.94        18.58         3.88         9.63        21.11        30.28 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KQ 
        3.48        88.87        34.06        57.90        12.23        94.88 
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-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J 
       66.54        10.22        17.42        40.08         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.74         6.58        13.15        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-BT-A3PH TCGA-BT-A42B 
        5.06        14.96         8.25        17.16         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A27C TCGA-CF-A3MF 
       36.43        28.41         1.94        23.01        13.97        12.59 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V TCGA-CF-A47W 
       12.13        13.08        10.95        12.66        12.46        12.10 
TCGA-CF-A47Y TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CF-A9FM 
       12.26        12.00        12.10        11.34        11.87        13.08 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       29.79        66.41        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX 
      142.78         4.80        13.58         8.15        20.81        10.55 
TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6X TCGA-E5-A2PC 
      163.30        15.02        13.58        18.81        15.35        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72         5.36         2.24        16.70         0.56         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A97P 
       26.96        26.24        24.66        13.68        14.07        14.37 
TCGA-E7-A97Q TCGA-FD-A3B3 TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
        8.09        32.02        16.77         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       27.98         5.52        14.96        19.33         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 
        2.70         7.10        13.35         2.27        10.85        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL 
       10.65         8.94         3.25        48.00        15.95        26.93 
TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       59.31         7.23         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       15.91         8.94        13.91         2.10         3.12        20.98 
TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
        2.20        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HO 
        7.00        14.27        21.34        19.10         8.48         1.51 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ 
       12.16        21.24         9.07        11.70        17.72         1.81 
TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-PQ-A6FN 
       16.27        11.80        15.32        15.58        21.07        16.67 
TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       16.54        76.01        78.25        69.34         3.02       112.83 
TCGA-UY-A9PA TCGA-UY-A9PB TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH 
       35.24        29.56        45.04         6.58        17.88        64.80 
TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG 
       79.66        66.41         5.98        16.27        92.98       110.60 
TCGA-XF-AAMT TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
        2.96        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RF 
       22.36        31.20        35.84        21.86        13.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA54 
       58.72         8.61        59.38        60.16        67.20        19.40 
TCGA-ZF-AA56 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
        8.52        54.21        29.49         5.52        10.65 

  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                          0.49                           0.56 
  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 
                        19.545                         16.670 
[1] "0.5 - 166.0 (19.5)" "0.6 - 165.7 (16.7)"
[1] "hr=" "1.2"
D64V2, 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
D64V3, 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
D64V4, 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 165  35  37   6
D64V5, multiclass
    clus
vv   DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  N0                           71                            165
  N1                           12                             35
  N2                           38                             37
  N3                            2                              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"
D64V6, 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
D64V7, 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
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED   127   3
  DEL PEAK 27(14Q24.1) WILD-TYPE 237  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED    127    3
  DEL PEAK 27(14Q24.1) WILD-TYPE  237   17
     clus
vv    DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  NO                           127                            237
  YES                            3                             17
[1] 2 2
[1] FALSE
D64V9, continuous
D64V10, continuous
D64V11, 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
D64V12, 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"
D64V13, 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(65) Variable = DEL PEAK 28(15Q13.1) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(15Q13.1) MUTATED    90  68
  DEL PEAK 28(15Q13.1) WILD-TYPE 137 110
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                           158                            247 
  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                            68                            110 
$`DEL PEAK 28(15Q13.1) MUTATED`
TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A42C TCGA-C4-A0EZ 
       15.12        26.14         8.35        20.48        28.70         8.98 
TCGA-CU-A0YR TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3X2 TCGA-DK-A6B2 TCGA-DK-A6B5 
       15.12        46.68         8.22        17.98        15.68        50.70 
TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-DK-AA74 TCGA-DK-AA75 
       36.66        52.01       165.73        13.64        56.15        11.18 
TCGA-E7-A541 TCGA-E7-A7DV TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A5BY 
       25.58         1.22        60.66        24.30        29.16         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TD TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-FJ-A3ZF 
       18.08        58.92        12.69         4.31        31.07        17.23 
TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3QF 
       11.08        17.62        19.13        24.92        10.92        20.28 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AB TCGA-KQ-A41P 
        8.58        19.07        22.72        25.02         2.76        35.97 
TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HD TCGA-XF-A8HF TCGA-XF-A8HG 
       14.24        33.14        86.83        97.45        97.12        15.35 
TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9T0 TCGA-XF-A9T3 
        3.22        15.98        34.45        14.93        26.27         2.24 
TCGA-XF-A9T5 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAN2 TCGA-YF-AA3M TCGA-ZF-A9RC 
       66.64        54.90         7.63        61.45        13.64        94.29 
TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA82 
       88.87        34.06        19.69         8.35        27.62        51.16 
TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 
       47.80         2.50        17.42        40.08         2.66         6.58 
TCGA-BT-A20J TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 
       19.04         8.25        16.18        17.56        36.43         1.94 
TCGA-CF-A47X TCGA-CU-A3QU TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I2 
       12.62         5.19        66.41        18.41       112.44         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A4IJ 
      142.78         8.15        15.02        12.03        43.59        22.16 
TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B3 
        0.56        24.03        13.68        12.95         8.09        32.02 
TCGA-FD-A3N5 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N 
       22.52        25.74        22.98         5.36        27.45         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-G2-A2EF TCGA-G2-A2EL TCGA-G2-A3IE 
        7.10        13.35        10.85        61.94        26.93        20.12 
TCGA-G2-AA3B TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GC-A6I1 TCGA-GD-A3OP TCGA-GD-A6C6 
       66.02        15.81        14.07         8.94         2.10         2.20 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        7.63        15.78         4.73        21.34        19.10         8.48 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ 
       19.40        38.60        12.16         9.07        11.70        17.72 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V 
        1.81        15.42        44.38        15.32        15.58        13.48 
TCGA-PQ-A6FN TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A9PA 
       16.67        17.62        37.05        22.68        76.01        35.24 
TCGA-UY-A9PB TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A9SG 
       29.56        17.82         6.21        45.04         1.87        48.62 
TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-AAMT TCGA-YF-AA3L TCGA-ZF-A9R9 TCGA-ZF-A9RF 
        5.98        23.64         2.96        11.97        28.41        64.08 
TCGA-ZF-A9RG TCGA-ZF-AA4N TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA58 
       58.72         2.89        59.38        67.20        35.41        54.21 
TCGA-ZF-AA5H TCGA-GU-AATO 
       29.49        10.65 

$`DEL PEAK 28(15Q13.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.27        16.77        33.83        12.39        14.89 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
       25.94         9.96        18.58        12.92         4.90        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2I6 
       13.58         2.14        19.00        16.70       130.88        87.32 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
       17.72        50.27        21.30        23.21         9.67        66.05 
TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-AA6L TCGA-DK-AA6S 
       64.18        53.29        76.60        67.36        38.24       166.03 
TCGA-DK-AA71 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-FD-A3B6 TCGA-FD-A3B7 
       13.64        20.32        15.35         0.92        33.04         4.01 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P 
       23.41        17.98        46.78        19.79        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX 
        3.62        15.58        26.73        53.88        10.78         5.69 
TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TG 
        6.28        62.86        18.81         6.15        12.36         3.06 
TCGA-FD-A6TI TCGA-G2-A2ES TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GU-A763 
        9.67        33.01        70.32        21.40        17.75        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QK TCGA-HQ-A5ND TCGA-K4-A3WU TCGA-K4-A4AC 
       32.98        19.82        27.35         9.01         3.45         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-S5-A6DX TCGA-UY-A9PH 
       27.68        52.73        50.56        46.98         1.84        51.32 
TCGA-XF-A8HE TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T2 
      125.49         4.21        12.76        11.90        21.04        18.90 
TCGA-XF-A9T6 TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMQ TCGA-XF-AAMR 
        2.10        13.74        10.82        11.31        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        44.32        30.94        86.30        18.58         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RE TCGA-ZF-AA53 TCGA-ZF-AA5P 
        9.63        21.11        30.28         3.48        57.90        12.23 
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-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-AA86 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
       10.22         7.33         6.74        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A2LA TCGA-BT-A3PH 
       19.50         5.06        14.96         5.06        17.16         4.67 
TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
       28.41        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-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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.87        13.08        29.79         1.84        21.86 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
       16.14        17.62        15.62        17.95         4.80        13.58 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        13.58        18.81        19.00 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83        29.72         5.36         2.24        16.70 
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-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N6 
       15.32        14.37        16.77         8.94        12.62        27.98 
TCGA-FD-A3SO TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A6TF TCGA-FJ-A3Z9 
        5.52        14.96        20.91        19.33         2.27        12.66 
TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
       10.65         8.94         3.25        48.00        15.95        59.31 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3RC TCGA-GC-A4ZW 
        7.23         6.94        29.36        20.71        15.91         0.49 
TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R 
       13.91        26.70         3.12        20.98        11.31        18.97 
TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OF 
       20.05         7.00        14.27        36.49         1.51        64.01 
TCGA-K4-A3WV TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LT-A8JT TCGA-PQ-A6FI 
       21.24        16.27        11.80         1.15        21.07        12.23 
TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A8OD 
       16.54        38.99        78.25        69.34         3.02       112.83 
TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL 
        3.85         6.58        17.88        64.80        79.66        66.41 
TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMW TCGA-XF-AAMX 
       28.24        16.27        92.98       110.60         8.32         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 
       56.48        27.06        75.39        18.84         0.66        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD TCGA-ZF-A9RM 
       25.41        31.20        35.84        21.86        13.41        47.84 
TCGA-ZF-A9RN TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       20.22         8.61        60.16        56.35        19.40         8.52 
TCGA-ZF-AA5N 
        5.52 

  DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE 
                          0.56                           0.49 
  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 
                         18.03                          16.83 
[1] "0.6 - 165.7 (18.0)" "0.5 - 166.0 (16.8)"
[1] "hr=" "1.1"
D65V2, 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
D65V3, 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
D65V4, 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 154  27  41   3
D65V5, multiclass
    clus
vv   DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  N0                           82                            154
  N1                           20                             27
  N2                           34                             41
  N3                            5                              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"
D65V6, 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
D65V7, 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
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(15Q13.1) MUTATED   145   5
  DEL PEAK 28(15Q13.1) WILD-TYPE 219  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(15Q13.1) MUTATED    145    5
  DEL PEAK 28(15Q13.1) WILD-TYPE  219   15
     clus
vv    DEL PEAK 28(15Q13.1) MUTATED DEL PEAK 28(15Q13.1) WILD-TYPE
  NO                           145                            219
  YES                            5                             15
[1] 2 2
[1] FALSE
D65V9, continuous
D65V10, continuous
D65V11, 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
D65V12, 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"
D65V13, 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(66) Variable = DEL PEAK 29(16P13.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16P13.3) MUTATED    97  77
  DEL PEAK 29(16P13.3) WILD-TYPE 130 101
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                           174                            231 
  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                            77                            101 
$`DEL PEAK 29(16P13.3) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A3PJ 
       16.27        16.77        15.12        26.14         8.35        25.94 
TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A3KJ TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN 
       28.70        12.92        18.48        46.68        87.32         8.22 
TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M 
       21.30         9.67        17.98        67.36        36.66        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B6 
      165.73       166.03        11.18        15.35        25.58        33.04 
TCGA-FD-A3SR TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A6TD TCGA-FD-A6TE 
       19.79        15.58        26.73         8.25        12.69        12.36 
TCGA-FD-A6TH TCGA-FJ-A3Z7 TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP 
        4.31        31.07        19.13        24.92        10.92        32.98 
TCGA-GV-A3JZ TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O 
       19.82        22.72        25.02         9.14        27.68        50.56 
TCGA-KQ-A41P TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N TCGA-XF-A8HF TCGA-XF-A8HG 
       35.97         1.84        33.14        86.83        97.12        15.35 
TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 
       34.45        14.93         4.21        11.90        21.04        26.27 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAML TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 
        2.24         2.10         7.63        44.32        61.45        86.30 
TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4T 
       18.58        13.64        21.11        94.29        88.87        19.69 
TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA81 
       57.90        24.13        11.97         8.35        27.62        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BT-A0S7 
       10.22        47.80         2.50        40.08         2.66         6.58 
TCGA-BT-A20R TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-C4-A0F6 
        5.06        17.16        16.18         4.67        36.43        23.01 
TCGA-CF-A1HS TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A9FF TCGA-CU-A3QU TCGA-CU-A5W6 
       12.56        12.66        11.34        11.87         5.19         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WX 
       21.86        18.41       142.78         4.80         8.15        10.55 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA76 TCGA-E5-A4U1 TCGA-E7-A5KE TCGA-E7-A6ME 
       15.02        13.58        12.03        38.83         0.56        24.03 
TCGA-FD-A3B3 TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A5BZ 
       32.02        25.74        22.98        20.91         5.36        27.45 
TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EF 
        2.70         7.10        13.35         2.27        10.85        61.94 
TCGA-G2-A2EL TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 
       26.93        20.12        15.91        14.07         0.49         8.94 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A766 
       26.70         2.10         2.20        18.97         7.63        15.78 
TCGA-GU-A767 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE 
        4.73        21.34        19.10         8.48        19.40        38.60 
TCGA-HQ-A2OF TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO 
       64.01         9.07        11.70        17.72         1.81        11.80 
TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FN TCGA-SY-A9G5 
        1.15        15.32        15.58        13.48        16.67        38.99 
TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA TCGA-UY-A9PB TCGA-UY-A9PD 
       22.68        69.34       112.83        35.24        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX 
        6.21         3.85         6.58        79.66         5.98        23.64 
TCGA-XF-A9SZ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       28.24         2.96         8.32         6.77        56.48        11.97 
TCGA-ZF-A9RF TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        47.84        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       67.20        56.35        19.40        54.21        29.49        10.65 

$`DEL PEAK 29(16P13.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A2LD TCGA-BT-A3PK 
      108.95        33.83        12.39        14.89        20.48         9.96 
TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 
        8.98        18.58         4.90        15.12        13.58         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU 
       19.00        16.70       130.88        17.72        50.27        23.21 
TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B2 TCGA-DK-A6B5 
       66.05        64.18        53.29        76.60        15.68        50.70 
TCGA-DK-AA6L TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DU 
       38.24        13.64        13.64        56.15        20.32         0.92 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
        1.22         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BS 
       29.16        46.78        12.85        27.35         3.62        53.88 
TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA 
       10.78         5.69        18.08        58.92         6.28        62.86 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P 
       18.81         6.15         3.06         9.67        17.23        11.08 
TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC TCGA-GU-A763 
       33.01        17.62        70.32        21.40        17.75        32.78 
TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A3WU 
       20.28        27.35         8.58        19.07         9.01         3.45 
TCGA-K4-A4AB TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A9PH TCGA-XF-A8HD 
        2.76        52.73        46.98        14.24        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SV TCGA-XF-A9T2 TCGA-XF-A9T5 
      125.49         3.22        15.98        12.76        18.90        66.64 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31        54.90        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RE 
       98.99        30.94         3.88         9.63        30.28         3.48 
TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O 
       34.06        12.23        94.88       104.65        44.94        16.83 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA83 
       17.16        34.98        50.04         0.62        51.16        66.54 
TCGA-5N-A9KM TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
       17.42         7.33         6.74        13.15        19.04        12.16 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A42B 
       17.88        19.50        14.96         5.06         8.25        17.56 
TCGA-BT-A42F TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A3MG 
       28.41         1.94        12.79        13.97        12.59        12.13 
TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X 
       13.08        12.16        10.95        12.46        12.10        12.62 
TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A8HY TCGA-CF-A9FM 
       12.26        13.12        12.00        12.10        11.34        13.08 
TCGA-CU-A3YL TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       29.79        66.41       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A3IL TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-AA6T 
       17.95         7.79        13.58        20.81       163.30        18.81 
TCGA-DK-AA6U TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4IJ 
       19.00        15.35        43.59        29.72         5.36        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-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A85H TCGA-E7-A8O7 TCGA-E7-A97P 
       24.66        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-A3SO TCGA-FD-A43S TCGA-FD-A5BU TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        5.52        14.96        19.33        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3B 
        3.25        48.00        15.95        59.31         7.23        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A6I3 TCGA-GD-A3OQ 
        6.94        29.36        20.71        15.81        13.91         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A764 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3QI 
       20.98        11.31        20.05         7.00        14.27        36.49 
TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R 
        1.51        12.16        21.24        15.42        16.27        44.38 
TCGA-LT-A8JT TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78O 
       21.07        12.23        16.54        17.62        37.05        76.01 
TCGA-UY-A78P TCGA-UY-A8OC TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
       78.25         3.02        45.04         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAN4 
       64.80        66.41        16.27        92.98       110.60        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RG TCGA-ZF-AA4W 
       35.84        21.86        28.41        13.41        58.72        60.16 
TCGA-ZF-AA52 TCGA-ZF-AA56 TCGA-ZF-AA5N 
       35.41         8.52         5.52 

  DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE 
                          0.49                           0.62 
  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 
                        18.195                         17.560 
[1] "0.5 - 166.0 (18.2)" "0.6 - 163.3 (17.6)"
[1] "hr=" "1.1"
D66V2, 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
D66V3, 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
D66V4, 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    91  16  43   2
  DEL PEAK 29(16P13.3) WILD-TYPE 145  31  32   6
D66V5, multiclass
    clus
vv   DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  N0                           91                            145
  N1                           16                             31
  N2                           43                             32
  N3                            2                              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"
D66V6, 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
D66V7, 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
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(16P13.3) MUTATED   153   5
  DEL PEAK 29(16P13.3) WILD-TYPE 211  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16P13.3) MUTATED    153    5
  DEL PEAK 29(16P13.3) WILD-TYPE  211   15
     clus
vv    DEL PEAK 29(16P13.3) MUTATED DEL PEAK 29(16P13.3) WILD-TYPE
  NO                           153                            211
  YES                            5                             15
[1] 2 2
[1] FALSE
D66V9, continuous
D66V10, continuous
D66V11, 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
D66V12, 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"
D66V13, 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(67) Variable = DEL PEAK 30(16Q23.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(16Q23.1) MUTATED    69  50
  DEL PEAK 30(16Q23.1) WILD-TYPE 158 128
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                           119                            286 
  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                            50                            128 
$`DEL PEAK 30(16Q23.1) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-CU-A0YN TCGA-DK-A1AC TCGA-DK-A2HX 
       16.27        16.77        15.12        12.92       130.88        46.68 
TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B6 
       87.32         8.22         9.67        17.98        67.36        36.66 
TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6W TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3SS 
       52.01       165.73        13.64        15.35        25.58        12.85 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FJ-A3Z7 TCGA-FT-A61P TCGA-GU-A42P 
        6.15        12.69        12.36        31.07        11.08        10.92 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-K4-A4AC TCGA-KQ-A41O TCGA-KQ-A41P TCGA-SY-A9G0 
       19.82        20.28         9.14        50.56        35.97        33.14 
TCGA-UY-A78N TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SP 
       86.83       125.49        97.12        15.35         3.22        14.93 
TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML 
       11.90        21.04        26.27         2.10        10.82         7.63 
TCGA-XF-AAN3 TCGA-XF-AAN7 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE 
       86.30        18.58        13.64        30.28        94.29         3.48 
TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA86 TCGA-BL-A0C8 
       19.69        57.90         0.62        41.75        10.22        40.08 
TCGA-CU-A3QU TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
        5.19         1.84        21.86        17.95         7.79       142.78 
TCGA-DK-A3WW TCGA-DK-AA6P TCGA-DK-AA6U TCGA-DK-AA76 TCGA-E7-A4IJ TCGA-E7-A677 
       20.81        15.02        19.00        12.03        22.16        26.96 
TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO 
       24.03        13.68        12.95         8.94        22.52         5.52 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A62N TCGA-FD-A62O TCGA-G2-A2EF TCGA-G2-A2EJ 
       22.98        20.91         2.70         7.10        61.94        48.00 
TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q 
       20.12        15.91        14.07         2.10         2.20        11.31 
TCGA-GU-A762 TCGA-GU-A766 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3QH 
        7.63        15.78         7.00        14.27        19.10         8.48 
TCGA-GV-A3QI TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A5RJ 
       36.49        19.40        38.60        21.24        11.70        17.72 
TCGA-K4-A6FZ TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI 
        1.81        44.38         1.15        15.58        13.48        12.23 
TCGA-UY-A8OB TCGA-UY-A9PA TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SI TCGA-XF-A9SX 
       69.34        35.24         3.85         6.58        79.66        23.64 
TCGA-XF-AAMG TCGA-XF-AAN0 TCGA-YC-A9TC TCGA-YF-AA3L TCGA-ZF-A9RF TCGA-ZF-AA4N 
      110.60        56.48         0.66        11.97        64.08         2.89 
TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 
        8.61        59.38        60.16        67.20        56.35 

$`DEL PEAK 30(16Q23.1) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T TCGA-BT-A20W 
      108.95        33.83        12.39        26.14        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL 
       20.48        25.94         9.96        28.70         8.98        18.58 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
        4.90        15.12        18.48        13.58         2.14        19.00 
TCGA-DK-A1AB TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3X1 
       16.70        17.72        50.27        21.30        23.21        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-AA6S TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E7-A7DU 
      166.03        13.64        56.15        11.18        20.32         0.92 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        1.22        33.04         4.01        60.66        24.30        23.41 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X 
       17.98        29.16        46.78        19.79        27.35         3.62 
TCGA-FD-A43Y TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY 
       15.58        26.73        53.88        10.78         5.69         8.25 
TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB TCGA-FD-A6TG 
       18.08        58.92         6.28        62.86        18.81         3.06 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        4.31         9.67        17.23        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP 
       21.40        19.13        17.75        24.92        32.78        32.98 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-HQ-A5ND TCGA-K4-A3WS 
       27.35         8.58        19.07        22.72         9.01        25.02 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X 
        3.45         2.76        27.68        52.73        46.98        14.24 
TCGA-S5-A6DX TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A9SK TCGA-XF-A9SM TCGA-XF-A9ST 
        1.84        51.32        97.45        15.98        34.45         4.21 
TCGA-XF-A9SV TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH 
       12.76        18.90         2.24        66.64        13.74        11.31 
TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 
       54.90        71.57        91.73        98.99        44.32        30.94 
TCGA-XF-AAN2 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-ZF-AA4R 
       61.45         3.88         9.63        21.11        88.87        34.06 
TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW 
       12.23        24.13        11.97        94.88       104.65         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-5N-A9KI TCGA-5N-A9KM TCGA-BL-A13I 
       51.16        66.54        47.80         2.50        17.42         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O 
        2.66         6.74         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-A3PH TCGA-BT-A42B TCGA-BT-A42E TCGA-BT-A42F 
       17.16        16.18         4.67        17.56        36.43        28.41 
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-A9FM TCGA-CU-A3YL TCGA-DK-A1A6 
       11.34        11.34        11.87        13.08        29.79        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK 
       18.41       112.44        16.14        17.62        15.62         4.80 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T 
       13.58         8.15        10.55       163.30        13.58        18.81 
TCGA-DK-AA6X TCGA-E5-A2PC TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ 
       15.35        43.59        38.83        29.72         5.36         2.24 
TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF 
       16.70         0.56         0.66        26.24         4.24        24.66 
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-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BV 
       12.62        27.98        25.74        14.96        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE 
       27.45        13.35         2.27        10.85        12.66        10.65 
TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB 
        8.94         3.25        15.95        26.93        59.31         7.23 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A4ZW 
       66.02         6.94        29.36        20.71        15.81         0.49 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
        8.94        13.91        26.70         3.12        20.98        18.97 
TCGA-GU-A764 TCGA-GU-A767 TCGA-GV-A3JW TCGA-H4-A2HO TCGA-HQ-A2OF TCGA-HQ-A5NE 
       20.05         4.73        21.34         1.51        64.01        12.16 
TCGA-K4-A5RH TCGA-K4-A6MB TCGA-K4-A83P TCGA-K4-AAQO TCGA-LC-A66R TCGA-LT-A8JT 
        9.07        15.42        16.27        11.80        15.32        21.07 
TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M 
       16.67        16.54        38.99        17.62        37.05        22.68 
TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD TCGA-UY-A9PB TCGA-UY-A9PD 
       76.01        78.25         3.02       112.83        29.56        17.82 
TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG TCGA-XF-A9SH 
        6.21        45.04         1.87        17.88        48.62        64.80 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMT 
       66.41         5.98        28.24        16.27        92.98         2.96 
TCGA-XF-AAMW TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-ZF-A9R0 
        8.32         6.77        27.06        75.39        18.84        22.36 
TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
       25.41        31.20        35.84        21.86        28.41        13.41 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       58.72        47.84        20.22        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21        29.49         5.52        10.65 

  DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE 
                          0.62                           0.49 
  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 
                         17.72                          17.62 
[1] "0.6 - 165.7 (17.7)" "0.5 - 166.0 (17.6)"
[1] "hr=" "1.1"
D67V2, 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
D67V3, 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
D67V4, 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 180  34  51   4
D67V5, multiclass
    clus
vv   DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  N0                           56                            180
  N1                           13                             34
  N2                           24                             51
  N3                            4                              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"
D67V6, 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
D67V7, 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
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(16Q23.1) MUTATED   107   5
  DEL PEAK 30(16Q23.1) WILD-TYPE 257  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(16Q23.1) MUTATED    107    5
  DEL PEAK 30(16Q23.1) WILD-TYPE  257   15
     clus
vv    DEL PEAK 30(16Q23.1) MUTATED DEL PEAK 30(16Q23.1) WILD-TYPE
  NO                           107                            257
  YES                            5                             15
[1] 2 2
[1] FALSE
D67V9, continuous
D67V10, continuous
D67V11, 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
D67V12, 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"
D67V13, 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(68) Variable = DEL PEAK 31(17P12) MUTATION ANALYSIS
D68V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(17P12) MUTATED   115  92
  DEL PEAK 31(17P12) WILD-TYPE 112  86
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                         207                          198 
  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                          92                           86 
$`DEL PEAK 31(17P12) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        16.27        15.12        12.39        26.14        14.89 
TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CU-A3KJ TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC 
        9.96         8.98        18.48         2.14        16.70       130.88 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
       46.68        87.32         8.22        17.72        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6B5 TCGA-DK-A6B6 
        9.67        66.05        17.98        64.18        50.70        36.66 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DU 
      165.73       166.03        11.18        15.35        25.58         0.92 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FD-A3SS TCGA-FD-A43P 
       60.66        24.30        29.16        46.78        12.85        27.35 
TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BY TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TB 
        3.62        26.73         8.25         6.28        62.86        18.81 
TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FJ-A3Z7 TCGA-G2-A3VY TCGA-G2-AA3D 
        6.15        12.69         3.06        31.07        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       21.40        19.13        24.92        10.92        32.98        19.82 
TCGA-GV-A3QF TCGA-GV-A40E TCGA-GV-A40G TCGA-HQ-A5ND TCGA-K4-A4AC TCGA-KQ-A41N 
       20.28         8.58        19.07         9.01         9.14        52.73 
TCGA-KQ-A41O TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH 
       50.56        46.98        14.24         1.84        33.14        51.32 
TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       97.45       125.49        97.12        15.35         3.22        15.98 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9T3 TCGA-XF-AAMF TCGA-XF-AAMJ TCGA-XF-AAMQ 
       14.93         4.21         2.24        10.82        54.90        71.57 
TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN3 TCGA-YF-AA3M 
       91.73        98.99        44.32        30.94        86.30        13.64 
TCGA-ZF-A9RE TCGA-ZF-A9RL TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KR 
        3.48        88.87        19.69        57.90        24.13       104.65 
TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-5N-A9KM 
       17.16        34.98         0.62        51.16        47.80        17.42 
TCGA-BL-A0C8 TCGA-BT-A20J TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20X TCGA-BT-A2LA 
       40.08        19.04        17.88        19.50         8.25        17.16 
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42E TCGA-C4-A0F0 TCGA-CF-A1HR TCGA-CF-A1HS 
       16.18         4.67        36.43         1.94        12.79        12.56 
TCGA-CF-A27C TCGA-CF-A3MG TCGA-CF-A3MI TCGA-CF-A47X TCGA-CF-A5UA TCGA-CU-A5W6 
       13.97        12.13        12.16        12.62        12.00         1.84 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-DK-A3IK TCGA-DK-A3IL 
       66.41        18.41       112.44        17.95         4.80        13.58 
TCGA-DK-AA6P TCGA-DK-AA6Q TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       15.02        13.58        19.00        15.35        12.03        43.59 
TCGA-E5-A4U1 TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A6ME 
       38.83        22.16         0.56        26.96         4.24        24.03 
TCGA-E7-A7PW TCGA-E7-A85H TCGA-E7-A97Q TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3SO 
       13.68        12.95         8.09        16.77         8.94         5.52 
TCGA-FD-A43N TCGA-FD-A43U TCGA-FD-A5BV TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK 
       22.98        20.91         5.36         7.10        13.35        10.85 
TCGA-FJ-A3ZE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IE 
       10.65        61.94        48.00        26.93        59.31        20.12 
TCGA-G2-AA3B TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       66.02        14.07         0.49        13.91        26.70         2.10 
TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A767 TCGA-GU-AATQ 
        2.20        11.31        18.97         7.63         4.73         7.00 
TCGA-GV-A3QH TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE TCGA-K4-A5RI 
        8.48        19.40        38.60        64.01        12.16        11.70 
TCGA-K4-A5RJ TCGA-K4-A6MB TCGA-K4-AAQO TCGA-KQ-A41S TCGA-PQ-A6FI TCGA-PQ-A6FN 
       17.72        15.42        11.80         1.15        12.23        16.67 
TCGA-SY-A9G5 TCGA-UY-A78M TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OC 
       38.99        22.68        76.01        78.25        69.34         3.02 
TCGA-UY-A8OD TCGA-UY-A9PD TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HH TCGA-XF-A9SG 
      112.83        17.82         6.21         3.85         1.87        48.62 
TCGA-XF-A9SI TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT 
       79.66         5.98        23.64        28.24       110.60         2.96 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
        8.32        56.48        11.97        22.36        25.41        31.20 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N 
       21.86        28.41        58.72        47.84        20.22         2.89 
TCGA-ZF-AA4W TCGA-ZF-AA51 TCGA-ZF-AA56 
       60.16        56.35         8.52 

$`DEL PEAK 31(17P12) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A42C 
       16.77        33.83         8.35        20.48        25.94        28.70 
TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1AA 
       18.58        12.92         4.90        15.12        13.58        19.00 
TCGA-DK-A3IU TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-AA6L 
       23.21        53.29        76.60        67.36        15.68        38.24 
TCGA-DK-AA6M TCGA-DK-AA6W TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DV 
       52.01        13.64        13.64        56.15        20.32         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43Y 
       33.04         4.01        23.41        17.98        19.79        15.58 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TE 
       53.88        10.78         5.69        18.08        58.92        12.36 
TCGA-FD-A6TH TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-GC-A3WC 
        4.31         9.67        17.23        11.08        33.01        17.75 
TCGA-GU-A763 TCGA-GV-A3QK TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB 
       32.78        27.35        22.72        25.02         3.45         2.76 
TCGA-K4-A54R TCGA-KQ-A41P TCGA-UY-A78N TCGA-XF-A9SM TCGA-XF-A9SV TCGA-XF-A9SW 
       27.68        35.97        86.83        34.45        12.76        11.90 
TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-A9T8 
       21.04        26.27        18.90        66.64         2.10        13.74 
TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 
       11.31         7.63        61.45        18.58         3.88         9.63 
TCGA-ZF-A9R2 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-AA4R TCGA-ZF-AA5P TCGA-2F-A9KP 
       21.11        30.28        94.29        34.06        12.23        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       94.88         8.35        44.94        16.83        27.62        50.04 
TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-5N-A9KI TCGA-BL-A13I TCGA-BL-A13J 
       41.75        66.54        10.22         2.50         7.33         2.66 
TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20R TCGA-BT-A20U 
        6.74         6.58        13.15        12.16         5.06        14.96 
TCGA-BT-A20V TCGA-BT-A42B TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A3MF TCGA-CF-A3MH 
        5.06        17.56        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-A9FM TCGA-CU-A3QU 
       12.10        11.34        11.34        11.87        13.08         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 
       29.79        21.86        16.14        17.62        15.62         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6T 
      142.78         8.15        20.81        10.55       163.30        18.81 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF TCGA-E7-A678 
       29.72         5.36         2.24        16.70         0.66        26.24 
TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B8 
       24.66        14.07        15.32        14.37        32.02        12.62 
TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A5BU TCGA-FD-A5BZ 
       22.52        27.98        25.74        14.96        19.33        27.45 
TCGA-FD-A62N TCGA-FD-A6TF TCGA-FJ-A3Z9 TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EK 
        2.70         2.27        12.66         8.94         3.25        15.95 
TCGA-G2-A3IB TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC 
        7.23         6.94        29.36        20.71        15.81        15.91 
TCGA-GC-A6I1 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JV 
        8.94         3.12        20.98        20.05        15.78        14.27 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QI TCGA-H4-A2HO TCGA-K4-A3WV TCGA-K4-A5RH 
       21.34        19.10        36.49         1.51        21.24         9.07 
TCGA-K4-A6FZ TCGA-K4-A83P TCGA-KQ-A41R TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81        16.27        44.38        15.32        15.58        21.07 
TCGA-MV-A51V TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A9PA TCGA-UY-A9PB 
       13.48        16.54        17.62        37.05        35.24        29.56 
TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SL TCGA-XF-A9T4 
       45.04         6.58        17.88        64.80        66.41        16.27 
TCGA-XF-AAME TCGA-XF-AAMX TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
       92.98         6.77        27.06        75.39        18.84         0.66 
TCGA-ZF-A9R5 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-AA4U TCGA-ZF-AA4V TCGA-ZF-AA4X 
       35.84        13.41        64.08         8.61        59.38        67.20 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-ZF-AA5N TCGA-GU-AATO 
       35.41        19.40        54.21        29.49         5.52        10.65 

  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE 
                        0.49                         0.66 
  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 
                      17.980                       16.735 
[1] "0.5 - 166.0 (18.0)" "0.7 - 163.3 (16.7)"
[1] "hr=" "1.1"
D68V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 31(17P12) MUTATED         1       61        70       75
  DEL PEAK 31(17P12) WILD-TYPE       1       68        70       60
D68V3, 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                          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 31(17P12) MUTATED         56 99 34
  DEL PEAK 31(17P12) WILD-TYPE       67 96 24
D68V4, multiclass
          clus
vv         DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  T0+T1+T2                         56                           67
  T3                               99                           96
  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 31(17P12) MUTATED   113  24  45   4
  DEL PEAK 31(17P12) WILD-TYPE 123  23  30   4
D68V5, multiclass
    clus
vv   DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  N0                        113                          123
  N1                         24                           23
  N2                         45                           30
  N3                          4                            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"
D68V6, binary
                              cls
clus                            0  1
  DEL PEAK 31(17P12) MUTATED   96  4
  DEL PEAK 31(17P12) WILD-TYPE 96  7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED     96    4
  DEL PEAK 31(17P12) WILD-TYPE   96    7
   clus
vv  DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  0                         96                           96
  1                          4                            7
[1] 2 2
[1] FALSE
D68V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(17P12) MUTATED    59 149
  DEL PEAK 31(17P12) WILD-TYPE  48 152
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED     59  149
  DEL PEAK 31(17P12) WILD-TYPE   48  152
        clus
vv       DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  FEMALE                         59                           48
  MALE                          149                          152
[1] 2 2
[1] FALSE
D68V8, binary
                              cls
clus                             0   1
  DEL PEAK 31(17P12) MUTATED   188   7
  DEL PEAK 31(17P12) WILD-TYPE 176  13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED    188    7
  DEL PEAK 31(17P12) WILD-TYPE  176   13
     clus
vv    DEL PEAK 31(17P12) MUTATED DEL PEAK 31(17P12) WILD-TYPE
  NO                         188                          176
  YES                          7                           13
[1] 2 2
[1] FALSE
D68V9, continuous
D68V10, continuous
D68V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(17P12) MUTATED      18                        12   164
  DEL PEAK 31(17P12) WILD-TYPE    25                        10   163
D68V12, multiclass
                           clus
vv                          DEL PEAK 31(17P12) MUTATED
  ASIAN                                             18
  BLACK OR AFRICAN AMERICAN                         12
  WHITE                                            164
                           clus
vv                          DEL PEAK 31(17P12) WILD-TYPE
  ASIAN                                               25
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              163
[1] 3 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 31(17P12) MUTATED     6 182
  DEL PEAK 31(17P12) WILD-TYPE   3 187
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(17P12) MUTATED      6  182
  DEL PEAK 31(17P12) WILD-TYPE    3  187
                        clus
vv                       DEL PEAK 31(17P12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                        182
                        clus
vv                       DEL PEAK 31(17P12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          187
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 32(18Q23) MUTATION ANALYSIS
D69V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(18Q23) MUTATED   108  71
  DEL PEAK 32(18Q23) WILD-TYPE 119 107
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         179                          226 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                          71                          107 
$`DEL PEAK 32(18Q23) MUTATED`
TCGA-4Z-AA7M TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A42C TCGA-CU-A0YN TCGA-CU-A0YR 
       16.27        26.14         8.35        28.70        12.92        15.12 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A2I6 
       13.58         2.14        16.70       130.88        46.68        87.32 
TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6B2 
        8.22        50.27        21.30        66.05        64.18        15.68 
TCGA-DK-A6B5 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA74 TCGA-E7-A541 
       50.70        52.01       165.73       166.03        56.15        25.58 
TCGA-E7-A7DV TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SQ 
        1.22         4.01        60.66        24.30        29.16        46.78 
TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A6TA TCGA-FD-A6TD TCGA-FD-A6TG TCGA-FD-A6TH 
       12.85        15.58        62.86        12.69         3.06         4.31 
TCGA-FJ-A3ZF TCGA-GC-A3BM TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-AATP TCGA-GV-A3JZ 
       17.23        21.40        24.92        10.92        32.98        19.82 
TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-KQ-A41N TCGA-KQ-A41Q TCGA-R3-A69X 
       19.07        22.72        25.02        52.73        46.98        14.24 
TCGA-SY-A9G0 TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9ST 
       33.14        97.12         3.22        15.98        14.93         4.21 
TCGA-XF-A9SW TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAML TCGA-XF-AAMQ 
       11.90        66.64         2.10        54.90         7.63        71.57 
TCGA-XF-AAMR TCGA-XF-AAMZ TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9RL 
       91.73        44.32        86.30        13.64        21.11        88.87 
TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-2F-A9KW TCGA-4Z-AA7R 
       57.90        24.13        94.88       104.65         8.35        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-BT-A0YX TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A2LA 
       17.42        40.08        13.15        19.04         5.06        17.16 
TCGA-BT-A42B TCGA-BT-A42E TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG TCGA-CF-A3MH 
       17.56        36.43        12.79        12.56        12.13        13.08 
TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A8HX TCGA-CF-A8HY TCGA-CF-A9FF 
       12.16        10.95        12.66        11.34        11.34        11.87 
TCGA-CU-A5W6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2I1 
        1.84        18.41       112.44        16.14        17.62        17.95 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6P TCGA-DK-AA6X TCGA-E5-A2PC 
        4.80        13.58         8.15        15.02        15.35        43.59 
TCGA-E7-A3X6 TCGA-E7-A5KE TCGA-E7-A677 TCGA-E7-A6MD TCGA-E7-A85H TCGA-E7-A97Q 
       29.72         0.56        26.96         4.24        12.95         8.09 
TCGA-FD-A3B4 TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A62N TCGA-FD-A62O 
       16.77         5.52        25.74        22.98         2.70         7.10 
TCGA-FD-A62S TCGA-G2-A2EF TCGA-G2-A3IE TCGA-G2-AA3B TCGA-G2-AA3F TCGA-GC-A3RC 
       13.35        61.94        20.12        66.02        29.36        15.91 
TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A3OP TCGA-GD-A3OS 
       14.07         0.49         8.94        13.91         2.10        20.98 
TCGA-GD-A6C6 TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 TCGA-GV-A3JW 
        2.20         7.63        20.05        15.78         4.73        21.34 
TCGA-GV-A3JX TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A5RH TCGA-K4-A5RI 
       19.10        19.40        38.60        64.01         9.07        11.70 
TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-KQ-A41S TCGA-LC-A66R TCGA-MV-A51V TCGA-PQ-A6FI 
       17.72        11.80         1.15        15.32        13.48        12.23 
TCGA-PQ-A6FN TCGA-SY-A9G5 TCGA-UY-A78O TCGA-UY-A8OB TCGA-UY-A9PB TCGA-UY-A9PD 
       16.67        38.99        76.01        69.34        29.56        17.82 
TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SX TCGA-XF-AAMG TCGA-XF-AAMT 
        6.21         3.85         6.58        23.64       110.60         2.96 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD 
        6.77        11.97        22.36        21.86        28.41        13.41 
TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA51 
       58.72        47.84         2.89         8.61        60.16        56.35 
TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA58 TCGA-ZF-AA5H TCGA-GU-AATO 
       35.41        19.40        54.21        29.49        10.65 

$`DEL PEAK 32(18Q23) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20T 
      108.95        16.77        15.12        33.83        12.39        14.89 
TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO 
       20.48        25.94         9.96         8.98        18.58         4.90 
TCGA-CU-A3KJ TCGA-DK-A1AA TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X2 
       18.48        19.00        17.72        23.21         9.67        17.98 
TCGA-DK-A6AW TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6L TCGA-DK-AA6W 
       53.29        76.60        67.36        36.66        38.24        13.64 
TCGA-DK-AA71 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A7DU TCGA-FD-A3B6 
       13.64        11.18        20.32        15.35         0.92        33.04 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       23.41        17.98        19.79        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 
       53.88        10.78         5.69         8.25        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TI TCGA-FJ-A3Z7 
        6.28        18.81         6.15        12.36         9.67        31.07 
TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D TCGA-GC-A3RB TCGA-GC-A3WC 
       11.08        33.01        17.62        70.32        19.13        17.75 
TCGA-GU-A763 TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-HQ-A5ND TCGA-K4-A3WU 
       32.78        20.28        27.35         8.58         9.01         3.45 
TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41O TCGA-KQ-A41P TCGA-S5-A6DX 
        2.76         9.14        27.68        50.56        35.97         1.84 
TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SM 
       86.83        51.32        97.45       125.49        15.35        34.45 
TCGA-XF-A9SV TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 TCGA-XF-A9T8 
       12.76        21.04        26.27        18.90         2.24        13.74 
TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMY TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 
       10.82        11.31        98.99        30.94        61.45        18.58 
TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R4 TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R 
        3.88         9.63        30.28        94.29         3.48        34.06 
TCGA-ZF-AA4T TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7Y 
       19.69        12.23        11.97        44.94        16.83        50.04 
TCGA-4Z-AA80 TCGA-4Z-AA81 TCGA-4Z-AA87 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM 
        0.62        41.75        47.80         7.33         2.66         6.74 
TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20V 
        6.58        12.16        17.88        19.50        14.96         5.06 
TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 
        8.25        16.18         4.67        28.41         1.94        23.01 
TCGA-CF-A27C TCGA-CF-A3MF TCGA-CF-A47V TCGA-CF-A47W TCGA-CF-A47X TCGA-CF-A47Y 
       13.97        12.59        12.46        12.10        12.62        12.26 
TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A7I0 TCGA-CF-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       13.12        12.00        12.10        13.08         5.19        29.79 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3WW 
       21.86        66.41        15.62         7.79       142.78        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA76 
       10.55       163.30        13.58        18.81        19.00        12.03 
TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       38.83         5.36        22.16         2.24        16.70         0.66 
TCGA-E7-A678 TCGA-E7-A6ME TCGA-E7-A6MF TCGA-E7-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 
       26.24        24.03        24.66        13.68        14.07        15.32 
TCGA-E7-A97P TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 
       14.37        32.02         8.94        12.62        22.52        27.98 
TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TF 
       14.96        20.91        19.33         5.36        27.45         2.27 
TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-FT-A3EE TCGA-G2-A2EJ 
       10.85        12.66        10.65         8.94         3.25        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-AA3C TCGA-GC-A3I6 
       15.95        26.93        59.31         7.23         6.94        20.71 
TCGA-GC-A3OO TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-AATQ 
       15.81        26.70         3.12        11.31        18.97         7.00 
TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A5NE TCGA-K4-A3WV 
       14.27         8.48        36.49         1.51        12.16        21.24 
TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P TCGA-KQ-A41R TCGA-LT-A5Z6 TCGA-LT-A8JT 
        1.81        15.42        16.27        44.38        15.58        21.07 
TCGA-S5-AA26 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OC 
       16.54        17.62        37.05        22.68        78.25         3.02 
TCGA-UY-A8OD TCGA-UY-A9PA TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SG 
      112.83        35.24        45.04         1.87        17.88        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SZ TCGA-XF-A9T4 
       64.80        79.66        66.41         5.98        28.24        16.27 
TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       92.98         8.32        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9RF TCGA-ZF-A9RN 
        0.66        25.41        31.20        35.84        64.08        20.22 
TCGA-ZF-AA4V TCGA-ZF-AA4X TCGA-ZF-AA56 TCGA-ZF-AA5N 
       59.38        67.20         8.52         5.52 

  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                        0.49                         0.62 
  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 
                      17.560                       17.735 
[1] "0.5 - 166.0 (17.6)" "0.6 - 163.3 (17.7)"
[1] "hr=" "1.3"
D69V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 32(18Q23) MUTATED         1       51        66       60
  DEL PEAK 32(18Q23) WILD-TYPE       1       78        74       75
D69V3, 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                          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
  DEL PEAK 32(18Q23) MUTATED         51  92  25
  DEL PEAK 32(18Q23) WILD-TYPE       72 103  33
D69V4, multiclass
          clus
vv         DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  T0+T1+T2                         51                           72
  T3                               92                          103
  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 32(18Q23) MUTATED   102  19  36   4
  DEL PEAK 32(18Q23) WILD-TYPE 134  28  39   4
D69V5, multiclass
    clus
vv   DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  N0                        102                          134
  N1                         19                           28
  N2                         36                           39
  N3                          4                            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"
D69V6, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED    85   1
  DEL PEAK 32(18Q23) WILD-TYPE 107  10
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED     85    1
  DEL PEAK 32(18Q23) WILD-TYPE  107   10
   clus
vv  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  0                         85                          107
  1                          1                           10
[1] 2 2
[1] FALSE
D69V7, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED    50 129
  DEL PEAK 32(18Q23) WILD-TYPE  57 172
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED     50  129
  DEL PEAK 32(18Q23) WILD-TYPE   57  172
        clus
vv       DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  FEMALE                         50                           57
  MALE                          129                          172
[1] 2 2
[1] FALSE
D69V8, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED   161   6
  DEL PEAK 32(18Q23) WILD-TYPE 203  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED    161    6
  DEL PEAK 32(18Q23) WILD-TYPE  203   14
     clus
vv    DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  NO                         161                          203
  YES                          6                           14
[1] 2 2
[1] FALSE
D69V9, continuous
D69V10, continuous
D69V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(18Q23) MUTATED      17                        11   145
  DEL PEAK 32(18Q23) WILD-TYPE    26                        11   182
D69V12, multiclass
                           clus
vv                          DEL PEAK 32(18Q23) MUTATED
  ASIAN                                             17
  BLACK OR AFRICAN AMERICAN                         11
  WHITE                                            145
                           clus
vv                          DEL PEAK 32(18Q23) WILD-TYPE
  ASIAN                                               26
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              182
[1] 3 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 32(18Q23) MUTATED     5 160
  DEL PEAK 32(18Q23) WILD-TYPE   4 209
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED      5  160
  DEL PEAK 32(18Q23) WILD-TYPE    4  209
                        clus
vv                       DEL PEAK 32(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        160
                        clus
vv                       DEL PEAK 32(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          209
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 33(19P13.3) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(19P13.3) MUTATED    75  70
  DEL PEAK 33(19P13.3) WILD-TYPE 152 108
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           145                            260 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                            70                            108 
$`DEL PEAK 33(19P13.3) MUTATED`
TCGA-BL-A5ZZ TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PK TCGA-C4-A0EZ 
       12.39        14.89         8.35        20.48         9.96         8.98 
TCGA-DK-A1A5 TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3X1 
        2.14        16.70        87.32        17.72        21.30        66.05 
TCGA-DK-A3X2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ 
       17.98        50.70        38.24        13.64        11.18        15.35 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
        1.22        33.04        24.30        23.41        17.98        29.16 
TCGA-FD-A3SS TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A6TB 
       12.85        15.58         8.25        18.08        58.92        18.81 
TCGA-FD-A6TC TCGA-FD-A6TE TCGA-FD-A6TH TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES 
        6.15        12.36         4.31        17.23        11.08        33.01 
TCGA-G2-A3VY TCGA-GC-A3RB TCGA-GC-A3YS TCGA-GU-A42P TCGA-GV-A3JZ TCGA-GV-A40G 
       17.62        19.13        24.92        10.92        19.82        19.07 
TCGA-HQ-A5ND TCGA-K4-A3WS TCGA-K4-A54R TCGA-KQ-A41Q TCGA-R3-A69X TCGA-UY-A78N 
        9.01        25.02        27.68        46.98        14.24        86.83 
TCGA-XF-A8HF TCGA-XF-A9SJ TCGA-XF-A9SM TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW 
       97.12         3.22        34.45         4.21        12.76        11.90 
TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMJ TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9R4 
       66.64         2.10        54.90        86.30        13.64        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-2F-A9KW 
       94.29        88.87        34.06        19.69        57.90         8.35 
TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA82 TCGA-4Z-AA87 TCGA-5N-A9KI TCGA-5N-A9KM 
       27.62         0.62        51.16        47.80         2.50        17.42 
TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42B 
       19.04         5.06         5.06        16.18         4.67        17.56 
TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A3MG 
       36.43        28.41        23.01        12.79        12.56        12.13 
TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A3IL TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 
       18.41       112.44        13.58        13.58        15.35        12.03 
TCGA-E5-A2PC TCGA-E7-A4IJ TCGA-E7-A85H TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B4 
       43.59        22.16        12.95        14.37         8.09        16.77 
TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A6TF TCGA-FJ-A3ZE 
        5.52        22.98         5.36        27.45         2.27        10.65 
TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-AA3F TCGA-GC-A3I6 
        8.94        61.94         7.23        20.12        29.36        20.71 
TCGA-GC-A6I1 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-AATQ TCGA-GV-A3JW 
        8.94        11.31        18.97         7.63         7.00        21.34 
TCGA-GV-A3JX TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-K4-A5RH TCGA-K4-A5RJ TCGA-K4-A6MB 
       19.10         1.51        19.40         9.07        17.72        15.42 
TCGA-KQ-A41S TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-S5-AA26 TCGA-SY-A9G5 
        1.15        13.48        12.23        16.67        16.54        38.99 
TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A78P TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA 
       37.05        22.68        78.25        69.34       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PF TCGA-XF-A8HB TCGA-XF-A9SG TCGA-XF-A9SH TCGA-XF-AAMG 
       29.56         3.85        45.04        48.62        64.80       110.60 
TCGA-XF-AAMT TCGA-XF-AAMX TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-AA4V TCGA-ZF-AA5H 
        2.96         6.77        28.41        47.84        59.38        29.49 
TCGA-GU-AATO 
       10.65 

$`DEL PEAK 33(19P13.3) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BT-A20N 
      108.95        16.27        16.77        15.12        33.83        26.14 
TCGA-BT-A3PJ TCGA-BT-A42C TCGA-CF-A9FL TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
       25.94        28.70        18.58        12.92         4.90        15.12 
TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AA TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN 
       18.48        13.58        19.00       130.88        46.68         8.22 
TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       50.27        23.21         9.67        64.18        53.29        76.60 
TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       67.36        15.68        36.66        52.01       165.73       166.03 
TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A541 TCGA-E7-A7DU TCGA-FD-A3B7 
       13.64        56.15        20.32        25.58         0.92         4.01 
TCGA-FD-A3NA TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A5BR 
       60.66        46.78        19.79        27.35         3.62        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A62P TCGA-FD-A6TA TCGA-FD-A6TD 
       53.88        10.78         5.69         6.28        62.86        12.69 
TCGA-FD-A6TG TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3WC 
        3.06         9.67        31.07        70.32        21.40        17.75 
TCGA-GU-A763 TCGA-GU-AATP TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA 
       32.78        32.98        20.28        27.35         8.58        22.72 
TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P 
        3.45         2.76         9.14        52.73        50.56        35.97 
TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG 
        1.84        33.14        51.32        97.45       125.49        15.35 
TCGA-XF-A9SK TCGA-XF-A9SP TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 TCGA-XF-A9T3 
       15.98        14.93        21.04        26.27        18.90         2.24 
TCGA-XF-A9T8 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAML TCGA-XF-AAMQ TCGA-XF-AAMR 
       13.74        10.82        11.31         7.63        71.57        91.73 
TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 TCGA-XF-AAN7 TCGA-XF-AAN8 
       98.99        44.32        30.94        61.45        18.58         3.88 
TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9RE TCGA-ZF-AA5P TCGA-2F-A9KO TCGA-2F-A9KP 
        9.63        21.11         3.48        12.23        24.13        11.97 
TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S 
       94.88       104.65        44.94        16.83        17.16        34.98 
TCGA-4Z-AA7Y TCGA-4Z-AA81 TCGA-4Z-AA83 TCGA-4Z-AA86 TCGA-BL-A0C8 TCGA-BL-A13I 
       50.04        41.75        66.54        10.22        40.08         7.33 
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.74         6.58        13.15        12.16        17.88 
TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X TCGA-BT-A2LA TCGA-C4-A0F0 TCGA-CF-A27C 
       19.50        14.96         8.25        17.16         1.94        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-A9FM TCGA-CU-A3QU TCGA-CU-A3YL 
       11.34        11.34        11.87        13.08         5.19        29.79 
TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        1.84        21.86        66.41        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3WW 
       17.95         7.79       142.78         4.80         8.15        20.81 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-E5-A4U1 
       10.55       163.30        15.02        18.81        19.00        38.83 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
       29.72         5.36         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-A7PW 
       26.96        26.24         4.24        24.03        24.66        13.68 
TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 
       14.07        15.32        32.02         8.94        12.62        22.52 
TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A62N 
       27.98        25.74        14.96        20.91        19.33         2.70 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FT-A3EE TCGA-G2-A2EJ 
        7.10        13.35        10.85        12.66         3.25        48.00 
TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3OO 
       15.95        26.93        59.31        66.02         6.94        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A4ZW TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07         0.49        13.91        26.70         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GD-A6C6 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
        3.12        20.98         2.20        20.05        15.78         4.73 
TCGA-GV-A3JV TCGA-GV-A3QH TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-HQ-A5NE 
       14.27         8.48        36.49        38.60        64.01        12.16 
TCGA-K4-A3WV TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A83P TCGA-K4-AAQO TCGA-KQ-A41R 
       21.24        11.70         1.81        16.27        11.80        44.38 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-LT-A8JT TCGA-UY-A78K TCGA-UY-A78O TCGA-UY-A8OC 
       15.32        15.58        21.07        17.62        76.01         3.02 
TCGA-UY-A9PD TCGA-UY-A9PE TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SI 
       17.82         6.21         6.58         1.87        17.88        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9SZ TCGA-XF-A9T4 TCGA-XF-AAME 
       66.41         5.98        23.64        28.24        16.27        92.98 
TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC 
        8.32        56.48        27.06        75.39        18.84         0.66 
TCGA-YF-AA3L TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 
       11.97        22.36        25.41        31.20        35.84        21.86 
TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       13.41        64.08        58.72        20.22         2.89         8.61 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N 
       54.21         5.52 

  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                          0.62                           0.49 
  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 
                         17.72                          17.39 
[1] "0.6 - 112.8 (17.7)" "0.5 - 166.0 (17.4)"
[1] "hr=" "1.2"
D70V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 33(19P13.3) MUTATED         0       34        52       59
  DEL PEAK 33(19P13.3) WILD-TYPE       2       95        88       76
D70V3, multiclass
           clus
vv          DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  STAGE I                              0                              2
  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         32  76  26
  DEL PEAK 33(19P13.3) WILD-TYPE       91 119  32
D70V4, multiclass
          clus
vv         DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  T0+T1+T2                           32                             91
  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 163  24  45   3
D70V5, multiclass
    clus
vv   DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  N0                           73                            163
  N1                           23                             24
  N2                           30                             45
  N3                            5                              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"
D70V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    53   7
  DEL PEAK 33(19P13.3) WILD-TYPE 139   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     53    7
  DEL PEAK 33(19P13.3) WILD-TYPE  139    4
   clus
vv  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  0                           53                            139
  1                            7                              4
[1] 2 2
[1] FALSE
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED    40 105
  DEL PEAK 33(19P13.3) WILD-TYPE  67 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED     40  105
  DEL PEAK 33(19P13.3) WILD-TYPE   67  196
        clus
vv       DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  FEMALE                           40                             67
  MALE                            105                            196
[1] 2 2
[1] FALSE
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED   135   4
  DEL PEAK 33(19P13.3) WILD-TYPE 229  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED    135    4
  DEL PEAK 33(19P13.3) WILD-TYPE  229   16
     clus
vv    DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  NO                           135                            229
  YES                            4                             16
[1] 2 2
[1] FALSE
D70V9, continuous
D70V10, continuous
D70V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(19P13.3) MUTATED      10                         9   120
  DEL PEAK 33(19P13.3) WILD-TYPE    33                        13   207
D70V12, multiclass
                           clus
vv                          DEL PEAK 33(19P13.3) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              120
                           clus
vv                          DEL PEAK 33(19P13.3) WILD-TYPE
  ASIAN                                                 33
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                207
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED     6 130
  DEL PEAK 33(19P13.3) WILD-TYPE   3 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED      6  130
  DEL PEAK 33(19P13.3) WILD-TYPE    3  239
                        clus
vv                       DEL PEAK 33(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          130
                        clus
vv                       DEL PEAK 33(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            239
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 34(22Q13.32) MUTATION ANALYSIS
D71V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 34(22Q13.32) MUTATED   103  84
  DEL PEAK 34(22Q13.32) WILD-TYPE 124  94
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                            187                             218 
  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                             84                              94 
$`DEL PEAK 34(22Q13.32) MUTATED`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0EZ 
       16.27        16.77         8.35        25.94        28.70         8.98 
TCGA-CU-A0YN TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
       12.92       130.88        46.68         8.22        17.72        21.30 
TCGA-DK-A3X2 TCGA-DK-A6B1 TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6M 
       17.98        67.36        15.68        50.70        38.24        52.01 
TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W TCGA-DK-AA75 TCGA-E5-A4TZ TCGA-E7-A541 
      165.73       166.03        13.64        11.18        15.35        25.58 
TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN 
        1.22        33.04        60.66        24.30        23.41        29.16 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FD-A43P TCGA-FD-A43Y TCGA-FD-A5BT TCGA-FD-A5BY 
       19.79        12.85        27.35        15.58        10.78         8.25 
TCGA-FD-A5C0 TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE 
       18.08         6.28        18.81         6.15        12.69        12.36 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A3VY TCGA-GC-A3YS TCGA-GU-AATP 
       31.07        17.23        11.08        17.62        24.92        32.98 
TCGA-GV-A40E TCGA-GV-A40G TCGA-GV-A6ZA TCGA-K4-A3WS TCGA-K4-A3WU TCGA-KQ-A41Q 
        8.58        19.07        22.72        25.02         3.45        46.98 
TCGA-UY-A78N TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
       86.83        97.12        15.35         3.22        15.98        34.45 
TCGA-XF-A9SP TCGA-XF-A9ST TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T3 
       14.93         4.21        11.90        21.04        26.27         2.24 
TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAML TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 
        2.10        10.82         7.63        98.99        44.32        61.45 
TCGA-XF-AAN3 TCGA-YF-AA3M TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T 
       86.30        13.64        94.29         3.48        34.06        19.69 
TCGA-ZF-AA5P TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7W TCGA-4Z-AA80 TCGA-4Z-AA81 
       12.23        11.97         8.35        27.62         0.62        41.75 
TCGA-4Z-AA86 TCGA-4Z-AA87 TCGA-BL-A13J TCGA-BT-A20J TCGA-BT-A20R TCGA-BT-A20V 
       10.22        47.80         2.66        19.04         5.06         5.06 
TCGA-BT-A42B TCGA-BT-A42E TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A3MI TCGA-CF-A47X 
       17.56        36.43         1.94        23.01        12.16        12.62 
TCGA-CF-A9FF TCGA-CU-A3QU TCGA-DK-A1A7 TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       11.87         5.19        18.41        17.95         7.79       142.78 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-AA6Q TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A2PC 
       13.58         8.15        13.58        15.35        12.03        43.59 
TCGA-E7-A4IJ TCGA-E7-A5KE TCGA-E7-A6ME TCGA-E7-A7PW TCGA-E7-A85H TCGA-FD-A3B3 
       22.16         0.56        24.03        13.68        12.95        32.02 
TCGA-FD-A3B4 TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SO TCGA-FD-A43N TCGA-FD-A43U 
       16.77         8.94        22.52         5.52        22.98        20.91 
TCGA-FD-A5BV TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A6TF TCGA-FD-A6TK TCGA-G2-A2EF 
        5.36        27.45         2.70         2.27        10.85        61.94 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3RC TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GC-A6I3 
        7.23        20.12        15.91         0.49         8.94        13.91 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A6C6 TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 
       26.70         2.10         2.20        11.31        18.97         7.63 
TCGA-GU-A764 TCGA-GU-A766 TCGA-GV-A3JX TCGA-H4-A2HQ TCGA-HQ-A5NE TCGA-K4-A5RH 
       20.05        15.78        19.10        19.40        12.16         9.07 
TCGA-K4-A5RI TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-KQ-A41R TCGA-KQ-A41S 
       11.70        17.72         1.81        15.42        44.38         1.15 
TCGA-LC-A66R TCGA-LT-A5Z6 TCGA-MV-A51V TCGA-PQ-A6FI TCGA-PQ-A6FN TCGA-SY-A9G5 
       15.32        15.58        13.48        12.23        16.67        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OD TCGA-UY-A9PA 
       17.62        37.05        22.68        69.34       112.83        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-UY-A9PF TCGA-XF-A8HC TCGA-XF-A9SG TCGA-XF-A9SX 
       29.56         6.21         3.85         6.58        48.62        23.64 
TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT TCGA-XF-AAMX TCGA-XF-AAN0 TCGA-YF-AA3L 
       28.24       110.60         2.96         6.77        56.48        11.97 
TCGA-ZF-A9R7 TCGA-ZF-A9R9 TCGA-ZF-A9RD TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM 
       21.86        28.41        13.41        64.08        58.72        47.84 
TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA5H 
        2.89         8.61        60.16        67.20        35.41        29.49 
TCGA-GU-AATO 
       10.65 

$`DEL PEAK 34(22Q13.32) WILD-TYPE`
TCGA-2F-A9KT TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20T 
      108.95        15.12        33.83        12.39        26.14        14.89 
TCGA-BT-A2LD TCGA-BT-A3PK TCGA-CF-A9FL TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
       20.48         9.96        18.58         4.90        15.12        18.48 
TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IS 
       13.58         2.14        19.00        16.70        87.32        50.27 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-DK-A6AV TCGA-DK-A6AW TCGA-DK-A6B0 
       23.21         9.67        66.05        64.18        53.29        76.60 
TCGA-DK-A6B6 TCGA-DK-AA71 TCGA-DK-AA74 TCGA-DK-AA77 TCGA-E7-A7DU TCGA-FD-A3B7 
       36.66        13.64        56.15        20.32         0.92         4.01 
TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43X TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BX 
       17.98        46.78         3.62        26.73        53.88         5.69 
TCGA-FD-A5C1 TCGA-FD-A6TA TCGA-FD-A6TG TCGA-FD-A6TH TCGA-FD-A6TI TCGA-G2-A2ES 
       58.92        62.86         3.06         4.31         9.67        33.01 
TCGA-G2-AA3D TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GU-A42P TCGA-GU-A763 
       70.32        21.40        19.13        17.75        10.92        32.78 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-HQ-A5ND TCGA-K4-A4AB TCGA-K4-A4AC 
       19.82        20.28        27.35         9.01         2.76         9.14 
TCGA-K4-A54R TCGA-KQ-A41N TCGA-KQ-A41O TCGA-KQ-A41P TCGA-R3-A69X TCGA-S5-A6DX 
       27.68        52.73        50.56        35.97        14.24         1.84 
TCGA-SY-A9G0 TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A9SV TCGA-XF-A9T2 
       33.14        51.32        97.45       125.49        12.76        18.90 
TCGA-XF-A9T5 TCGA-XF-A9T8 TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAMQ TCGA-XF-AAMR 
       66.64        13.74        11.31        54.90        71.57        91.73 
TCGA-XF-AAN1 TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       30.94        18.58         3.88         9.63        21.11        30.28 
TCGA-ZF-A9RL TCGA-ZF-AA53 TCGA-2F-A9KO TCGA-2F-A9KQ TCGA-2F-A9KR TCGA-4Z-AA7N 
       88.87        57.90        24.13        94.88       104.65        44.94 
TCGA-4Z-AA7O TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7Y TCGA-4Z-AA82 TCGA-4Z-AA83 
       16.83        17.16        34.98        50.04        51.16        66.54 
TCGA-5N-A9KI TCGA-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 
        2.50        17.42        40.08         7.33         6.74         6.58 
TCGA-BT-A0YX TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20U TCGA-BT-A20X 
       13.15        12.16        17.88        19.50        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A3PH TCGA-BT-A42F TCGA-CF-A1HR TCGA-CF-A1HS 
       17.16        16.18         4.67        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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 
       11.34        11.34        13.08        29.79         1.84        21.86 
TCGA-DK-A1A6 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A3IK 
       66.41       112.44        16.14        17.62        15.62         4.80 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U 
       20.81        10.55       163.30        15.02        18.81        19.00 
TCGA-E5-A4U1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KF 
       38.83        29.72         5.36         2.24        16.70         0.66 
TCGA-E7-A677 TCGA-E7-A678 TCGA-E7-A6MD TCGA-E7-A6MF TCGA-E7-A7XN TCGA-E7-A8O7 
       26.96        26.24         4.24        24.66        14.07        15.32 
TCGA-E7-A97P TCGA-E7-A97Q TCGA-FD-A3B8 TCGA-FD-A3N6 TCGA-FD-A3SP TCGA-FD-A43S 
       14.37         8.09        12.62        27.98        25.74        14.96 
TCGA-FD-A5BU TCGA-FD-A62O TCGA-FD-A62S TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
       19.33         7.10        13.35        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EL TCGA-G2-A2EO TCGA-G2-AA3B 
        3.25        48.00        15.95        26.93        59.31        66.02 
TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RD TCGA-GD-A3OQ 
        6.94        29.36        20.71        15.81        14.07         3.12 
TCGA-GD-A3OS TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3QH 
       20.98         4.73         7.00        14.27        21.34         8.48 
TCGA-GV-A3QI TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-HQ-A2OF TCGA-K4-A3WV TCGA-K4-A83P 
       36.49         1.51        38.60        64.01        21.24        16.27 
TCGA-K4-AAQO TCGA-LT-A8JT TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC 
       11.80        21.07        16.54        76.01        78.25         3.02 
TCGA-UY-A9PD TCGA-XF-A8HB TCGA-XF-A8HH TCGA-XF-A8HI TCGA-XF-A9SH TCGA-XF-A9SI 
       17.82        45.04         1.87        17.88        64.80        79.66 
TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN4 
       66.41         5.98        16.27        92.98         8.32        27.06 
TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 
       75.39        18.84         0.66        22.36        25.41        31.20 
TCGA-ZF-A9R5 TCGA-ZF-A9RN TCGA-ZF-AA4V TCGA-ZF-AA51 TCGA-ZF-AA54 TCGA-ZF-AA56 
       35.84        20.22        59.38        56.35        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N 
       54.21         5.52 

  DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE 
                           0.49                            0.66 
  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 
                          16.77                           17.93 
[1] "0.5 - 166.0 (16.8)" "0.7 - 163.3 (17.9)"
[1] "hr=" "1.1"
D71V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 34(22Q13.32) MUTATED         0       53        64       71
  DEL PEAK 34(22Q13.32) WILD-TYPE       2       76        76       64
D71V3, multiclass
           clus
vv          DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  STAGE I                               0                               2
  STAGE II                             53                              76
  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
D71V4, 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    99  21  46   3
  DEL PEAK 34(22Q13.32) WILD-TYPE 137  26  29   5
D71V5, multiclass
    clus
vv   DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  N0                            99                             137
  N1                            21                              26
  N2                            46                              29
  N3                             3                               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"
D71V6, 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
D71V7, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED    48 140
  DEL PEAK 34(22Q13.32) WILD-TYPE  59 161
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED     48  140
  DEL PEAK 34(22Q13.32) WILD-TYPE   59  161
        clus
vv       DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  FEMALE                            48                              59
  MALE                             140                             161
[1] 2 2
[1] FALSE
D71V8, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED   168   5
  DEL PEAK 34(22Q13.32) WILD-TYPE 196  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED    168    5
  DEL PEAK 34(22Q13.32) WILD-TYPE  196   15
     clus
vv    DEL PEAK 34(22Q13.32) MUTATED DEL PEAK 34(22Q13.32) WILD-TYPE
  NO                            168                             196
  YES                             5                              15
[1] 2 2
[1] FALSE
D71V9, continuous
D71V10, continuous
D71V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(22Q13.32) MUTATED      12                        12   157
  DEL PEAK 34(22Q13.32) WILD-TYPE    31                        10   170
D71V12, multiclass
                           clus
vv                          DEL PEAK 34(22Q13.32) MUTATED
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               157
                           clus
vv                          DEL PEAK 34(22Q13.32) WILD-TYPE
  ASIAN                                                  31
  BLACK OR AFRICAN AMERICAN                              10
  WHITE                                                 170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                                 cls
clus                                0   1
  DEL PEAK 34(22Q13.32) MUTATED     6 169
  DEL PEAK 34(22Q13.32) WILD-TYPE   3 200
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.32) MUTATED      6  169
  DEL PEAK 34(22Q13.32) WILD-TYPE    3  200
                        clus
vv                       DEL PEAK 34(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           169
                        clus
vv                       DEL PEAK 34(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             200
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 35(XP11.3) MUTATION ANALYSIS
D72V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 35(XP11.3) MUTATED    52  39
  DEL PEAK 35(XP11.3) WILD-TYPE 175 139
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           91                           314 
  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                           39                           139 
$`DEL PEAK 35(XP11.3) MUTATED`
TCGA-2F-A9KT TCGA-4Z-AA7M TCGA-4Z-AA84 TCGA-BT-A20T TCGA-CU-A0YN TCGA-DK-A1A5 
      108.95        16.27        15.12        14.89        12.92         2.14 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A2I6 TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV 
       19.00        16.70        87.32        50.27        21.30         9.67 
TCGA-DK-A6B2 TCGA-DK-A6B5 TCGA-DK-AA6L TCGA-DK-AA6R TCGA-DK-AA6S TCGA-DK-AA6W 
       15.68        50.70        38.24       165.73       166.03        13.64 
TCGA-E7-A7DU TCGA-E7-A7DV TCGA-FD-A3B6 TCGA-FD-A3SN TCGA-FD-A3SR TCGA-FD-A3SS 
        0.92         1.22        33.04        29.16        19.79        12.85 
TCGA-FD-A43Y TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FD-A6TC TCGA-G2-A3VY TCGA-HQ-A5ND 
       15.58         8.25        62.86         6.15        17.62         9.01 
TCGA-K4-A3WS TCGA-KQ-A41O TCGA-XF-A8HF TCGA-XF-A9SM TCGA-XF-A9SP TCGA-XF-A9T8 
       25.02        50.56        97.12        34.45        14.93        13.74 
TCGA-XF-AAML TCGA-XF-AAN1 TCGA-ZF-A9RL TCGA-ZF-AA4R TCGA-2F-A9KQ TCGA-2F-A9KW 
        7.63        30.94        88.87        34.06        94.88         8.35 
TCGA-4Z-AA7O TCGA-4Z-AA7S TCGA-5N-A9KI TCGA-BL-A13J TCGA-BT-A20P TCGA-BT-A20V 
       16.83        34.98         2.50         2.66        17.88         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-A3QU TCGA-DK-A1AD TCGA-DK-AA6Q 
       12.62        12.10        11.34         5.19       112.44        13.58 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-FD-A3B4 TCGA-FD-A62N TCGA-FD-A6TF TCGA-G2-A2EL 
       43.59        29.72        16.77         2.70         2.27        26.93 
TCGA-G2-A3IB TCGA-G2-AA3F TCGA-GC-A4ZW TCGA-GD-A3OS TCGA-GV-A3JX TCGA-GV-A3QH 
        7.23        29.36         0.49        20.98        19.10         8.48 
TCGA-GV-A3QI TCGA-HQ-A2OF TCGA-K4-A5RJ TCGA-K4-A6FZ TCGA-K4-AAQO TCGA-LT-A5Z6 
       36.49        64.01        17.72         1.81        11.80        15.58 
TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OC TCGA-UY-A8OD 
       12.23        16.54        76.01        78.25         3.02       112.83 
TCGA-XF-A9SZ TCGA-XF-AAMT TCGA-XF-AAMW TCGA-ZF-A9R9 TCGA-ZF-AA51 TCGA-ZF-AA56 
       28.24         2.96         8.32        28.41        56.35         8.52 
TCGA-ZF-AA58 
       54.21 

$`DEL PEAK 35(XP11.3) WILD-TYPE`
TCGA-4Z-AA7Q TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N TCGA-BT-A20W TCGA-BT-A2LD 
       16.77        33.83        12.39        26.14         8.35        20.48 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C TCGA-C4-A0EZ TCGA-CF-A9FL TCGA-CU-A0YO 
       25.94         9.96        28.70         8.98        18.58         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A72E TCGA-DK-A1AC TCGA-DK-A2HX TCGA-DK-A3IN 
       15.12        18.48        13.58       130.88        46.68         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3X1 TCGA-DK-A3X2 TCGA-DK-A6AV TCGA-DK-A6AW 
       17.72        23.21        66.05        17.98        64.18        53.29 
TCGA-DK-A6B0 TCGA-DK-A6B1 TCGA-DK-A6B6 TCGA-DK-AA6M TCGA-DK-AA71 TCGA-DK-AA74 
       76.60        67.36        36.66        52.01        13.64        56.15 
TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-FD-A3B7 TCGA-FD-A3NA 
       11.18        20.32        15.35        25.58         4.01        60.66 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SQ TCGA-FD-A43P TCGA-FD-A43X 
       24.30        23.41        17.98        46.78        27.35         3.62 
TCGA-FD-A5BR TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 
       26.73        53.88        10.78         5.69        18.08        58.92 
TCGA-FD-A62P TCGA-FD-A6TB TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
        6.28        18.81        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-AA3D 
        9.67        31.07        17.23        11.08        33.01        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A42P TCGA-GU-A763 
       21.40        19.13        17.75        24.92        10.92        32.78 
TCGA-GU-AATP TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
       32.98        19.82        20.28        27.35         8.58        19.07 
TCGA-GV-A6ZA TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-K4-A54R TCGA-KQ-A41N 
       22.72         3.45         2.76         9.14        27.68        52.73 
TCGA-KQ-A41P TCGA-KQ-A41Q TCGA-R3-A69X TCGA-S5-A6DX TCGA-SY-A9G0 TCGA-UY-A78N 
       35.97        46.98        14.24         1.84        33.14        86.83 
TCGA-UY-A9PH TCGA-XF-A8HD TCGA-XF-A8HE TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK 
       51.32        97.45       125.49        15.35         3.22        15.98 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T5 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ 
        2.24        66.64         2.10        10.82        11.31        54.90 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN2 TCGA-XF-AAN3 
       71.57        91.73        98.99        44.32        61.45        86.30 
TCGA-XF-AAN7 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R2 TCGA-ZF-A9R4 
       18.58         3.88         9.63        13.64        21.11        30.28 
TCGA-ZF-A9RC TCGA-ZF-A9RE TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
       94.29         3.48        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KR TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7W TCGA-4Z-AA7Y 
       11.97       104.65        44.94        17.16        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-5N-A9KM TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       17.42        40.08         7.33         6.74         6.58        13.15 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20X 
       19.04        12.16        19.50         5.06        14.96         8.25 
TCGA-BT-A2LA TCGA-BT-A2LB TCGA-BT-A42F TCGA-C4-A0F0 TCGA-C4-A0F6 TCGA-CF-A1HR 
       17.16        16.18        28.41         1.94        23.01        12.79 
TCGA-CF-A1HS TCGA-CF-A3MF TCGA-CF-A3MI TCGA-CF-A47S TCGA-CF-A47T TCGA-CF-A47V 
       12.56        12.59        12.16        10.95        12.66        12.46 
TCGA-CF-A47W TCGA-CF-A47Y TCGA-CF-A5U8 TCGA-CF-A5UA TCGA-CF-A8HY TCGA-CF-A9FF 
       12.10        12.26        13.12        12.00        11.34        11.87 
TCGA-CF-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 
       13.08        29.79         1.84        21.86        66.41        18.41 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        17.95         7.79       142.78 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
        4.80        13.58         8.15        20.81        10.55       163.30 
TCGA-DK-AA6P TCGA-DK-AA6T TCGA-DK-AA6U TCGA-DK-AA6X TCGA-DK-AA76 TCGA-E5-A4U1 
       15.02        18.81        19.00        15.35        12.03        38.83 
TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 TCGA-E7-A5KE TCGA-E7-A5KF 
        5.36        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-A7PW 
       26.96        26.24         4.24        24.03        24.66        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-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO TCGA-FD-A3SP 
        8.94        12.62        22.52        27.98         5.52        25.74 
TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV TCGA-FD-A5BZ 
       22.98        14.96        20.91        19.33         5.36        27.45 
TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TK TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 
        7.10        13.35        10.85        12.66        10.65         8.94 
TCGA-FT-A3EE TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IE 
        3.25        61.94        48.00        15.95        59.31        20.12 
TCGA-G2-AA3B TCGA-G2-AA3C TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD 
       66.02         6.94        20.71        15.81        15.91        14.07 
TCGA-GC-A6I1 TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A6C6 
        8.94        13.91        26.70         2.10         3.12         2.20 
TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 TCGA-GU-A767 
       11.31        18.97         7.63        20.05        15.78         4.73 
TCGA-GU-AATQ TCGA-GV-A3JV TCGA-GV-A3JW TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        7.00        14.27        21.34         1.51        19.40        38.60 
TCGA-HQ-A5NE TCGA-K4-A3WV TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6MB TCGA-K4-A83P 
       12.16        21.24         9.07        11.70        15.42        16.27 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-MV-A51V TCGA-PQ-A6FN 
       44.38         1.15        15.32        21.07        13.48        16.67 
TCGA-SY-A9G5 TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A9PA 
       38.99        17.62        37.05        22.68        69.34        35.24 
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-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-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 TCGA-XF-AAME TCGA-XF-AAMG TCGA-XF-AAMX 
        5.98        23.64        16.27        92.98       110.60         6.77 
TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H TCGA-YC-A9TC TCGA-YF-AA3L 
       56.48        27.06        75.39        18.84         0.66        11.97 
TCGA-ZF-A9R0 TCGA-ZF-A9R1 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
       22.36        25.41        31.20        35.84        21.86        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RM TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U 
       64.08        58.72        47.84        20.22         2.89         8.61 
TCGA-ZF-AA4V TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA5H 
       59.38        60.16        67.20        35.41        19.40        29.49 
TCGA-ZF-AA5N TCGA-GU-AATO 
        5.52        10.65 

  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE 
                         0.49                          0.56 
  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 
                       16.700                        17.915 
[1] "0.5 - 166.0 (16.7)" "0.6 - 163.3 (17.9)"
[1] "hr=" "1.1"
D72V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 35(XP11.3) MUTATED         0       27        33       31
  DEL PEAK 35(XP11.3) WILD-TYPE       2      102       107      104
D72V3, 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                          33                           107
  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  44  16
  DEL PEAK 35(XP11.3) WILD-TYPE      100 151  42
D72V4, multiclass
          clus
vv         DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  T0+T1+T2                          23                           100
  T3                                44                           151
  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    51  14  14   2
  DEL PEAK 35(XP11.3) WILD-TYPE 185  33  61   6
D72V5, multiclass
    clus
vv   DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  N0                          51                           185
  N1                          14                            33
  N2                          14                            61
  N3                           2                             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"
D72V6, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    43   2
  DEL PEAK 35(XP11.3) WILD-TYPE 149   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     43    2
  DEL PEAK 35(XP11.3) WILD-TYPE  149    9
   clus
vv  DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  0                          43                           149
  1                           2                             9
[1] 2 2
[1] FALSE
D72V7, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    24  67
  DEL PEAK 35(XP11.3) WILD-TYPE  83 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     24   67
  DEL PEAK 35(XP11.3) WILD-TYPE   83  234
        clus
vv       DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  FEMALE                          24                            83
  MALE                            67                           234
[1] 2 2
[1] FALSE
D72V8, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED    81   5
  DEL PEAK 35(XP11.3) WILD-TYPE 283  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED     81    5
  DEL PEAK 35(XP11.3) WILD-TYPE  283   15
     clus
vv    DEL PEAK 35(XP11.3) MUTATED DEL PEAK 35(XP11.3) WILD-TYPE
  NO                           81                           283
  YES                           5                            15
[1] 2 2
[1] FALSE
D72V9, continuous
D72V10, continuous
D72V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(XP11.3) MUTATED       8                         7    72
  DEL PEAK 35(XP11.3) WILD-TYPE    35                        15   255
D72V12, multiclass
                           clus
vv                          DEL PEAK 35(XP11.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              72
                           clus
vv                          DEL PEAK 35(XP11.3) WILD-TYPE
  ASIAN                                                35
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                               cls
clus                              0   1
  DEL PEAK 35(XP11.3) MUTATED     1  82
  DEL PEAK 35(XP11.3) WILD-TYPE   8 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 35(XP11.3) MUTATED      1   82
  DEL PEAK 35(XP11.3) WILD-TYPE    8  287
                        clus
vv                       DEL PEAK 35(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          82
                        clus
vv                       DEL PEAK 35(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           287
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 36(XQ21.33) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(XQ21.33) MUTATED    55  29
  DEL PEAK 36(XQ21.33) WILD-TYPE 172 149
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            84                            321 
  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                            29                            149 
$`DEL PEAK 36(XQ21.33) MUTATED`
TCGA-2F-A9KT TCGA-BT-A20T TCGA-BT-A42C TCGA-CU-A3KJ TCGA-DK-A1AB TCGA-DK-A1AC 
      108.95        14.89        28.70        18.48        16.70       130.88 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A6B5 TCGA-DK-AA6W TCGA-DK-AA71 TCGA-E7-A7DU 
       50.27        21.30        50.70        13.64        13.64         0.92 
TCGA-FD-A3SN TCGA-FD-A3SS TCGA-FD-A5BY TCGA-FD-A6TA TCGA-FJ-A3Z7 TCGA-GU-A42P 
       29.16        12.85         8.25        62.86        31.07        10.92 
TCGA-GV-A40G TCGA-K4-A54R TCGA-KQ-A41O TCGA-S5-A6DX TCGA-XF-A9SP TCGA-XF-A9T5 
       19.07        27.68        50.56         1.84        14.93        66.64 
TCGA-XF-A9T8 TCGA-XF-AAN7 TCGA-ZF-A9R2 TCGA-ZF-A9RL TCGA-2F-A9KQ TCGA-2F-A9KR 
       13.74        18.58        21.11        88.87        94.88       104.65 
TCGA-4Z-AA7O TCGA-4Z-AA80 TCGA-BT-A20V TCGA-BT-A20X TCGA-BT-A2LB TCGA-BT-A3PH 
       16.83         0.62         5.06         8.25        16.18         4.67 
TCGA-BT-A42B TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A47X TCGA-CF-A7I0 TCGA-CF-A8HX 
       17.56        12.56        13.97        12.62        12.10        11.34 
TCGA-CU-A3QU TCGA-DK-AA6Q TCGA-DK-AA6T TCGA-DK-AA76 TCGA-E5-A2PC TCGA-E7-A3X6 
        5.19        13.58        18.81        12.03        43.59        29.72 
TCGA-E7-A85H TCGA-FD-A3B4 TCGA-FT-A3EE TCGA-G2-A2EL TCGA-G2-A3IB TCGA-G2-AA3B 
       12.95        16.77         3.25        26.93         7.23        66.02 
TCGA-GC-A4ZW TCGA-GC-A6I1 TCGA-GD-A6C6 TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QH 
        0.49         8.94         2.20        21.34        19.10         8.48 
TCGA-GV-A3QI TCGA-HQ-A2OE TCGA-K4-A3WV TCGA-K4-A5RJ TCGA-K4-AAQO TCGA-LT-A5Z6 
       36.49        38.60        21.24        17.72        11.80        15.58 
TCGA-MV-A51V TCGA-PQ-A6FI TCGA-S5-AA26 TCGA-UY-A78O TCGA-UY-A78P TCGA-UY-A8OD 
       13.48        12.23        16.54        76.01        78.25       112.83 
TCGA-UY-A9PD TCGA-UY-A9PF TCGA-XF-A8HI TCGA-XF-A9SZ TCGA-XF-AAMG TCGA-XF-AAMT 
       17.82         3.85        17.88        28.24       110.60         2.96 
TCGA-XF-AAMX TCGA-YF-AA3L TCGA-ZF-A9R1 TCGA-ZF-A9R9 TCGA-ZF-A9RM TCGA-ZF-AA5H 
        6.77        11.97        25.41        28.41        47.84        29.49 

$`DEL PEAK 36(XQ21.33) WILD-TYPE`
TCGA-4Z-AA7M TCGA-4Z-AA7Q TCGA-4Z-AA84 TCGA-4Z-AA89 TCGA-BL-A5ZZ TCGA-BT-A20N 
       16.27        16.77        15.12        33.83        12.39        26.14 
TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-C4-A0EZ TCGA-CF-A9FL 
        8.35        20.48        25.94         9.96         8.98        18.58 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A72E TCGA-DK-A1A5 TCGA-DK-A1AA 
       12.92         4.90        15.12        13.58         2.14        19.00 
TCGA-DK-A2HX TCGA-DK-A2I6 TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IU TCGA-DK-A3IV 
       46.68        87.32         8.22        17.72        23.21         9.67 
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-A6B6 TCGA-DK-AA6L TCGA-DK-AA6M TCGA-DK-AA6R TCGA-DK-AA6S 
       15.68        36.66        38.24        52.01       165.73       166.03 
TCGA-DK-AA74 TCGA-DK-AA75 TCGA-DK-AA77 TCGA-E5-A4TZ TCGA-E7-A541 TCGA-E7-A7DV 
       56.15        11.18        20.32        15.35        25.58         1.22 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       33.04         4.01        60.66        24.30        23.41        17.98 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A43P TCGA-FD-A43X TCGA-FD-A43Y TCGA-FD-A5BR 
       46.78        19.79        27.35         3.62        15.58        26.73 
TCGA-FD-A5BS TCGA-FD-A5BT TCGA-FD-A5BX TCGA-FD-A5C0 TCGA-FD-A5C1 TCGA-FD-A62P 
       53.88        10.78         5.69        18.08        58.92         6.28 
TCGA-FD-A6TB TCGA-FD-A6TC TCGA-FD-A6TD TCGA-FD-A6TE TCGA-FD-A6TG TCGA-FD-A6TH 
       18.81         6.15        12.69        12.36         3.06         4.31 
TCGA-FD-A6TI TCGA-FJ-A3ZF TCGA-FT-A61P TCGA-G2-A2ES TCGA-G2-A3VY TCGA-G2-AA3D 
        9.67        17.23        11.08        33.01        17.62        70.32 
TCGA-GC-A3BM TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GU-A763 TCGA-GU-AATP 
       21.40        19.13        17.75        24.92        32.78        32.98 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A6ZA TCGA-HQ-A5ND 
       19.82        20.28        27.35         8.58        22.72         9.01 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A4AB TCGA-K4-A4AC TCGA-KQ-A41N TCGA-KQ-A41P 
       25.02         3.45         2.76         9.14        52.73        35.97 
TCGA-KQ-A41Q TCGA-R3-A69X TCGA-SY-A9G0 TCGA-UY-A78N TCGA-UY-A9PH TCGA-XF-A8HD 
       46.98        14.24        33.14        86.83        51.32        97.45 
TCGA-XF-A8HE TCGA-XF-A8HF TCGA-XF-A8HG TCGA-XF-A9SJ TCGA-XF-A9SK TCGA-XF-A9SM 
      125.49        97.12        15.35         3.22        15.98        34.45 
TCGA-XF-A9ST TCGA-XF-A9SV TCGA-XF-A9SW TCGA-XF-A9SY TCGA-XF-A9T0 TCGA-XF-A9T2 
        4.21        12.76        11.90        21.04        26.27        18.90 
TCGA-XF-A9T3 TCGA-XF-A9T6 TCGA-XF-AAMF TCGA-XF-AAMH TCGA-XF-AAMJ TCGA-XF-AAML 
        2.24         2.10        10.82        11.31        54.90         7.63 
TCGA-XF-AAMQ TCGA-XF-AAMR TCGA-XF-AAMY TCGA-XF-AAMZ TCGA-XF-AAN1 TCGA-XF-AAN2 
       71.57        91.73        98.99        44.32        30.94        61.45 
TCGA-XF-AAN3 TCGA-XF-AAN8 TCGA-YC-A8S6 TCGA-YF-AA3M TCGA-ZF-A9R4 TCGA-ZF-A9RC 
       86.30         3.88         9.63        13.64        30.28        94.29 
TCGA-ZF-A9RE TCGA-ZF-AA4R TCGA-ZF-AA4T TCGA-ZF-AA53 TCGA-ZF-AA5P TCGA-2F-A9KO 
        3.48        34.06        19.69        57.90        12.23        24.13 
TCGA-2F-A9KP TCGA-2F-A9KW TCGA-4Z-AA7N TCGA-4Z-AA7R TCGA-4Z-AA7S TCGA-4Z-AA7W 
       11.97         8.35        44.94        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-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-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q 
        6.58        13.15        19.04        12.16        17.88        19.50 
TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A2LA TCGA-BT-A42E TCGA-BT-A42F TCGA-C4-A0F0 
        5.06        14.96        17.16        36.43        28.41         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-A9FM TCGA-CU-A3YL TCGA-CU-A5W6 
       12.00        11.34        11.87        13.08        29.79         1.84 
TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       21.86        66.41        18.41       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       15.62        17.95         7.79       142.78         4.80        13.58 
TCGA-DK-A3IM TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-AA6P TCGA-DK-AA6U 
        8.15        20.81        10.55       163.30        15.02        19.00 
TCGA-DK-AA6X TCGA-E5-A4U1 TCGA-E7-A3Y1 TCGA-E7-A4IJ TCGA-E7-A4XJ TCGA-E7-A519 
       15.35        38.83         5.36        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-A7PW TCGA-E7-A7XN TCGA-E7-A8O7 TCGA-E7-A97P TCGA-E7-A97Q 
       24.66        13.68        14.07        15.32        14.37         8.09 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3N6 TCGA-FD-A3SO 
       32.02         8.94        12.62        22.52        27.98         5.52 
TCGA-FD-A3SP TCGA-FD-A43N TCGA-FD-A43S TCGA-FD-A43U TCGA-FD-A5BU TCGA-FD-A5BV 
       25.74        22.98        14.96        20.91        19.33         5.36 
TCGA-FD-A5BZ TCGA-FD-A62N TCGA-FD-A62O TCGA-FD-A62S TCGA-FD-A6TF TCGA-FD-A6TK 
       27.45         2.70         7.10        13.35         2.27        10.85 
TCGA-FJ-A3Z9 TCGA-FJ-A3ZE TCGA-FJ-A871 TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
       12.66        10.65         8.94        61.94        48.00        15.95 
TCGA-G2-A2EO TCGA-G2-A3IE TCGA-G2-AA3C TCGA-G2-AA3F TCGA-GC-A3I6 TCGA-GC-A3OO 
       59.31        20.12         6.94        29.36        20.71        15.81 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A6I3 TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       15.91        14.07        13.91        26.70         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42Q TCGA-GU-A42R TCGA-GU-A762 TCGA-GU-A764 TCGA-GU-A766 
       20.98        11.31        18.97         7.63        20.05        15.78 
TCGA-GU-A767 TCGA-GU-AATQ TCGA-GV-A3JV TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OF 
        4.73         7.00        14.27         1.51        19.40        64.01 
TCGA-HQ-A5NE TCGA-K4-A5RH TCGA-K4-A5RI TCGA-K4-A6FZ TCGA-K4-A6MB TCGA-K4-A83P 
       12.16         9.07        11.70         1.81        15.42        16.27 
TCGA-KQ-A41R TCGA-KQ-A41S TCGA-LC-A66R TCGA-LT-A8JT TCGA-PQ-A6FN TCGA-SY-A9G5 
       44.38         1.15        15.32        21.07        16.67        38.99 
TCGA-UY-A78K TCGA-UY-A78L TCGA-UY-A78M TCGA-UY-A8OB TCGA-UY-A8OC TCGA-UY-A9PA 
       17.62        37.05        22.68        69.34         3.02        35.24 
TCGA-UY-A9PB TCGA-UY-A9PE TCGA-XF-A8HB TCGA-XF-A8HC TCGA-XF-A8HH TCGA-XF-A9SG 
       29.56         6.21        45.04         6.58         1.87        48.62 
TCGA-XF-A9SH TCGA-XF-A9SI TCGA-XF-A9SL TCGA-XF-A9SU TCGA-XF-A9SX TCGA-XF-A9T4 
       64.80        79.66        66.41         5.98        23.64        16.27 
TCGA-XF-AAME TCGA-XF-AAMW TCGA-XF-AAN0 TCGA-XF-AAN4 TCGA-XF-AAN5 TCGA-YC-A89H 
       92.98         8.32        56.48        27.06        75.39        18.84 
TCGA-YC-A9TC TCGA-ZF-A9R0 TCGA-ZF-A9R3 TCGA-ZF-A9R5 TCGA-ZF-A9R7 TCGA-ZF-A9RD 
        0.66        22.36        31.20        35.84        21.86        13.41 
TCGA-ZF-A9RF TCGA-ZF-A9RG TCGA-ZF-A9RN TCGA-ZF-AA4N TCGA-ZF-AA4U TCGA-ZF-AA4V 
       64.08        58.72        20.22         2.89         8.61        59.38 
TCGA-ZF-AA4W TCGA-ZF-AA4X TCGA-ZF-AA51 TCGA-ZF-AA52 TCGA-ZF-AA54 TCGA-ZF-AA56 
       60.16        67.20        56.35        35.41        19.40         8.52 
TCGA-ZF-AA58 TCGA-ZF-AA5N TCGA-GU-AATO 
       54.21         5.52        10.65 

  DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE 
                          0.49                           0.56 
  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                         17.720 
[1] "0.5 - 130.9 (17.2)" "0.6 - 166.0 (17.7)"
[1] "hr=" "1.4"
D73V2, 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
D73V3, 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
D73V4, 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 184  37  60   7
D73V5, multiclass
    clus
vv   DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  N0                           52                            184
  N1                           10                             37
  N2                           15                             60
  N3                            1                              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"
D73V6, 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
D73V7, 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
D73V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(XQ21.33) MUTATED    74   5
  DEL PEAK 36(XQ21.33) WILD-TYPE 290  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XQ21.33) MUTATED     74    5
  DEL PEAK 36(XQ21.33) WILD-TYPE  290   15
     clus
vv    DEL PEAK 36(XQ21.33) MUTATED DEL PEAK 36(XQ21.33) WILD-TYPE
  NO                            74                            290
  YES                            5                             15
[1] 2 2
[1] FALSE
D73V9, continuous
D73V10, continuous
D73V11, 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
D73V12, 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"
D73V13, 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
