[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTHNSC-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/HNSC-TP/10005940/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/10013755/transformed.cor.cli.txt"

nPatients in clinical file=423, in cluster file=511, common to both=417
[1]  73 417
[1] "AMP PEAK  1(2Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           86                           331 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           86                           331 
[1] "AMP PEAK  2(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           90                           327 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           90                           327 
[1] "AMP PEAK  3(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           306                            111 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           306                            111 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           190                            227 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           190                            227 
[1] "AMP PEAK  5(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                        165                         252 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                        165                         252 
[1] "AMP PEAK  6(6P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                           81                           336 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                           81                           336 
[1] "AMP PEAK  7(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         75                         342 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         75                         342 
[1] "AMP PEAK  8(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          177                           240 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          177                           240 
[1] "AMP PEAK  9(7Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                          141                           276 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                          141                           276 
[1] "AMP PEAK 10(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                           125                            292 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                           125                            292 
[1] "AMP PEAK 11(8Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                           244                            173 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                           244                            173 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           305                            112 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           305                            112 
[1] "AMP PEAK 13(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                          103                           314 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                          103                           314 
[1] "AMP PEAK 14(9P23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                        103                         314 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                        103                         314 
[1] "AMP PEAK 15(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                          113                           304 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                          113                           304 
[1] "AMP PEAK 16(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                          139                           278 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                          139                           278 
[1] "AMP PEAK 17(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                          87                          330 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                          87                          330 
[1] "AMP PEAK 18(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           190                            227 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           190                            227 
[1] "AMP PEAK 19(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                            131                             286 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                            131                             286 
[1] "AMP PEAK 20(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                          81                          336 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                          81                          336 
[1] "AMP PEAK 21(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                            90                            327 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                            90                            327 
[1] "AMP PEAK 22(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                          84                          333 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                          84                          333 
[1] "AMP PEAK 23(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                            89                            328 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                            89                            328 
[1] "AMP PEAK 24(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          68                          349 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          68                          349 
[1] "AMP PEAK 25(18P11.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                            122                             295 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                            122                             295 
[1] "AMP PEAK 26(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                            82                            335 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                            82                            335 
[1] "AMP PEAK 27(20P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           156                            261 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           156                            261 
[1] "AMP PEAK 28(20Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            183                             234 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            183                             234 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        117                         300 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        117                         300 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            78                            339 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            78                            339 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          102                           315 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          102                           315 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         38                         379 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         38                         379 
[1] "DEL PEAK  4(2Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           58                           359 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           58                           359 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           88                           329 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           88                           329 
[1] "DEL PEAK  6(2Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          126                           291 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          126                           291 
[1] "DEL PEAK  7(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                          301                           116 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                          301                           116 
[1] "DEL PEAK  8(3P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE 
                          281                           136 
  DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE 
                          281                           136 
[1] "DEL PEAK  9(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                          171                           246 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                          171                           246 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          134                           283 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          134                           283 
[1] "DEL PEAK 11(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE 
                          171                           246 
  DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE 
                          171                           246 
[1] "DEL PEAK 12(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                          171                           246 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                          171                           246 
[1] "DEL PEAK 13(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE 
                        181                         236 
  DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE 
                        181                         236 
[1] "DEL PEAK 14(5Q35.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE 
                          160                           257 
  DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE 
                          160                           257 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           339 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           339 
[1] "DEL PEAK 16(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           65                           352 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           65                           352 
[1] "DEL PEAK 17(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                          105                           312 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                          105                           312 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          241                           176 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          241                           176 
[1] "DEL PEAK 19(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                        186                         231 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                        186                         231 
[1] "DEL PEAK 20(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                          236                           181 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                          236                           181 
[1] "DEL PEAK 21(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE 
                            76                            341 
  DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE 
                            76                            341 
[1] "DEL PEAK 22(9Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE 
                           62                           355 
  DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE 
                           62                           355 
[1] "DEL PEAK 23(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           135                            282 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           135                            282 
[1] "DEL PEAK 24(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE 
                            126                             291 
  DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE 
                            126                             291 
[1] "DEL PEAK 25(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            100                             317 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            100                             317 
[1] "DEL PEAK 26(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           129                            288 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           129                            288 
[1] "DEL PEAK 27(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE 
                           195                            222 
  DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE 
                           195                            222 
[1] "DEL PEAK 28(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             50                             367 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             50                             367 
[1] "DEL PEAK 29(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE 
                            180                             237 
  DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE 
                            180                             237 
[1] "DEL PEAK 30(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           170                            247 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           170                            247 
[1] "DEL PEAK 31(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE 
                            52                            365 
  DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE 
                            52                            365 
[1] "DEL PEAK 32(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE 
                             55                             362 
  DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE 
                             55                             362 
[1] "DEL PEAK 33(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                            95                            322 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                            95                            322 
[1] "DEL PEAK 34(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE 
                            81                            336 
  DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE 
                            81                            336 
[1] "DEL PEAK 35(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE 
                            58                            359 
  DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE 
                            58                            359 
[1] "DEL PEAK 36(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE 
                           218                            199 
  DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE 
                           218                            199 
[1] "DEL PEAK 37(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                         232                          185 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                         232                          185 
[1] "DEL PEAK 38(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           139                            278 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           139                            278 
[1] "DEL PEAK 39(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE 
                             81                             336 
  DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE 
                             81                             336 
[1] "DEL PEAK 40(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                           167                            250 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                           167                            250 
[1] "DEL PEAK 41(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE 
                             74                             343 
  DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE 
                             74                             343 
[1] "DEL PEAK 42(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE 
                          118                           299 
  DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE 
                          118                           299 
[1] "DEL PEAK 43(XP21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE 
                          121                           296 
  DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE 
                          121                           296 
[1] "DEL PEAK 44(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE 
                            61                            356 
  DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE 
                            61                            356 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 417 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415           NA          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
         384          113          236          895          513          351 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BB-4217 TCGA-BB-4223 
         216           NA          182           NA          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
        2161          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642          369          395          240           NA 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268           NA          488          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
         173           NA         1081           NA           NA           NA 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
          NA           NA           NA           NA          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          424          629          433          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98           NA          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
         224          318          611          394          119           NA 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 
         526          484          348          175          367           NA 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
        1466         1207          654           NA         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
          NA         1000         1057          985           NA           NA 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
          NA          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968           NA          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
          NA          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521           NA         1050         1125           NA 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514           NA          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479           NA         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245           NA          105           NA 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972           NA         1036 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
          NA          796           NA          997         1430           NA 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         4241          522         3930         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         3270         2886         2327         2784 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
          NA           NA           NA           NA         3835           NA 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
          NA           NA         3837         3381           NA           NA 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
          NA           NA           NA         3497         1724           NA 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        1444         1095          954          797           NA           NA 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
          NA           NA           NA           NA           NA         1099 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
          NA           NA           NA           NA           NA         4335 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
          NA           NA           NA          851           NA           NA 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
          NA          750           NA          717          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         237          828           NA          773          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548           NA          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
          14           13           NA            6           NA          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
          25           NA           NA           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
         360          412           NA          440           NA          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
          56          111          112          254          910           NA 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
        1652          721           NA         1120           NA          578 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
        1917           NA           NA           NA           NA           NA 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
         400          553          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-UF-A7JV 
         225           64           NA 
Variable 1:'AGE':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=147,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=267,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=18,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "NUMBERPACKYEARSSMOKED"                 
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 417 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 40 108  85 131 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 40 108  85 131 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 40 108  85 131 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 40 108  85 131 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
136  56 129   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
136  56 129   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
136  56 129   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
136  56 129   7 
PATHOLOGY.M.STAGE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=81, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=25, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(2Q11.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(2Q11.2) MUTATED    45  23
  AMP PEAK  1(2Q11.2) WILD-TYPE 212  75
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           68                           287 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           23                            75 
$`AMP PEAK  1(2Q11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5555 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BB-7864 
         283          415          520          384          895          687 
TCGA-BB-7870 TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4740 
        1153         1955          452          613          240          811 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 
        1988          512         1980          630          629           45 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W 
         424          224          318          119          225          348 
TCGA-CQ-5332 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7365 
         317          358          514         1969          354         1191 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 
        1440          105          759         1954          907         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5973 
         522         1950         3295          584         1978         2641 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6960 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
        1952         1959         1969         1095          797         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A6JE 
        1976         1099         1957         1947         1959          750 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7588 
         237          828          128          104          516         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-7229 TCGA-HD-A6HZ TCGA-HD-A6I0 
         575          299            6            2          111           33 
TCGA-KU-A66T TCGA-QK-A6IJ 
         210           64 

$`AMP PEAK  1(2Q11.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462         1983          276          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1762          725          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 
         644          451           63          113          236          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         351          216          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         638          428          436          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
         799          721          485          142          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
         993          642          369          395         1960         1330 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1268          488          173         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1966         1966         1975          413          290          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         433          594          629          432           98         1970 
TCGA-CN-6022 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         202          611          394          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         443          447          526          484          175          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1007          509         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1971          362          311          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1956         1435         1245         1960 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1979          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
         796          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5439 
         181         1077          911         1472         1438          546 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         701         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6942 
         641         1899         1970         1948         1969         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 
        1948         1969         1966         1957         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 
        1945         1987         1979         1724         1444          954 
TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 
        1967         1974         1948         1955         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1945         1954         1970          717          317          321 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         568          106          112         1778         1081         1030 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         548          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340          564          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 
          58          133          414          403            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          49           10         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         588          360          412          440          351          360 
TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         224           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         357          245          218          228          225 

  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                            2                             3 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                         3295                          3837 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          621                           629 
[1] "2.0 - 3295.0 (621.0)" "3.0 - 3837.0 (629.0)"
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  1(2Q11.2) MUTATED         2        7        15        49         1
  AMP PEAK  1(2Q11.2) WILD-TYPE      22       56        56       143         8
D1V3, multiclass
           clus
vv          AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  STAGE I                             2                            22
  STAGE II                            7                            56
  STAGE III                          15                            56
  STAGE IVA                          49                           143
  STAGE IVB                           1                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  1(2Q11.2) MUTATED    3 13 23 35
  AMP PEAK  1(2Q11.2) WILD-TYPE 37 95 62 96
D1V4, multiclass
    clus
vv   AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  T1                           3                            37
  T2                          13                            95
  T3                          23                            62
  T4                          35                            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                             N0  N1  N2  N3
  AMP PEAK  1(2Q11.2) MUTATED    26   9  32   1
  AMP PEAK  1(2Q11.2) WILD-TYPE 110  47  97   6
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  N0                          26                           110
  N1                           9                            47
  N2                          32                            97
  N3                           1                             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(2Q11.2) MUTATED   17  9
  AMP PEAK  1(2Q11.2) WILD-TYPE 91 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     17    9
  AMP PEAK  1(2Q11.2) WILD-TYPE   91   39
    clus
vv   AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  M0                          17                            91
  MX                           9                            39
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED    21  65
  AMP PEAK  1(2Q11.2) WILD-TYPE 100 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     21   65
  AMP PEAK  1(2Q11.2) WILD-TYPE  100  231
        clus
vv       AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  FEMALE                          21                           100
  MALE                            65                           231
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(2Q11.2) MUTATED                                      86
  AMP PEAK  1(2Q11.2) WILD-TYPE                                   324
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  1(2Q11.2) MUTATED                                                             0
  AMP PEAK  1(2Q11.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  1(2Q11.2) MUTATED                                                     0
  AMP PEAK  1(2Q11.2) WILD-TYPE                                                   6
D1V8, multiclass
                                                             clus
vv                                                            AMP PEAK  1(2Q11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                86
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   0
                                                             clus
vv                                                            AMP PEAK  1(2Q11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 324
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED    18  68
  AMP PEAK  1(2Q11.2) WILD-TYPE  61 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     18   68
  AMP PEAK  1(2Q11.2) WILD-TYPE   61  270
     clus
vv    AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  NO                           18                            61
  YES                          68                           270
[1] 2 2
[1] FALSE
D1V10, continuous
D1V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(2Q11.2) MUTATED                                  1     2
  AMP PEAK  1(2Q11.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(2Q11.2) MUTATED                           9    72
  AMP PEAK  1(2Q11.2) WILD-TYPE                        24   289
D1V12, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     72
                                  clus
vv                                 AMP PEAK  1(2Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      289
[1] 4 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(2Q11.2) MUTATED     5  77
  AMP PEAK  1(2Q11.2) WILD-TYPE  13 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED      5   77
  AMP PEAK  1(2Q11.2) WILD-TYPE   13  304
                        clus
vv                       AMP PEAK  1(2Q11.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       AMP PEAK  1(2Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           304
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(2Q31.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(2Q31.2) MUTATED    44  27
  AMP PEAK  2(2Q31.2) WILD-TYPE 213  71
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           71                           284 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           27                            71 
$`AMP PEAK  2(2Q31.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6D8 
         283          415         1983          384          895          513 
TCGA-BB-7864 TCGA-BB-8596 TCGA-CN-4728 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-6012 
         687         1955          613         1988         1980          629 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W 
        1970          224          611          119          225          348 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
        1399          317          985         1959          613          608 
TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7383 
         358          514         1191          105           30         1954 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
         907         1955          522         1950         3295          584 
TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7091 
        1978          215         1969         1959         1969         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
        1970         1970         1724         1095          797         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 
        1976         1099         1955         1957         1947         1959 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5629 
         237          828          701          128          104          516 
TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
        1965          299            6           10          111           33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-KU-A66T TCGA-MT-A67D TCGA-P3-A6T8 
         360          412          210           56          400 

$`AMP PEAK  2(2Q31.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462          276          248          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
         520          725          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DA 
         644          451           63          113          236          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 
         133          558          310          536          423          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
        1153          428          436          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
         799          721          485          142          452          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         462          993          642          369          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
        1960         1330          811         1268          488          512 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1975          413          290          630          424          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 
         594          629           45          432           98          202 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         424          318          394          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         443          447          526          484          175          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
         341          129          870         1000         1057         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         901          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 
         548          393          391          303         2562         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        1435         1440         1245         1960         1979          759 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
         889          972         1968         1036          796          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
         911         1472         1438          546         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1970         1948         1952         3835         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 
        1957         1969         1959         3837         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 
        1939         1945         1987         1979         1444          954 
TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1967         1974         1948         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          317          321 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         773          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         106          112         1778         1081         1030          548 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340          564          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
          25           37           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          11           49         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W 
         588          440          351          360          224           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          34          392          111          112          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
        1968          553          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                            6                             2 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                         3295                          3837 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                        687.0                         623.5 
[1] "6.0 - 3295.0 (687.0)" "2.0 - 3837.0 (623.5)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  2(2Q31.2) MUTATED         2       13        13        47         2
  AMP PEAK  2(2Q31.2) WILD-TYPE      22       50        58       145         7
D2V3, multiclass
           clus
vv          AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  STAGE I                             2                            22
  STAGE II                           13                            50
  STAGE III                          13                            58
  STAGE IVA                          47                           145
  STAGE IVB                           2                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  2(2Q31.2) MUTATED    4 21 20 33
  AMP PEAK  2(2Q31.2) WILD-TYPE 36 87 65 98
D2V4, multiclass
    clus
vv   AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  T1                           4                            36
  T2                          21                            87
  T3                          20                            65
  T4                          33                            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                             N0  N1  N2  N3
  AMP PEAK  2(2Q31.2) MUTATED    25   8  33   1
  AMP PEAK  2(2Q31.2) WILD-TYPE 111  48  96   6
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  N0                          25                           111
  N1                           8                            48
  N2                          33                            96
  N3                           1                             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"
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(2Q31.2) MUTATED   15 14
  AMP PEAK  2(2Q31.2) WILD-TYPE 93 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     15   14
  AMP PEAK  2(2Q31.2) WILD-TYPE   93   34
    clus
vv   AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  M0                          15                            93
  MX                          14                            34
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED    22  68
  AMP PEAK  2(2Q31.2) WILD-TYPE  99 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     22   68
  AMP PEAK  2(2Q31.2) WILD-TYPE   99  228
        clus
vv       AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  FEMALE                          22                            99
  MALE                            68                           228
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2Q31.2) MUTATED                                      89
  AMP PEAK  2(2Q31.2) WILD-TYPE                                   321
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  2(2Q31.2) MUTATED                                                             0
  AMP PEAK  2(2Q31.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  2(2Q31.2) MUTATED                                                     1
  AMP PEAK  2(2Q31.2) WILD-TYPE                                                   5
D2V8, multiclass
                                                             clus
vv                                                            AMP PEAK  2(2Q31.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                89
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            AMP PEAK  2(2Q31.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 321
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED    17  73
  AMP PEAK  2(2Q31.2) WILD-TYPE  62 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     17   73
  AMP PEAK  2(2Q31.2) WILD-TYPE   62  265
     clus
vv    AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  NO                           17                            62
  YES                          73                           265
[1] 2 2
[1] FALSE
D2V10, continuous
D2V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(2Q31.2) MUTATED                                  1     1
  AMP PEAK  2(2Q31.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2Q31.2) MUTATED                           9    75
  AMP PEAK  2(2Q31.2) WILD-TYPE                        24   286
D2V12, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     75
                                  clus
vv                                 AMP PEAK  2(2Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED     8  78
  AMP PEAK  2(2Q31.2) WILD-TYPE  10 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED      8   78
  AMP PEAK  2(2Q31.2) WILD-TYPE   10  303
                        clus
vv                       AMP PEAK  2(2Q31.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          78
                        clus
vv                       AMP PEAK  2(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           303
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q26.33) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  3(3Q26.33) MUTATED   182  77
  AMP PEAK  3(3Q26.33) WILD-TYPE  75  21
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           259                             96 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                            77                             21 
$`AMP PEAK  3(3Q26.33) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         283          415         1983          276          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1762          520          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         644          451           63          384          113          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         895          513          351         2878          278          140 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
         133          310          423          687         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
         436         1955          624            5            4          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          369          395          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988          488          512          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         413          290          630          629          433          594 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
         224          318          611          394          119          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
          46          443          447          225          526          348 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6223 
         367         1466         1422          317         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
         985         1959         1959          815         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         509          901          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         545          393          391          608         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 
        1663         1152         1777         1521         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
        1971          514         1969          362          311          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
         234          379          350          479         1435         1191 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
        1245         1960          105         1979          759           30 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968         1036         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         392          907          216          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
         584          546         1978         2327         2437          519 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
         406         2641         1840          215         1665          641 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6952 
        1948         1969         1952         1959         1969         1966 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7100 
        1957         1959         3837         1959         1970         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1939         1945         1987         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7433 
        1948         1955         1957         1947         1972         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 
        1958         1959         1954          750          317          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 
         828          292          701          491          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         112          104         1778          516         1030          548 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         575          622          299          368          324          340 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7229 
         384           14           13            6          133            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           5           25           37           55           44           24 
TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61E 
          25           49           10          111         1057          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W 
         360          412          440          351          210           14 
TCGA-MT-A51X TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW 
          34          112          254          910         1652         1120 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
        1954         1968          400          553          357          228 
TCGA-QK-A6IJ 
          64 

$`AMP PEAK  3(3Q26.33) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         462         1288          725          216          182          187 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7866 TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-5370 
         558          536          638          799          642         1975 
TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5324 
         424          629          432          484          175         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CD TCGA-CQ-A4CH 
         870         1461         1309          877          548          303 
TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7373 
         799         1966          345         1956         1440          889 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         972          796          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5976 
         930          156         2886         1958          701         1478 
TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6960 
        1315         1899         1970         3835         1948         1969 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7427 TCGA-CV-7428 
        1970         1936         1979         1724         1937         1973 
TCGA-CV-7432 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN 
        1937         1981          851         1945         1970          717 
TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-DQ-5625 
         321          773           77          154          568         1081 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-F7-7848 TCGA-H7-7774 TCGA-H7-8501 
        1965          775          369          564          407           58 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
         414          403           11           33          485          122 
TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         441          360          224          392           56          111 
TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
         721          578         1917          245          218          225 

  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                             2                             11 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                          3837                           3835 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           594                            749 
[1] "2.0 - 3837.0 (594.0)"  "11.0 - 3835.0 (749.0)"
[1] "hr=" "1.2"
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  3(3Q26.33) MUTATED        15       38        55       145         8
  AMP PEAK  3(3Q26.33) WILD-TYPE       9       25        16        47         1
D3V3, multiclass
           clus
vv          AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  STAGE I                             15                              9
  STAGE II                            38                             25
  STAGE III                           55                             16
  STAGE IVA                          145                             47
  STAGE IVB                            8                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  3(3Q26.33) MUTATED   28 73 66 98
  AMP PEAK  3(3Q26.33) WILD-TYPE 12 35 19 33
D3V4, multiclass
    clus
vv   AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  T1                           28                             12
  T2                           73                             35
  T3                           66                             19
  T4                           98                             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  3(3Q26.33) MUTATED    93  42 103   6
  AMP PEAK  3(3Q26.33) WILD-TYPE  43  14  26   1
D3V5, multiclass
    clus
vv   AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  N0                           93                             43
  N1                           42                             14
  N2                          103                             26
  N3                            6                              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"
D3V6, binary
                                cls
clus                              0  1
  AMP PEAK  3(3Q26.33) MUTATED   78 33
  AMP PEAK  3(3Q26.33) WILD-TYPE 30 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     78   33
  AMP PEAK  3(3Q26.33) WILD-TYPE   30   15
    clus
vv   AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  M0                           78                             30
  MX                           33                             15
[1] 2 2
[1] FALSE
D3V7, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED    77 229
  AMP PEAK  3(3Q26.33) WILD-TYPE  44  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     77  229
  AMP PEAK  3(3Q26.33) WILD-TYPE   44   67
        clus
vv       AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  FEMALE                           77                             44
  MALE                            229                             67
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(3Q26.33) MUTATED                                     302
  AMP PEAK  3(3Q26.33) WILD-TYPE                                   108
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  3(3Q26.33) MUTATED                                                             0
  AMP PEAK  3(3Q26.33) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  3(3Q26.33) MUTATED                                                     4
  AMP PEAK  3(3Q26.33) WILD-TYPE                                                   2
D3V8, multiclass
                                                             clus
vv                                                            AMP PEAK  3(3Q26.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                302
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            AMP PEAK  3(3Q26.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  108
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED    62 244
  AMP PEAK  3(3Q26.33) WILD-TYPE  17  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     62  244
  AMP PEAK  3(3Q26.33) WILD-TYPE   17   94
     clus
vv    AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  NO                            62                             17
  YES                          244                             94
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(3Q26.33) MUTATED                                  1     8
  AMP PEAK  3(3Q26.33) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q26.33) MUTATED                          27   260
  AMP PEAK  3(3Q26.33) WILD-TYPE                         6   101
D3V12, multiclass
                                  clus
vv                                 AMP PEAK  3(3Q26.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     260
                                  clus
vv                                 AMP PEAK  3(3Q26.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                       101
[1] 4 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(3Q26.33) MUTATED    13 279
  AMP PEAK  3(3Q26.33) WILD-TYPE   5 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     13  279
  AMP PEAK  3(3Q26.33) WILD-TYPE    5  102
                        clus
vv                       AMP PEAK  3(3Q26.33) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          279
                        clus
vv                       AMP PEAK  3(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            102
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(5P15.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(5P15.33) MUTATED   119  47
  AMP PEAK  4(5P15.33) WILD-TYPE 138  51
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           166                            189 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            47                             51 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5555 
         462          283          415         1983          276          520 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         725         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
          63          384          113          236          895          513 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
         216          182          187         2878          278          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-8596 TCGA-BB-8601 
         558          310          687          638         1955          624 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
           5          721          485          452          392          462 
TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5359 
         993          395          240         1960         1330         1980 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 
        1977         1966          630          424          432           98 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 
         424          318          394          119          429          443 
TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5330 TCGA-CQ-6221 TCGA-CQ-6224 
         447          526          348          896         1000          985 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 
        1378          509         1963          548          608         2562 
TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1663         1777         1966         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
        1969          379          479         1956         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7390 
        1245         1960         1036         1954          392          907 
TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 
         946          216          156          181         1472          522 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
        3295         1438          546         1978         2327         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6941 
         519          406         2641         1970         1952         1959 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1969         1957         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 
        1970         1939         1945         1987         1724         1095 
TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A6JE TCGA-CX-7086 
         797         1976         1947         1959          750          237 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5629 
         292          701          106          128         1778          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 
        1030          548         1965          575          775          299 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 
         368          340          585            3           14           13 
TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 
           6          133            5           37           55           25 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61O 
         111         1057          485          588          440          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA 
         224          210           14           34           56         1652 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
         357          218          228           64 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5557 TCGA-BA-A6DA 
         248          722         1288         1762          623          351 
TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         140          536          423         1153          428          436 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 
           4          799          142          613          642          369 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988          488          512          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1081         1980         1966         1975          413          290 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 
         629          433          594          629           45         1970 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63T 
         202          224          611          432           46          225 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         484          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
         870         1057         1959         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5247 
         613          545          393          391          303          358 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 
        1152          799         1521         1050          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7370 
         345          354          234          350         1435          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7393 
         796          997         1430         1951          913          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 
         898          930         1077          911         1955         1950 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 
         584         2886         1958          701         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
         215         1315         1665          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7099 
        1969         3835         1948         1966         1969         1936 
TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        1959         1979         1444          954         1967         1960 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 
        1099         1974         1948         1955         1957         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1973         1972         1937         1984         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7082 
         851         1945         1954         1970          717          317 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         321          828          773           77          491          154 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-7591 TCGA-DQ-7593 
         568          112          104         1081          622          369 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         324          564          490          658           15           92 
TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
         384          407           58          414          403            2 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          25           44           24           11           49           10 
TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L 
          33          122          441          360          412          351 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910          721 
TCGA-P3-A6T0 TCGA-QK-A6IF TCGA-QK-A6II 
         578          245          225 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             3                              2 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                          3837                           3835 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         555.5                          701.0 
[1] "3.0 - 3837.0 (555.5)" "2.0 - 3835.0 (701.0)"
[1] "hr=" "1.2"
D4V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  4(5P15.33) MUTATED         7       26        36        84         5
  AMP PEAK  4(5P15.33) WILD-TYPE      17       37        35       108         4
D4V3, multiclass
           clus
vv          AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  STAGE I                              7                             17
  STAGE II                            26                             37
  STAGE III                           36                             35
  STAGE IVA                           84                            108
  STAGE IVB                            5                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  4(5P15.33) MUTATED   14 52 39 55
  AMP PEAK  4(5P15.33) WILD-TYPE 26 56 46 76
D4V4, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  T1                           14                             26
  T2                           52                             56
  T3                           39                             46
  T4                           55                             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                             N0 N1 N2 N3
  AMP PEAK  4(5P15.33) MUTATED   49 31 58  3
  AMP PEAK  4(5P15.33) WILD-TYPE 87 25 71  4
D4V5, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  N0                           49                             87
  N1                           31                             25
  N2                           58                             71
  N3                            3                              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"
D4V6, binary
                                cls
clus                              0  1
  AMP PEAK  4(5P15.33) MUTATED   47 26
  AMP PEAK  4(5P15.33) WILD-TYPE 61 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     47   26
  AMP PEAK  4(5P15.33) WILD-TYPE   61   22
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  M0                           47                             61
  MX                           26                             22
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    46 144
  AMP PEAK  4(5P15.33) WILD-TYPE  75 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     46  144
  AMP PEAK  4(5P15.33) WILD-TYPE   75  152
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                           46                             75
  MALE                            144                            152
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                     186
  AMP PEAK  4(5P15.33) WILD-TYPE                                   224
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  4(5P15.33) MUTATED                                                             1
  AMP PEAK  4(5P15.33) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  4(5P15.33) MUTATED                                                     3
  AMP PEAK  4(5P15.33) WILD-TYPE                                                   3
D4V8, multiclass
                                                             clus
vv                                                            AMP PEAK  4(5P15.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                186
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            AMP PEAK  4(5P15.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  224
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    42 148
  AMP PEAK  4(5P15.33) WILD-TYPE  37 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     42  148
  AMP PEAK  4(5P15.33) WILD-TYPE   37  190
     clus
vv    AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  NO                            42                             37
  YES                          148                            190
[1] 2 2
[1] FALSE
D4V10, continuous
D4V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(5P15.33) MUTATED                                  1     3
  AMP PEAK  4(5P15.33) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5P15.33) MUTATED                          17   163
  AMP PEAK  4(5P15.33) WILD-TYPE                        16   198
D4V12, multiclass
                                  clus
vv                                 AMP PEAK  4(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     163
                                  clus
vv                                 AMP PEAK  4(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED     9 175
  AMP PEAK  4(5P15.33) WILD-TYPE   9 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      9  175
  AMP PEAK  4(5P15.33) WILD-TYPE    9  206
                        clus
vv                       AMP PEAK  4(5P15.33) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          175
                        clus
vv                       AMP PEAK  4(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            206
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5P12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(5P12) MUTATED   106  39
  AMP PEAK  5(5P12) WILD-TYPE 151  59
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                        145                         210 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                         39                          59 
$`AMP PEAK  5(5P12) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
         462          283          276          520          725         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
        1747          190          644          384          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          187         2878 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         133          310         1153         1955          624            5 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 
         452          392          462          993          240         1960 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 
        1988          512         1977         1966          630          424 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         432           98          424          224          318          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W 
         119          429          443          447          526          348 
TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4CA 
        1466          896          870          985          509         1963 
TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
         548         2562         1777         1966         1125         1971 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
         514          354          379         1956         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 
        1245         1960         1036         1954          392          946 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 
         156          181         1472          522         1950         1438 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         1978         2327         2437          519          406 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6941 
        2641          215         1315         1970         1952         1959 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1969         1957         1959         3837         1959         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7424 
        1939         1945         1987         1095          797         1947 
TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 
         750          237          292          701          106          128 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 
         516         1030          548          575          775          299 
TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-HD-7753 
         340          585            3           14           13            5 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E 
          37           55           25          111          485          588 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         440          360          224          210           14           34 
TCGA-MT-A67D TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
          56          254         1652         1120         1954         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH 
        1968          400          553          357          218          228 
TCGA-QK-A6IJ 
          64 

$`AMP PEAK  5(5P12) WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         415         1983          248          722         1288         1762 
TCGA-BA-5557 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-4224 TCGA-BB-4225 
         623          451           63          113          278          140 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
         558          536          423          687          638          428 
TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         436            4          799          721          485          142 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 
         613          642          369          395         1330          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1268          488          173         1980         1081         1980 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
        1966         1975          413          290          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6989 
         594          629           45         1970          202          611 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         432           46          225          484          175          367 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
        1207          654         1660         1422         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
         341          129         1000         1057         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
         815         1461         1378         1007         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
         877          968         1960          613          545          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
         799         1521         1050         1969          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7370 
         345          234          350          479         1435          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
         796          997         1430         1951          907          913 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
         908          898          930          216         1077          911 
TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 
        1955         3295          584         2886         1958          701 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
        1478         1840         1665          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7097 
        1969         3835         1948         1966         1969         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 
        1936         1959         1979         1724         1444          954 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1984         1958         1959         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 
        1954         1970          717          317          321          828 
TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 
         773           77          491          154          568          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7593 
         104         1778         1081         1965          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          92          384            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 
         414          403            2           25           44           24 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          11           49           10           33         1057          122 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-MT-A67A TCGA-MT-A67F 
         441          360          412          351          392          111 
TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-QK-A6IF TCGA-QK-A6II 
         112          910          721          578          245          225 

  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                          3                           2 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                       3837                        3835 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                        526                         709 
[1] "3.0 - 3837.0 (526.0)" "2.0 - 3835.0 (709.0)"
[1] "hr=" "1.1"
D5V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  5(5P12) MUTATED         8       22        33        77         4
  AMP PEAK  5(5P12) WILD-TYPE      16       41        38       115         5
D5V3, multiclass
           clus
vv          AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  STAGE I                           8                          16
  STAGE II                         22                          41
  STAGE III                        33                          38
  STAGE IVA                        77                         115
  STAGE IVB                         4                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  AMP PEAK  5(5P12) MUTATED   13 43 38 50
  AMP PEAK  5(5P12) WILD-TYPE 27 65 47 81
D5V4, multiclass
    clus
vv   AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  T1                        13                          27
  T2                        43                          65
  T3                        38                          47
  T4                        50                          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                          N0 N1 N2 N3
  AMP PEAK  5(5P12) MUTATED   47 27 54  3
  AMP PEAK  5(5P12) WILD-TYPE 89 29 75  4
D5V5, multiclass
    clus
vv   AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  N0                        47                          89
  N1                        27                          29
  N2                        54                          75
  N3                         3                           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"
D5V6, binary
                             cls
clus                           0  1
  AMP PEAK  5(5P12) MUTATED   42 24
  AMP PEAK  5(5P12) WILD-TYPE 66 24
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED     42   24
  AMP PEAK  5(5P12) WILD-TYPE   66   24
    clus
vv   AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  M0                        42                          66
  MX                        24                          24
[1] 2 2
[1] FALSE
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(5P12) MUTATED    42 123
  AMP PEAK  5(5P12) WILD-TYPE  79 173
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED     42  123
  AMP PEAK  5(5P12) WILD-TYPE   79  173
        clus
vv       AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  FEMALE                        42                          79
  MALE                         123                         173
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(5P12) MUTATED                                     162
  AMP PEAK  5(5P12) WILD-TYPE                                   248
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  5(5P12) MUTATED                                                             1
  AMP PEAK  5(5P12) WILD-TYPE                                                           0
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  5(5P12) MUTATED                                                     2
  AMP PEAK  5(5P12) WILD-TYPE                                                   4
D5V8, multiclass
                                                             clus
vv                                                            AMP PEAK  5(5P12) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             162
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 2
                                                             clus
vv                                                            AMP PEAK  5(5P12) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               248
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                             cls
clus                            0   1
  AMP PEAK  5(5P12) MUTATED    40 125
  AMP PEAK  5(5P12) WILD-TYPE  39 213
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED     40  125
  AMP PEAK  5(5P12) WILD-TYPE   39  213
     clus
vv    AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  NO                         40                          39
  YES                       125                         213
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(5P12) MUTATED                                  1     4
  AMP PEAK  5(5P12) WILD-TYPE                                0     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5P12) MUTATED                          15   140
  AMP PEAK  5(5P12) WILD-TYPE                        18   221
D5V12, multiclass
                                  clus
vv                                 AMP PEAK  5(5P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               15
  WHITE                                                  140
                                  clus
vv                                 AMP PEAK  5(5P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                             cls
clus                            0   1
  AMP PEAK  5(5P12) MUTATED     8 152
  AMP PEAK  5(5P12) WILD-TYPE  10 229
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED      8  152
  AMP PEAK  5(5P12) WILD-TYPE   10  229
                        clus
vv                       AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  HISPANIC OR LATINO                             8                          10
  NOT HISPANIC OR LATINO                       152                         229
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(6P12.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(6P12.1) MUTATED    50  19
  AMP PEAK  6(6P12.1) WILD-TYPE 207  79
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                           69                           286 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                           19                            79 
$`AMP PEAK  6(6P12.1) MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-7870 
         283          520          190          384          113         1153 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4736 TCGA-CN-5356 TCGA-CN-5365 
           5          721          485          395          512         1980 
TCGA-CN-5367 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-A63U 
        1966           98          202          424          611          526 
TCGA-CN-A63W TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-7067 
         348         1422         1399          317          129          509 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6487 TCGA-CR-7368 
        1960         1963          393          358          234         1245 
TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 
         392          946          181          911         1955         1950 
TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6945 
        1438         2886         2327         1840         1665         1969 
TCGA-CV-6954 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7418 
        1957         1939         1724          954         1967         1955 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JE TCGA-D6-6823 TCGA-DQ-5624 TCGA-DQ-5625 
        1959         1981          750          701         1778         1081 
TCGA-DQ-7589 TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 
         575            6          133            5           37           55 
TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D 
          33          588          351          210           14           56 
TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-QK-A6IG 
        1120         1917          218 

$`AMP PEAK  6(6P12.1) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          725          623         1636         1747 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         644          451           63          236          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         351          216          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687          638          428          436         1955          624 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
           4          799          142          452          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
         462          993          642          369          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
        1330          811         1268         1988          488          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 
        1980         1081         1977         1966         1975          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          424          629          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 
         629           45          432         1970          224          318 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          119          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         447          225          484          175          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 
        1207          654         1660          896          341          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1461         1378         1007         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
         968          613          545          548          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         608         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 
        1969          362          311          345          354          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479         1956         1435         1191         1440 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
        1430         1951          907          913          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 
         930          216          156         1077         1472          522 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5443 TCGA-CV-5444 
        3295          584          546         1978         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
         519          406          701         2641         1478          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1315          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1952         1959         3835         1948         1966         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1959         1945         1987         1979         1444         1095 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
         797         1960         1976         1099         1974         1948 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1957         1947         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1984         1958          851         1945         1954         1970 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         292           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         128          112          104          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1965          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 
         407           58          414          403            2           25 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
         111         1057          485          122          441          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51X TCGA-MT-A67A 
         412          440          360          224           34          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1652          721 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1954          578         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         245          228          225           64 

  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                            5                             2 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                         2886                          3837 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                        588.0                         629.5 
[1] "5.0 - 2886.0 (588.0)" "2.0 - 3837.0 (629.5)"
[1] "hr=" "1.1"
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  6(6P12.1) MUTATED         4       13        15        36         2
  AMP PEAK  6(6P12.1) WILD-TYPE      20       50        56       156         7
D6V3, multiclass
           clus
vv          AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  STAGE I                             4                            20
  STAGE II                           13                            50
  STAGE III                          15                            56
  STAGE IVA                          36                           156
  STAGE IVB                           2                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  6(6P12.1) MUTATED     6  21  23  22
  AMP PEAK  6(6P12.1) WILD-TYPE  34  87  62 109
D6V4, multiclass
    clus
vv   AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  T1                           6                            34
  T2                          21                            87
  T3                          23                            62
  T4                          22                           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                             N0  N1  N2  N3
  AMP PEAK  6(6P12.1) MUTATED    27  10  27   2
  AMP PEAK  6(6P12.1) WILD-TYPE 109  46 102   5
D6V5, multiclass
    clus
vv   AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  N0                          27                           109
  N1                          10                            46
  N2                          27                           102
  N3                           2                             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"
D6V6, binary
                               cls
clus                             0  1
  AMP PEAK  6(6P12.1) MUTATED   18  9
  AMP PEAK  6(6P12.1) WILD-TYPE 90 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED     18    9
  AMP PEAK  6(6P12.1) WILD-TYPE   90   39
    clus
vv   AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  M0                          18                            90
  MX                           9                            39
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(6P12.1) MUTATED    23  58
  AMP PEAK  6(6P12.1) WILD-TYPE  98 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED     23   58
  AMP PEAK  6(6P12.1) WILD-TYPE   98  238
        clus
vv       AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  FEMALE                          23                            98
  MALE                            58                           238
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(6P12.1) MUTATED                                      80
  AMP PEAK  6(6P12.1) WILD-TYPE                                   330
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  6(6P12.1) MUTATED                                                             0
  AMP PEAK  6(6P12.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  6(6P12.1) MUTATED                                                     1
  AMP PEAK  6(6P12.1) WILD-TYPE                                                   5
D6V8, multiclass
                                                             clus
vv                                                            AMP PEAK  6(6P12.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                80
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            AMP PEAK  6(6P12.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 330
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                               cls
clus                              0   1
  AMP PEAK  6(6P12.1) MUTATED    11  70
  AMP PEAK  6(6P12.1) WILD-TYPE  68 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED     11   70
  AMP PEAK  6(6P12.1) WILD-TYPE   68  268
     clus
vv    AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  NO                           11                            68
  YES                          70                           268
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(6P12.1) MUTATED                                  0     1
  AMP PEAK  6(6P12.1) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(6P12.1) MUTATED                          11    66
  AMP PEAK  6(6P12.1) WILD-TYPE                        22   295
D6V12, multiclass
                                  clus
vv                                 AMP PEAK  6(6P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     66
                                  clus
vv                                 AMP PEAK  6(6P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      295
[1] 4 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(6P12.1) MUTATED     3  75
  AMP PEAK  6(6P12.1) WILD-TYPE  15 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED      3   75
  AMP PEAK  6(6P12.1) WILD-TYPE   15  306
                        clus
vv                       AMP PEAK  6(6P12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          75
                        clus
vv                       AMP PEAK  6(6P12.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           306
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(6Q12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(6Q12) MUTATED    46  16
  AMP PEAK  7(6Q12) WILD-TYPE 211  82
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         62                         293 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         16                          82 
$`AMP PEAK  7(6Q12) MUTATED`
TCGA-BA-4075 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-7862 TCGA-BB-7870 TCGA-C9-A47Z 
         283          384          113          536         1153            5 
TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5367 
         721          395          811          512         1980         1966 
TCGA-CN-6010 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5329 
         630          202          424          526          348         1422 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CE 
        1399          317          129          509         1963          393 
TCGA-CR-5247 TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-7370 TCGA-CR-7389 
         358         1969          234          350          105          392 
TCGA-CR-7397 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5973 
         216         1955         1950         1978         2327         2641 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7248 
        1840         1665         1957         1724          954         1967 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 
        1958         1959         1981         1954          750          317 
TCGA-CX-7219 TCGA-D6-6823 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-HD-7229 TCGA-HD-7917 
         828          701         1778         1081            2           37 
TCGA-HD-8224 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W 
          55           33          588          351          210           14 
TCGA-MT-A67D TCGA-QK-A6IG 
          56          218 

$`AMP PEAK  7(6Q12) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 
        1747          190          644          451           63          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        2878          278          140          133          558          310 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         624            4          799          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         240         1960         1330         1268         1988          488 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5370 
         173         1980         1081         1977         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         413          290          424          629          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 
         629           45          432           98         1970          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          119          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
          46          443          447          225          484          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 
         367         1466         1207          654         1660          896 
TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         341          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
         901          877          968         1960          613          545 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         548          391          303          608         2562         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971          514          362          311          345 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         354          379          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         908          898          930          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
         911         1472          522         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         2886         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
         701         1478          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1969         1966         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
        1945         1987         1979         1444         1095          797 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1957         1947         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 
        1984          851         1945         1970          717          321 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         237          773          292           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5629 
         568          106          128          112          104          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 
         133          414          403            5           25           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
        1057          485          122          441          360          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         440          360          224           34          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          228          225           64 

  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          2                           3 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                       2641                        3837 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                        562                         629 
[1] "2.0 - 2641.0 (562.0)" "3.0 - 3837.0 (629.0)"
[1] "hr=" "1.1"
D7V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  7(6Q12) MUTATED         3       12        13        34         1
  AMP PEAK  7(6Q12) WILD-TYPE      21       51        58       158         8
D7V3, multiclass
           clus
vv          AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  STAGE I                           3                          21
  STAGE II                         12                          51
  STAGE III                        13                          58
  STAGE IVA                        34                         158
  STAGE IVB                         1                           8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  7(6Q12) MUTATED     4  20  18  23
  AMP PEAK  7(6Q12) WILD-TYPE  36  88  67 108
D7V4, multiclass
    clus
vv   AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  T1                         4                          36
  T2                        20                          88
  T3                        18                          67
  T4                        23                         108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  7(6Q12) MUTATED    25   9  23   1
  AMP PEAK  7(6Q12) WILD-TYPE 111  47 106   6
D7V5, multiclass
    clus
vv   AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  N0                        25                         111
  N1                         9                          47
  N2                        23                         106
  N3                         1                           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"
D7V6, binary
                             cls
clus                           0  1
  AMP PEAK  7(6Q12) MUTATED   16  6
  AMP PEAK  7(6Q12) WILD-TYPE 92 42
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED     16    6
  AMP PEAK  7(6Q12) WILD-TYPE   92   42
    clus
vv   AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  M0                        16                          92
  MX                         6                          42
[1] 2 2
[1] FALSE
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(6Q12) MUTATED    25  50
  AMP PEAK  7(6Q12) WILD-TYPE  96 246
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED     25   50
  AMP PEAK  7(6Q12) WILD-TYPE   96  246
        clus
vv       AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  FEMALE                        25                          96
  MALE                          50                         246
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(6Q12) MUTATED                                      75
  AMP PEAK  7(6Q12) WILD-TYPE                                   335
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  7(6Q12) MUTATED                                                             0
  AMP PEAK  7(6Q12) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  7(6Q12) MUTATED                                                     0
  AMP PEAK  7(6Q12) WILD-TYPE                                                   6
D7V8, multiclass
                                                             clus
vv                                                            AMP PEAK  7(6Q12) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                              75
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 0
                                                             clus
vv                                                            AMP PEAK  7(6Q12) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               335
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                             cls
clus                            0   1
  AMP PEAK  7(6Q12) MUTATED     9  66
  AMP PEAK  7(6Q12) WILD-TYPE  70 272
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED      9   66
  AMP PEAK  7(6Q12) WILD-TYPE   70  272
     clus
vv    AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  NO                          9                          70
  YES                        66                         272
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(6Q12) MUTATED                                  0     1
  AMP PEAK  7(6Q12) WILD-TYPE                                1     9
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(6Q12) MUTATED                           8    62
  AMP PEAK  7(6Q12) WILD-TYPE                        25   299
D7V12, multiclass
                                  clus
vv                                 AMP PEAK  7(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                8
  WHITE                                                   62
                                  clus
vv                                 AMP PEAK  7(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    299
[1] 4 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(6Q12) MUTATED     4  66
  AMP PEAK  7(6Q12) WILD-TYPE  14 315
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED      4   66
  AMP PEAK  7(6Q12) WILD-TYPE   14  315
                        clus
vv                       AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             4                          14
  NOT HISPANIC OR LATINO                        66                         315
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7P11.2) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7P11.2) MUTATED    99  47
  AMP PEAK  8(7P11.2) WILD-TYPE 158  51
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          146                           209 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                           47                            51 
$`AMP PEAK  8(7P11.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 
         462          283          415          248          520          451 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7870 
         384          236          182          278          423         1153 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 
        1955          624            5          799          142          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 
         462          993          240         1960         1330          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1980         1977         1980         1966         1966 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
         424          629          433           98          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63T 
         224          318          394          429          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 
         484          348          367         1422          896          129 
TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
         815          509         1309          901         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 
        1963          303         1971          514         1969          354 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7377 
        1435         1191         1440          105          889         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
        1036          796          392          907          216          156 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
        1955          522         1950          546         1978         2327 
TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        2437         1478          215         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 
        1959         1969         1957         1969         3837         1959 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 
        1970         1939         1945         1987         1724         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
         954          797         1967         1955         1957         1947 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
        1959         1981          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5625 
         701          154          568          128         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 
         516          548         1965          575          299          564 
TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-A6C4 TCGA-HD-7229 
         490           92          585            3          414            2 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7631 
           5           37           24           49          111          122 
TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         441          412          360          210           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
         392           56          112         1954         1968          400 
TCGA-QK-A6IH TCGA-QK-A6II 
         228          225 

$`AMP PEAK  8(7P11.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
        1983          276          722         1288         1762          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 
         623         1636         1747          190          644           63 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 
         113          895          513          351          216          187 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          140          133          558          310          536 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4723 
         687          638          428          436            4          721 
TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         485          452          613          642          369          395 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5370 
         811         1268         1988          488         1081         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         413          290          630          594          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
         432         1970          611          119          432           46 
TCGA-CN-A498 TCGA-CN-A63U TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         443          526          175         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 
        1660         1399          317          341          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 
        1057          985         1959         1959         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1007          877          968          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         391          608         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          311          345          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
         479         1956         1245         1960         1979          759 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
          30          972         1954          997         1430         1951 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 
         913          946          908          898          930          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1077          911         1472         3295         1438          584 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2886         1958          519          406          701         2641 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840         1315         1665          641         1899         1970 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7097 TCGA-CV-7099 
        3835         1948         1966         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1959         1979         1444         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1974         1948         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1984         1958          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 
         750          717          317          321           77          491 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         106          112          104         1030          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G 
         369          368          324          340          658           15 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
         133          403           25           55           44           25 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E 
          11           10           33         1057          485          588 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A67F TCGA-MZ-A6I9 
         360          440          351          224          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1652          721         1120          578         1917 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IJ 
         553          357          245          218           64 

  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                            2                             4 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                         3837                          3835 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          547                           658 
[1] "2.0 - 3837.0 (547.0)" "4.0 - 3835.0 (658.0)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  8(7P11.2) MUTATED         9       28        31        88         6
  AMP PEAK  8(7P11.2) WILD-TYPE      15       35        40       104         3
D8V3, multiclass
           clus
vv          AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  STAGE I                             9                            15
  STAGE II                           28                            35
  STAGE III                          31                            40
  STAGE IVA                          88                           104
  STAGE IVB                           6                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  8(7P11.2) MUTATED   11 46 44 61
  AMP PEAK  8(7P11.2) WILD-TYPE 29 62 41 70
D8V4, multiclass
    clus
vv   AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  T1                          11                            29
  T2                          46                            62
  T3                          44                            41
  T4                          61                            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                            N0 N1 N2 N3
  AMP PEAK  8(7P11.2) MUTATED   59 22 60  4
  AMP PEAK  8(7P11.2) WILD-TYPE 77 34 69  3
D8V5, multiclass
    clus
vv   AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  N0                          59                            77
  N1                          22                            34
  N2                          60                            69
  N3                           4                             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"
D8V6, binary
                               cls
clus                             0  1
  AMP PEAK  8(7P11.2) MUTATED   43 22
  AMP PEAK  8(7P11.2) WILD-TYPE 65 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     43   22
  AMP PEAK  8(7P11.2) WILD-TYPE   65   26
    clus
vv   AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  M0                          43                            65
  MX                          22                            26
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    53 124
  AMP PEAK  8(7P11.2) WILD-TYPE  68 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     53  124
  AMP PEAK  8(7P11.2) WILD-TYPE   68  172
        clus
vv       AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  FEMALE                          53                            68
  MALE                           124                           172
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(7P11.2) MUTATED                                     176
  AMP PEAK  8(7P11.2) WILD-TYPE                                   234
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  8(7P11.2) MUTATED                                                             1
  AMP PEAK  8(7P11.2) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  8(7P11.2) MUTATED                                                     0
  AMP PEAK  8(7P11.2) WILD-TYPE                                                   6
D8V8, multiclass
                                                             clus
vv                                                            AMP PEAK  8(7P11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               176
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   0
                                                             clus
vv                                                            AMP PEAK  8(7P11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 234
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    35 142
  AMP PEAK  8(7P11.2) WILD-TYPE  44 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     35  142
  AMP PEAK  8(7P11.2) WILD-TYPE   44  196
     clus
vv    AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  NO                           35                            44
  YES                         142                           196
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(7P11.2) MUTATED                                  1     4
  AMP PEAK  8(7P11.2) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7P11.2) MUTATED                          18   150
  AMP PEAK  8(7P11.2) WILD-TYPE                        15   211
D8V12, multiclass
                                  clus
vv                                 AMP PEAK  8(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    150
                                  clus
vv                                 AMP PEAK  8(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                      211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED     8 162
  AMP PEAK  8(7P11.2) WILD-TYPE  10 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED      8  162
  AMP PEAK  8(7P11.2) WILD-TYPE   10  219
                        clus
vv                       AMP PEAK  8(7P11.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         162
                        clus
vv                       AMP PEAK  8(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           219
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(7Q21.3) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(7Q21.3) MUTATED    72  44
  AMP PEAK  9(7Q21.3) WILD-TYPE 185  54
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                          116                           239 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                           44                            54 
$`AMP PEAK  9(7Q21.3) MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DE 
         283          190          451          384          236          182 
TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4727 
         423         1153         1955          624          799          452 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 
         392          369         1960         1330          811          512 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1081         1977         1980         1966         1966 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6023 
         630          424          629          433           98          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63T 
         224          318          611          429          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-7067 TCGA-CQ-7069 
         484          348          367          317          509          901 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-6478 TCGA-CR-6491 TCGA-CR-7367 
        1960          613          358         1969          350         1440 
TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 
         105         1954         1951          392          907          181 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
        1955          522         1950         3295         1438          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6935 
        1978         2327         2437          215         1970         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7101 
        1952         1959         1969         1969         3837         1939 
TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 
        1724          797         1967         1976         1099         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JE 
        1957         1947         1984         1959         1981          750 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 
         237          828          773          154          568          128 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 
        1081          516          548         1965          575          299 
TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8502 
         490           92          585            3            6          133 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 
           5           37           55          111         1057          122 
TCGA-IQ-A61H TCGA-IQ-A61O TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G 
         412          360           14           34          392          112 
TCGA-P3-A6SX TCGA-P3-A6T4 
        1954         1968 

$`AMP PEAK  9(7Q21.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 
        1747          644           63          113          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         351          216          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 
         133          558          310          536          687          638 
TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
         428          436            5            4          721          485 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
         142          613          462          993          642          395 
TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5370 
         240         1268         1988          488         1980         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         413          290          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
        1970          202          394          119          432           46 
TCGA-CN-A498 TCGA-CN-A63U TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         443          526          175         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 
         815         1461         1378         1007         1309          877 
TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         968         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          608         2562         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
         514          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
         379          479         1956         1435         1191         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1960         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 
        1968         1036          796          997         1430          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 
        1077          911         1472          584         2886         1958 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6942 
        1315         1665          641         1899         1948         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1948         1966         1957         1959         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1945         1987         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 
        1444         1095          954         1960         1974         1948 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45O 
        1937         1973         1972         1937         1958          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1945         1954         1970          717          317          321 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 
         292          701           77          491          106          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
         104         1778         1030          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          340          564          658           15 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
         384           14           13          407           58          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
         403            2           25           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 
          11           49           10           33          485          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A66T 
         588          360          440          351          224          210 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          254          910         1652          721 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1120          578         1917          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         245          218          228          225           64 

  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                            3                             2 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                         3837                          3835 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                          580                           644 
[1] "3.0 - 3837.0 (580.0)" "2.0 - 3835.0 (644.0)"
[1] "hr=" "1.3"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  9(7Q21.3) MUTATED         8       18        25        69         4
  AMP PEAK  9(7Q21.3) WILD-TYPE      16       45        46       123         5
D9V3, multiclass
           clus
vv          AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  STAGE I                             8                            16
  STAGE II                           18                            45
  STAGE III                          25                            46
  STAGE IVA                          69                           123
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  9(7Q21.3) MUTATED   11 28 33 52
  AMP PEAK  9(7Q21.3) WILD-TYPE 29 80 52 79
D9V4, multiclass
    clus
vv   AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  T1                          11                            29
  T2                          28                            80
  T3                          33                            52
  T4                          52                            79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  9(7Q21.3) MUTATED   44 16 47  4
  AMP PEAK  9(7Q21.3) WILD-TYPE 92 40 82  3
D9V5, multiclass
    clus
vv   AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  N0                          44                            92
  N1                          16                            40
  N2                          47                            82
  N3                           4                             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"
D9V6, binary
                               cls
clus                             0  1
  AMP PEAK  9(7Q21.3) MUTATED   28 17
  AMP PEAK  9(7Q21.3) WILD-TYPE 80 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED     28   17
  AMP PEAK  9(7Q21.3) WILD-TYPE   80   31
    clus
vv   AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  M0                          28                            80
  MX                          17                            31
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(7Q21.3) MUTATED    37 104
  AMP PEAK  9(7Q21.3) WILD-TYPE  84 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED     37  104
  AMP PEAK  9(7Q21.3) WILD-TYPE   84  192
        clus
vv       AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  FEMALE                          37                            84
  MALE                           104                           192
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(7Q21.3) MUTATED                                     140
  AMP PEAK  9(7Q21.3) WILD-TYPE                                   270
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  9(7Q21.3) MUTATED                                                             1
  AMP PEAK  9(7Q21.3) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  9(7Q21.3) MUTATED                                                     0
  AMP PEAK  9(7Q21.3) WILD-TYPE                                                   6
D9V8, multiclass
                                                             clus
vv                                                            AMP PEAK  9(7Q21.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               140
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   0
                                                             clus
vv                                                            AMP PEAK  9(7Q21.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 270
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                               cls
clus                              0   1
  AMP PEAK  9(7Q21.3) MUTATED    32 109
  AMP PEAK  9(7Q21.3) WILD-TYPE  47 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED     32  109
  AMP PEAK  9(7Q21.3) WILD-TYPE   47  229
     clus
vv    AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  NO                           32                            47
  YES                         109                           229
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(7Q21.3) MUTATED                                  1     1
  AMP PEAK  9(7Q21.3) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(7Q21.3) MUTATED                          20   118
  AMP PEAK  9(7Q21.3) WILD-TYPE                        13   243
D9V12, multiclass
                                  clus
vv                                 AMP PEAK  9(7Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                    118
                                  clus
vv                                 AMP PEAK  9(7Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      243
[1] 4 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(7Q21.3) MUTATED     8 128
  AMP PEAK  9(7Q21.3) WILD-TYPE  10 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED      8  128
  AMP PEAK  9(7Q21.3) WILD-TYPE   10  253
                        clus
vv                       AMP PEAK  9(7Q21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         128
                        clus
vv                       AMP PEAK  9(7Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(8P11.23) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(8P11.23) MUTATED    83  31
  AMP PEAK 10(8P11.23) WILD-TYPE 174  67
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                           114                            241 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                            31                             67 
$`AMP PEAK 10(8P11.23) MUTATED`
TCGA-BA-4075 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         283         1288         1747          190          451           63 
TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         236          187         2878          278          140          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         310          536          687         1153          428         1955 
TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
         624          799          485          613          392          993 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 
        1330          811          488          512         1980          630 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 
         629           45           98          202          394          119 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CQ-5324 TCGA-CQ-6229 TCGA-CQ-7068 TCGA-CQ-7069 
         225          484         1207          815         1309          901 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 
         613          393          391          608         2562         1777 
TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6487 
        1521         1971          514         1969          345          234 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 
        1435         1191         1440          105           30         1036 
TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
         796          392          907          181         1955          522 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 
        1978         2327         1665          641         1970         1948 
TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1952         1969         1957         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 
        1970         1936         1959         1987         1095          954 
TCGA-CV-7254 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 
        1976         1957         1972         1959         1981         1954 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-8568 
         750          317          237          773          154          106 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
         112          104         1778          516          548         1965 
TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A634 TCGA-IQ-A61O 
         585            6            5           37           10          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5QE 
         224          210           14           56          112          721 

$`AMP PEAK 10(8P11.23) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
        1762          520          725          623         1636          644 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         384          113          895          513          351          216 
TCGA-BA-A6DE TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A47Z 
         182          133          423          638          436            5 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4733 
           4          721          142          452          462          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
         369          395          240         1960         1268         1988 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        1975          413          290          424          433          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         629          432         1970          424          224          318 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         611          432          429           46          443          447 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5325 
         526          348          175          367         1466          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7071 
        1959         1461         1378         1007          509          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
         968         1960         1963          545          548          303 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 
         358         1663         1152          799         1966         1050 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
        1125          362          311          354          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
         479         1956         1245         1960         1979          759 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         889          972         1968         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
        1951          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 
         216          156         1077          911         1472         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 
        3295         1438          584          546         2886         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6941 
        1840          215         1315         1899         1969         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7101 
        3835         1948         1966         1969         1959         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7248 
        1945         1979         1724         1444          797         1967 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 
        1960         1099         1974         1948         1955         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1937         1973         1937         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 
        1945         1970          717          321          828          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 TCGA-DQ-5625 
         701           77          491          568          128         1081 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1030          575          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340          564          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          15           92            3          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
         407           58          133          414          403            2 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         441          588          360          412          440          351 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          34          392          111          254          910         1652 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ 
          64 

  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                             5                              2 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                          3837                           3835 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                         629.5                          623.0 
[1] "5.0 - 3837.0 (629.5)" "2.0 - 3835.0 (623.0)"
[1] "hr=" "1.3"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 10(8P11.23) MUTATED         5       23        26        53         0
  AMP PEAK 10(8P11.23) WILD-TYPE      19       40        45       139         9
D10V3, multiclass
           clus
vv          AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  STAGE I                              5                             19
  STAGE II                            23                             40
  STAGE III                           26                             45
  STAGE IVA                           53                            139
  STAGE IVB                            0                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 10(8P11.23) MUTATED    9 41 23 34
  AMP PEAK 10(8P11.23) WILD-TYPE 31 67 62 97
D10V4, multiclass
    clus
vv   AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  T1                            9                             31
  T2                           41                             67
  T3                           23                             62
  T4                           34                             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                             N0 N1 N2 N3
  AMP PEAK 10(8P11.23) MUTATED   40 17 35  0
  AMP PEAK 10(8P11.23) WILD-TYPE 96 39 94  7
D10V5, multiclass
    clus
vv   AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  N0                           40                             96
  N1                           17                             39
  N2                           35                             94
  N3                            0                              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"
D10V6, binary
                                cls
clus                              0  1
  AMP PEAK 10(8P11.23) MUTATED   30 11
  AMP PEAK 10(8P11.23) WILD-TYPE 78 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED     30   11
  AMP PEAK 10(8P11.23) WILD-TYPE   78   37
    clus
vv   AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  M0                           30                             78
  MX                           11                             37
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(8P11.23) MUTATED    35  90
  AMP PEAK 10(8P11.23) WILD-TYPE  86 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED     35   90
  AMP PEAK 10(8P11.23) WILD-TYPE   86  206
        clus
vv       AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  FEMALE                           35                             86
  MALE                             90                            206
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(8P11.23) MUTATED                                     121
  AMP PEAK 10(8P11.23) WILD-TYPE                                   289
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 10(8P11.23) MUTATED                                                             1
  AMP PEAK 10(8P11.23) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 10(8P11.23) MUTATED                                                     3
  AMP PEAK 10(8P11.23) WILD-TYPE                                                   3
D10V8, multiclass
                                                             clus
vv                                                            AMP PEAK 10(8P11.23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                121
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            AMP PEAK 10(8P11.23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  289
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(8P11.23) MUTATED    27  98
  AMP PEAK 10(8P11.23) WILD-TYPE  52 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED     27   98
  AMP PEAK 10(8P11.23) WILD-TYPE   52  240
     clus
vv    AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  NO                            27                             52
  YES                           98                            240
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(8P11.23) MUTATED                                  0     0
  AMP PEAK 10(8P11.23) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(8P11.23) MUTATED                          14   108
  AMP PEAK 10(8P11.23) WILD-TYPE                        19   253
D10V12, multiclass
                                  clus
vv                                 AMP PEAK 10(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     108
                                  clus
vv                                 AMP PEAK 10(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                                cls
clus                               0   1
  AMP PEAK 10(8P11.23) MUTATED     5 112
  AMP PEAK 10(8P11.23) WILD-TYPE  13 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED      5  112
  AMP PEAK 10(8P11.23) WILD-TYPE   13  269
                        clus
vv                       AMP PEAK 10(8P11.23) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       AMP PEAK 10(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            269
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(8Q11.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(8Q11.21) MUTATED   152  56
  AMP PEAK 11(8Q11.21) WILD-TYPE 105  42
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                           208                            147 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                            56                             42 
$`AMP PEAK 11(8Q11.21) MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
         283          248          520          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         190          451           63          384          113          236 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
         310          423          687         1153          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721          485 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
         142          613          392          993          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1960         1330          811         1988          488          512 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1980         1977         1966         1966         1975          413 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 
         629          433          594           98          202          224 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         394          119          432           46          443          447 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 
         225          484          348         1207          654         1422 
TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         896          985         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007          509         1309          901          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 
         613          545          393          391          608         2562 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 
        1777         1521         1966         1125          514         1969 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 
         345          354          234          379         1956         1191 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
        1440         1960          105          759          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036          796         1954         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 
         907          181         1077         1955         1950         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
         584         1978         2886         2327         2437          519 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        2641         1478         1840         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1948         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1966         1969         3837         1959         1970         1970 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7254 
        1987         1724         1444          954          797         1976 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JD 
        1947         1973         1958         1981         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         750          717          317          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         292          701          154          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
         104         1778         1081          516         1030         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         575          299          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
          92          585            3           13            6           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 
         133          414            2           37           55           24 
TCGA-HD-8635 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H 
          25           10         1057          485          588          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         440          351          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A5QE TCGA-QK-A64Z TCGA-QK-A652 
          34          112         1652          721          553          357 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         218          228          225           64 

$`AMP PEAK 11(8Q11.21) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          276          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
        1762          725          644          895          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-CN-4727 
         216          182          536          638          428          452 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5360 
         462          642          369         1268          173         1081 
TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 
        1980          290          630          424          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 
         432         1970          424          318          611          429 
TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5331 
         526          175          367         1466         1660         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6228 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5247 
        1959          877         1963          548          303          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6480 
        1663         1152          799         1050         1971          362 
TCGA-CR-6481 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 
         311          350          479         1435         1245         1979 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         889           30          997          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 
         898          930          216          156          911         1472 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 
         522         3295          546         1958          406          701 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6954 TCGA-CV-6961 
         215         1315         1970         1969         1957         1959 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7242 
        1936         1959         1939         1945         1979         1095 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1960         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
        1957         1937         1972         1937         1984         1959 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         851         1945          321           77          491          568 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         548          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-7774 TCGA-H7-A6C5 TCGA-HD-7753 
         340          384           14          407          403            5 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 
          25           44           11           49          111           33 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         122          441          360          392           56          111 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         254          910         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IF 
        1968          400          245 

  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                             2                              5 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                          3837                           3295 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                         623.5                          630.0 
[1] "2.0 - 3837.0 (623.5)" "5.0 - 3295.0 (630.0)"
[1] "hr=" "1.3"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 11(8Q11.21) MUTATED        16       35        52       107         5
  AMP PEAK 11(8Q11.21) WILD-TYPE       8       28        19        85         4
D11V3, multiclass
           clus
vv          AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  STAGE I                             16                              8
  STAGE II                            35                             28
  STAGE III                           52                             19
  STAGE IVA                          107                             85
  STAGE IVB                            5                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 11(8Q11.21) MUTATED   26 62 56 72
  AMP PEAK 11(8Q11.21) WILD-TYPE 14 46 29 59
D11V4, multiclass
    clus
vv   AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  T1                           26                             14
  T2                           62                             46
  T3                           56                             29
  T4                           72                             59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  AMP PEAK 11(8Q11.21) MUTATED   76 39 76  3
  AMP PEAK 11(8Q11.21) WILD-TYPE 60 17 53  4
D11V5, multiclass
    clus
vv   AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  N0                           76                             60
  N1                           39                             17
  N2                           76                             53
  N3                            3                              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"
D11V6, binary
                                cls
clus                              0  1
  AMP PEAK 11(8Q11.21) MUTATED   69 26
  AMP PEAK 11(8Q11.21) WILD-TYPE 39 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED     69   26
  AMP PEAK 11(8Q11.21) WILD-TYPE   39   22
    clus
vv   AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  M0                           69                             39
  MX                           26                             22
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q11.21) MUTATED    72 172
  AMP PEAK 11(8Q11.21) WILD-TYPE  49 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED     72  172
  AMP PEAK 11(8Q11.21) WILD-TYPE   49  124
        clus
vv       AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  FEMALE                           72                             49
  MALE                            172                            124
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(8Q11.21) MUTATED                                     240
  AMP PEAK 11(8Q11.21) WILD-TYPE                                   170
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 11(8Q11.21) MUTATED                                                             1
  AMP PEAK 11(8Q11.21) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 11(8Q11.21) MUTATED                                                     3
  AMP PEAK 11(8Q11.21) WILD-TYPE                                                   3
D11V8, multiclass
                                                             clus
vv                                                            AMP PEAK 11(8Q11.21) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                240
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            AMP PEAK 11(8Q11.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  170
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q11.21) MUTATED    44 200
  AMP PEAK 11(8Q11.21) WILD-TYPE  35 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED     44  200
  AMP PEAK 11(8Q11.21) WILD-TYPE   35  138
     clus
vv    AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  NO                            44                             35
  YES                          200                            138
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(8Q11.21) MUTATED                                  1     7
  AMP PEAK 11(8Q11.21) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8Q11.21) MUTATED                          17   210
  AMP PEAK 11(8Q11.21) WILD-TYPE                        16   151
D11V12, multiclass
                                  clus
vv                                 AMP PEAK 11(8Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     210
                                  clus
vv                                 AMP PEAK 11(8Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       151
[1] 4 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(8Q11.21) MUTATED    13 221
  AMP PEAK 11(8Q11.21) WILD-TYPE   5 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED     13  221
  AMP PEAK 11(8Q11.21) WILD-TYPE    5  160
                        clus
vv                       AMP PEAK 11(8Q11.21) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          221
                        clus
vv                       AMP PEAK 11(8Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            160
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED   182  75
  AMP PEAK 12(8Q24.21) WILD-TYPE  75  23
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           257                             98 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            75                             23 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 
         283          415          248          722         1288          520 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         623         1636         1747          190          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
         384          113          236          895          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 
         133          558          423          687         1153          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
        1955          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
         485          142          452          613          392          993 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
         395          240         1960         1330          811         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         488          512         1980         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1966         1975          413          629          433          594 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          98          202          424          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          119          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CQ-5324 
         447          225          526          484          348         1207 
TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
         654         1422          896         1399          317          129 
TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
         870          985         1959         1959          815         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-A4C6 
        1378         1007          509         1309          901          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1960          613          545          548          393          391 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
         608         2562          358         1777         1521         1966 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6484 
        1125         1971          514         1969          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
         234          379          350         1956         1191         1440 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1960          105          759           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036          796         1954         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
         907          216          181         1077         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
         522         1950         3295         1438          584         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 
        2886         2327         2437          519          406         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1966         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1936         1945         1987         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7418 
        1095          954          797         1967         1976         1955 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1947         1937         1973         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1981         1945         1954         1970          750          717 
TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         317          237          828          773          292          701 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
          77          154          106          128          112          104 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
         575          299          564          490          658           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
         585            3           14           13            6           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 
         133          414            2            5           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 
          44           24           25           10          111         1057 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         485          588          360          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A6I9 
         210           14           34           56          112          254 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1652          721          578         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          218          228          225           64 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6869 
         462         1983          276         1762          725          644 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-CN-4730 TCGA-CN-4733 
         310          536          638          428          462          642 
TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 
         369         1268          173         1081          290          630 
TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-A63Y 
         424          629           45          432         1970          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5333 TCGA-CQ-6221 TCGA-CQ-6223 
         367         1466         1660          341         1000         1057 
TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         877         1963          303         1663         1152          799 
TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 
        1050          362          311          479         1435         1245 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1979          889          997          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5439 TCGA-CV-5443 
         898          930          156          911          546         1958 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
         701         2641         1970         1957         1969         1959 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1959         1939         1960         1099         1974         1948 
TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-A45O TCGA-CX-7085 TCGA-D6-6825 
        1957         1972         1937          851          321          491 
TCGA-D6-6827 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         568          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-A6C5 TCGA-HD-7754 
         340           15          384          407          403           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61H 
          11           49           33          122          441          412 
TCGA-IQ-A61J TCGA-MT-A67A TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX 
         440          392          111          910         1120         1954 
TCGA-P3-A6T2 TCGA-QK-A6IF 
        1917          245 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                             2                             11 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          3837                           2641 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         611.0                          672.5 
[1] "2.0 - 3837.0 (611.0)"  "11.0 - 2641.0 (672.5)"
[1] "hr=" "1"  
D12V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 12(8Q24.21) MUTATED        18       41        53       147         8
  AMP PEAK 12(8Q24.21) WILD-TYPE       6       22        18        45         1
D12V3, multiclass
           clus
vv          AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  STAGE I                             18                              6
  STAGE II                            41                             22
  STAGE III                           53                             18
  STAGE IVA                          147                             45
  STAGE IVB                            8                              1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 12(8Q24.21) MUTATED   29 74 67 99
  AMP PEAK 12(8Q24.21) WILD-TYPE 11 34 18 32
D12V4, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  T1                           29                             11
  T2                           74                             34
  T3                           67                             18
  T4                           99                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 12(8Q24.21) MUTATED    88  40 107   6
  AMP PEAK 12(8Q24.21) WILD-TYPE  48  16  22   1
D12V5, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  N0                           88                             48
  N1                           40                             16
  N2                          107                             22
  N3                            6                              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"
D12V6, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   82 34
  AMP PEAK 12(8Q24.21) WILD-TYPE 26 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     82   34
  AMP PEAK 12(8Q24.21) WILD-TYPE   26   14
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  M0                           82                             26
  MX                           34                             14
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    89 216
  AMP PEAK 12(8Q24.21) WILD-TYPE  32  80
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     89  216
  AMP PEAK 12(8Q24.21) WILD-TYPE   32   80
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                           89                             32
  MALE                            216                             80
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8Q24.21) MUTATED                                     300
  AMP PEAK 12(8Q24.21) WILD-TYPE                                   110
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 12(8Q24.21) MUTATED                                                             1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 12(8Q24.21) MUTATED                                                     4
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                   2
D12V8, multiclass
                                                             clus
vv                                                            AMP PEAK 12(8Q24.21) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                300
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            AMP PEAK 12(8Q24.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  110
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    59 246
  AMP PEAK 12(8Q24.21) WILD-TYPE  20  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     59  246
  AMP PEAK 12(8Q24.21) WILD-TYPE   20   92
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                            59                             20
  YES                          246                             92
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(8Q24.21) MUTATED                                  1     8
  AMP PEAK 12(8Q24.21) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED                          26   259
  AMP PEAK 12(8Q24.21) WILD-TYPE                         7   102
D12V12, multiclass
                                  clus
vv                                 AMP PEAK 12(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     259
                                  clus
vv                                 AMP PEAK 12(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                       102
[1] 4 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(8Q24.21) MUTATED    16 277
  AMP PEAK 12(8Q24.21) WILD-TYPE   2 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     16  277
  AMP PEAK 12(8Q24.21) WILD-TYPE    2  104
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          277
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            104
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(9P24.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(9P24.1) MUTATED    61  21
  AMP PEAK 13(9P24.1) WILD-TYPE 196  77
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           82                           273 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           21                            77 
$`AMP PEAK 13(9P24.1) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BB-7870 
         725          623         1747          113          351         1153 
TCGA-C9-A47Z TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
           5          488         1977         1975          413          630 
TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CQ-5325 
         424           45          424          119          432          654 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
        1422          896         1057          815         1461         1309 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6487 
         968         1960          548         1777         1969          234 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7382 
        1956         1440          105         1979          889          796 
TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 
         392          930          181          522         3295         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 
        2886         2327         1958          519         1840          641 
TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-7099 TCGA-CV-7254 
        1899         1959         3835         1966         1936         1976 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN 
        1937         1973         1958         1945         1970          717 
TCGA-D6-6516 TCGA-DQ-5625 TCGA-F7-A50G TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8502 
         773         1081           15            3          407          133 
TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
           2           37           24           10           33         1057 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F 
         588          412          351           14          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T2 
         112          254         1120         1917 

$`AMP PEAK 13(9P24.1) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
         722         1288         1762          520         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451           63          384          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         513          216          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687          638          428          436         1955          624 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1988          512          173         1980         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1966         1966          290          629          433          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
         629          432           98         1970          202          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         318          611          394          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         447          225          526          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 
         367         1466         1207         1660         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 
         341          129          870         1000          985         1959 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 
        1959         1378         1007          509          901          877 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
         613         1963          545          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
         362          311          345          354          379          350 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 
         479         1435         1191         1245         1960          759 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 
          30          972         1968         1036         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         898          216          156         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 
        1955         1950         1438          584          546         2437 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
         406          701         2641         1478          215         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6943 
        1665         1970         1948         1969         1952         1948 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1969         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1970         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1960         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
        1957         1947         1972         1937         1984         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7085 
        1981          851         1954          750          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          828          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          112          104 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1778          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
         340          564          490          658           92          585 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 
         384           14           13            6           58          414 
TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
         403            5           25           55           44           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          11           49          111          485          122          441 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X 
         360          440          360          224          210           34 
TCGA-MT-A67D TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 
          56          910         1652          721         1954          578 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                            2                             4 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                         3835                          3837 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                        784.5                         608.0 
[1] "2.0 - 3835.0 (784.5)" "4.0 - 3837.0 (608.0)"
[1] "hr=" "1.5"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 13(9P24.1) MUTATED         8       17        16        48         4
  AMP PEAK 13(9P24.1) WILD-TYPE      16       46        55       144         5
D13V3, multiclass
           clus
vv          AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  STAGE I                             8                            16
  STAGE II                           17                            46
  STAGE III                          16                            55
  STAGE IVA                          48                           144
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK 13(9P24.1) MUTATED   10 22 25 36
  AMP PEAK 13(9P24.1) WILD-TYPE 30 86 60 95
D13V4, multiclass
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  T1                          10                            30
  T2                          22                            86
  T3                          25                            60
  T4                          36                            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                             N0  N1  N2  N3
  AMP PEAK 13(9P24.1) MUTATED    33  14  31   4
  AMP PEAK 13(9P24.1) WILD-TYPE 103  42  98   3
D13V5, multiclass
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  N0                          33                           103
  N1                          14                            42
  N2                          31                            98
  N3                           4                             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"
D13V6, binary
                               cls
clus                             0  1
  AMP PEAK 13(9P24.1) MUTATED   25 13
  AMP PEAK 13(9P24.1) WILD-TYPE 83 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     25   13
  AMP PEAK 13(9P24.1) WILD-TYPE   83   35
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  M0                          25                            83
  MX                          13                            35
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED    42  61
  AMP PEAK 13(9P24.1) WILD-TYPE  79 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     42   61
  AMP PEAK 13(9P24.1) WILD-TYPE   79  235
        clus
vv       AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  FEMALE                          42                            79
  MALE                            61                           235
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(9P24.1) MUTATED                                     102
  AMP PEAK 13(9P24.1) WILD-TYPE                                   308
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 13(9P24.1) MUTATED                                                             0
  AMP PEAK 13(9P24.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 13(9P24.1) MUTATED                                                     1
  AMP PEAK 13(9P24.1) WILD-TYPE                                                   5
D13V8, multiclass
                                                             clus
vv                                                            AMP PEAK 13(9P24.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               102
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            AMP PEAK 13(9P24.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 308
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED    14  89
  AMP PEAK 13(9P24.1) WILD-TYPE  65 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     14   89
  AMP PEAK 13(9P24.1) WILD-TYPE   65  249
     clus
vv    AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  NO                           14                            65
  YES                          89                           249
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(9P24.1) MUTATED                                  0     2
  AMP PEAK 13(9P24.1) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(9P24.1) MUTATED                           7    90
  AMP PEAK 13(9P24.1) WILD-TYPE                        26   271
D13V12, multiclass
                                  clus
vv                                 AMP PEAK 13(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     90
                                  clus
vv                                 AMP PEAK 13(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED     8  92
  AMP PEAK 13(9P24.1) WILD-TYPE  10 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED      8   92
  AMP PEAK 13(9P24.1) WILD-TYPE   10  289
                        clus
vv                       AMP PEAK 13(9P24.1) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       AMP PEAK 13(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           289
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(9P23) MUTATION ANALYSIS
D14V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 14(9P23) MUTATED    61  25
  AMP PEAK 14(9P23) WILD-TYPE 196  73
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                         86                         269 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                         25                          73 
$`AMP PEAK 14(9P23) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-C9-A47Z 
         725          623         1747          113          351            5 
TCGA-CN-4725 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5370 
         485          488         1980         1977         1966         1975 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 
         630          424           45          424          119          432 
TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 
         654         1422          896         1057          985          815 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 
        1461         1309          968         1960          548         1777 
TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7382 
        1969          234         1956          105         1979          796 
TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 
         392          930          181         1955          522         3295 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 
        1978         2886         2327          519         1840          641 
TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
        1899         1959         1966         3837         1970         1936 
TCGA-CV-7102 TCGA-CV-7243 TCGA-CV-7254 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 
        1945          954         1976         1937         1973         1958 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-D6-6516 TCGA-DQ-5625 TCGA-DQ-7589 TCGA-F7-A50G 
        1945         1970          773         1081          575           15 
TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A634 
           3          407          133           37           24           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-MT-A51W TCGA-MT-A67A 
          33         1057          588          412           14          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-QK-A6IF 
         111          112          254         1120         1917          245 
TCGA-QK-A6IG TCGA-QK-A6IJ 
         218           64 

$`AMP PEAK 14(9P23) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
         722         1288         1762          520         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451           63          384          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         513          216          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
         624            4          799          721          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 
        1988          512          173         1081         1980         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         413          290          629          433          594          629 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
         432           98         1970          202          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         611          394          429           46          443          447 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         225          526          484          348          175          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1466         1207         1660         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 
         129          870         1000         1959         1959         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1007          509          901          877          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         545          393          391          303          608         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
         358         1663         1152          799         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
        1050         1125         1971          514          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
         345          354          379          350          479         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 
        1191         1440         1245         1960          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 
          30          972         1968         1036         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         898          216          156         1077          911         1472 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5444 
        1950         1438          584          546         1958         2437 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
         406          701         2641         1478          215         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
        1665         1970         1948         1969         1952         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
        1948         1969         1957         1969         1959         1959 
TCGA-CV-7095 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1970         1959         1939         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1444         1095          797         1967         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 
        1974         1948         1955         1957         1947         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A461 
        1937         1984         1959         1981          851         1954 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          317          321          237          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 
         106          128          112          104         1778          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548         1965          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658           92          585          384           14           13 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
           6           58          414          403            2            5 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          25           55           44           25           11           49 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J 
         111          485          122          441          360          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D 
         351          360          224          210           34           56 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 
         910         1652          721         1954          578         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          357          228          225 

  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                          3                           2 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                       3837                        3835 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                      805.5                       608.0 
[1] "3.0 - 3837.0 (805.5)" "2.0 - 3835.0 (608.0)"
[1] "hr=" "1.4"
D14V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 14(9P23) MUTATED         7       18        17        46         4
  AMP PEAK 14(9P23) WILD-TYPE      17       45        54       146         5
D14V3, multiclass
           clus
vv          AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  STAGE I                           7                          17
  STAGE II                         18                          45
  STAGE III                        17                          54
  STAGE IVA                        46                         146
  STAGE IVB                         4                           5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  AMP PEAK 14(9P23) MUTATED    9 26 24 33
  AMP PEAK 14(9P23) WILD-TYPE 31 82 61 98
D14V4, multiclass
    clus
vv   AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  T1                         9                          31
  T2                        26                          82
  T3                        24                          61
  T4                        33                          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                           N0  N1  N2  N3
  AMP PEAK 14(9P23) MUTATED    28  15  33   4
  AMP PEAK 14(9P23) WILD-TYPE 108  41  96   3
D14V5, multiclass
    clus
vv   AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  N0                        28                         108
  N1                        15                          41
  N2                        33                          96
  N3                         4                           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"
D14V6, binary
                             cls
clus                           0  1
  AMP PEAK 14(9P23) MUTATED   26 13
  AMP PEAK 14(9P23) WILD-TYPE 82 35
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED     26   13
  AMP PEAK 14(9P23) WILD-TYPE   82   35
    clus
vv   AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  M0                        26                          82
  MX                        13                          35
[1] 2 2
[1] FALSE
D14V7, binary
                             cls
clus                            0   1
  AMP PEAK 14(9P23) MUTATED    39  64
  AMP PEAK 14(9P23) WILD-TYPE  82 232
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED     39   64
  AMP PEAK 14(9P23) WILD-TYPE   82  232
        clus
vv       AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  FEMALE                        39                          82
  MALE                          64                         232
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P23) MUTATED                                     102
  AMP PEAK 14(9P23) WILD-TYPE                                   308
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 14(9P23) MUTATED                                                             0
  AMP PEAK 14(9P23) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 14(9P23) MUTATED                                                     1
  AMP PEAK 14(9P23) WILD-TYPE                                                   5
D14V8, multiclass
                                                             clus
vv                                                            AMP PEAK 14(9P23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             102
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 1
                                                             clus
vv                                                            AMP PEAK 14(9P23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               308
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                             cls
clus                            0   1
  AMP PEAK 14(9P23) MUTATED    16  87
  AMP PEAK 14(9P23) WILD-TYPE  63 251
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED     16   87
  AMP PEAK 14(9P23) WILD-TYPE   63  251
     clus
vv    AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  NO                         16                          63
  YES                        87                         251
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(9P23) MUTATED                                  0     2
  AMP PEAK 14(9P23) WILD-TYPE                                1     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(9P23) MUTATED                           6    92
  AMP PEAK 14(9P23) WILD-TYPE                        27   269
D14V12, multiclass
                                  clus
vv                                 AMP PEAK 14(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                6
  WHITE                                                   92
                                  clus
vv                                 AMP PEAK 14(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    269
[1] 4 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(9P23) MUTATED     7  93
  AMP PEAK 14(9P23) WILD-TYPE  11 288
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED      7   93
  AMP PEAK 14(9P23) WILD-TYPE   11  288
                        clus
vv                       AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  HISPANIC OR LATINO                             7                          11
  NOT HISPANIC OR LATINO                        93                         288
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(9P13.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(9P13.3) MUTATED    69  26
  AMP PEAK 15(9P13.3) WILD-TYPE 188  72
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                           95                           260 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                           26                            72 
$`AMP PEAK 15(9P13.3) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DA 
         725          623         1747          384          113          351 
TCGA-BB-4224 TCGA-BB-7870 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 
         278         1153          613          240          488         1980 
TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6023 
        1977         1975          630          424          629          424 
TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5330 
         224          119          432          225         1422          896 
TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         985          815         1461         1309          968         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CI TCGA-CR-6467 TCGA-CR-6488 TCGA-CR-7368 TCGA-CR-7370 
        1963          608         1777          379         1245          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7390 TCGA-CR-7395 
        1979          759          889          972          907          930 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 
         181         1077          522         1950         3295          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1978         2886         2327         2437          519          406 
TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-7095 
        1840          641         1899         1959         1966         1970 
TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7254 TCGA-CV-7427 
        1936         1987         1724         1444         1976         1937 
TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CX-7219 TCGA-D6-6516 TCGA-DQ-5625 
        1958         1945         1970          828          773         1081 
TCGA-DQ-5629 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-H7-7774 
         516          490           15           92            3          407 
TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-A634 TCGA-HD-A6I0 
         133           37           55           24           10           33 
TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         485          351           14           34          392          111 
TCGA-MT-A67G TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IG 
         112         1120         1917          553          218 

$`AMP PEAK 15(9P13.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
         722         1288         1762          520         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         644          451           63          236          895          513 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
         216          182          187         2878          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
         799          721          485          142          452          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         462          993          642          369          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1988          512          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1081         1980         1966         1966          413          290 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 
        1970          202          318          611          394          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
          46          443          447          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129          870         1000 
TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1057         1959         1959         1378         1007          509 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         901          877          613          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         391          303         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
         799         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         234          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1440         1960           30         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
        1954          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 
         946          908          898          216          156          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5443 TCGA-CV-5971 
        1472         1955         1438          584         1958          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        2641         1478          215         1315         1665         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1948         1969         1952         3835         1948         1969 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7243 
        1959         1939         1945         1979         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
         797         1967         1960         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1947         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A461 TCGA-CV-A6JE 
        1984         1959         1981          851         1954          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 
         717          317          321          237          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         112          104         1778         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         575          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61V 
         324          340          564          658          585          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 
          14           13            6           58          414          403 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 
           2            5           25           44           25           11 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          49          111         1057          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         360          412          440          360          224          210 
TCGA-MT-A67D TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX 
          56          254          910         1652          721         1954 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
         578         1968          400          357          245          228 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                            3                             2 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                         3295                          3837 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                        759.0                         602.5 
[1] "3.0 - 3295.0 (759.0)" "2.0 - 3837.0 (602.5)"
[1] "hr=" "1.3"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 15(9P13.3) MUTATED         8       22        16        55         5
  AMP PEAK 15(9P13.3) WILD-TYPE      16       41        55       137         4
D15V3, multiclass
           clus
vv          AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  STAGE I                             8                            16
  STAGE II                           22                            41
  STAGE III                          16                            55
  STAGE IVA                          55                           137
  STAGE IVB                           5                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK 15(9P13.3) MUTATED   11 31 25 39
  AMP PEAK 15(9P13.3) WILD-TYPE 29 77 60 92
D15V4, multiclass
    clus
vv   AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  T1                          11                            29
  T2                          31                            77
  T3                          25                            60
  T4                          39                            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                            N0 N1 N2 N3
  AMP PEAK 15(9P13.3) MUTATED   38 16 35  4
  AMP PEAK 15(9P13.3) WILD-TYPE 98 40 94  3
D15V5, multiclass
    clus
vv   AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  N0                          38                            98
  N1                          16                            40
  N2                          35                            94
  N3                           4                             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"
D15V6, binary
                               cls
clus                             0  1
  AMP PEAK 15(9P13.3) MUTATED   33 12
  AMP PEAK 15(9P13.3) WILD-TYPE 75 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED     33   12
  AMP PEAK 15(9P13.3) WILD-TYPE   75   36
    clus
vv   AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  M0                          33                            75
  MX                          12                            36
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P13.3) MUTATED    37  76
  AMP PEAK 15(9P13.3) WILD-TYPE  84 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED     37   76
  AMP PEAK 15(9P13.3) WILD-TYPE   84  220
        clus
vv       AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  FEMALE                          37                            84
  MALE                            76                           220
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(9P13.3) MUTATED                                     111
  AMP PEAK 15(9P13.3) WILD-TYPE                                   299
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 15(9P13.3) MUTATED                                                             0
  AMP PEAK 15(9P13.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 15(9P13.3) MUTATED                                                     2
  AMP PEAK 15(9P13.3) WILD-TYPE                                                   4
D15V8, multiclass
                                                             clus
vv                                                            AMP PEAK 15(9P13.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               111
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            AMP PEAK 15(9P13.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 299
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P13.3) MUTATED    20  93
  AMP PEAK 15(9P13.3) WILD-TYPE  59 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED     20   93
  AMP PEAK 15(9P13.3) WILD-TYPE   59  245
     clus
vv    AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  NO                           20                            59
  YES                          93                           245
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(9P13.3) MUTATED                                  0     1
  AMP PEAK 15(9P13.3) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(9P13.3) MUTATED                           7   101
  AMP PEAK 15(9P13.3) WILD-TYPE                        26   260
D15V12, multiclass
                                  clus
vv                                 AMP PEAK 15(9P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                    101
                                  clus
vv                                 AMP PEAK 15(9P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P13.3) MUTATED     8 100
  AMP PEAK 15(9P13.3) WILD-TYPE  10 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED      8  100
  AMP PEAK 15(9P13.3) WILD-TYPE   10  281
                        clus
vv                       AMP PEAK 15(9P13.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       AMP PEAK 15(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           281
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(9Q34.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(9Q34.3) MUTATED    76  37
  AMP PEAK 16(9Q34.3) WILD-TYPE 181  61
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                          113                           242 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                           37                            61 
$`AMP PEAK 16(9Q34.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         283         1983          248          520          725          623 
TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BB-4224 TCGA-BB-7872 
        1747          451          113          351          278          436 
TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4741 
         624          721          452          613          993         1268 
TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6010 
         488         1980         1977         1966         1966          630 
TCGA-CN-6011 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6996 
         424         1970          424          224          119          432 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5332 
         225          348         1466          654          896          317 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 
        1000         1057          815         1461         1309          968 
TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6491 TCGA-CR-7365 
        1960          548         1777          514          350         1191 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7402 
        1245         1960          105          889         1036          911 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
        1950         3295          584          546         1978         2327 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 
        2437          519          406         1840          215          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6952 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 
        1899         1970         1966         1936         1959         1987 
TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 
        1724          797         1099         1948         1957         1937 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1972         1937         1958         1945         1954         1970 
TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 TCGA-DQ-5625 
         317          828          773          701          128         1081 
TCGA-DQ-7589 TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7917 
         575            3          407          133            2           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-A61J 
          55           44           10          111           33          440 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6SW 
         351           14          392           56          112         1120 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A6II 
        1917          400          553          218          225 

$`AMP PEAK 16(9Q34.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462          415          276          722         1288         1762 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
        1636          190          644           63          384          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         895          513          216          182          187         2878 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-C9-A47Z 
         687          638         1153          428         1955            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
           4          799          485          142          392          462 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642          369          395          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 
         811         1988          512          173         1081         1980 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1975          413          290          629          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6988 
         629           45          432           98          202          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         611          394          429           46          443          447 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5327 
         526          484          175          367         1207         1660 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 
        1422         1399          341          129          870          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
        1959         1959         1378         1007          509          901 
TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
         877          613         1963          545          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
         799         1521         1966         1050         1125         1971 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7371 
         379          479         1956         1435         1440         1979 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 
         759           30          972         1968          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         997         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 
         181         1077         1472         1955          522         1438 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
        2886         1958          701         2641         1478         1315 
TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1665         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1969         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 
        1959         1970         1970         1939         1945         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444         1095          954         1967         1960         1976 
TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7435 
        1974         1955         1947         1973         1984         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 
        1981          851          750          717          321          237 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         292           77          491          154          568          106 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         112          104         1778          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1965          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          92          585          384           14           13            6 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8634 
          58          414          403            5           25           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          25           11           49         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66S 
         441          588          360          412          360          224 
TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
         210           34          111          254          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IF 
         721         1954          578         1968          357          245 
TCGA-QK-A6IH TCGA-QK-A6IJ 
         228           64 

  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                            2                             4 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                         3295                          3837 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                        701.0                         609.5 
[1] "2.0 - 3295.0 (701.0)" "4.0 - 3837.0 (609.5)"
[1] "hr=" "1.2"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 16(9Q34.3) MUTATED         7       20        20        74         6
  AMP PEAK 16(9Q34.3) WILD-TYPE      17       43        51       118         3
D16V3, multiclass
           clus
vv          AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  STAGE I                             7                            17
  STAGE II                           20                            43
  STAGE III                          20                            51
  STAGE IVA                          74                           118
  STAGE IVB                           6                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK 16(9Q34.3) MUTATED   10 30 29 59
  AMP PEAK 16(9Q34.3) WILD-TYPE 30 78 56 72
D16V4, multiclass
    clus
vv   AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  T1                          10                            30
  T2                          30                            78
  T3                          29                            56
  T4                          59                            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                            N0 N1 N2 N3
  AMP PEAK 16(9Q34.3) MUTATED   45 18 47  5
  AMP PEAK 16(9Q34.3) WILD-TYPE 91 38 82  2
D16V5, multiclass
    clus
vv   AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  N0                          45                            91
  N1                          18                            38
  N2                          47                            82
  N3                           5                             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"
D16V6, binary
                               cls
clus                             0  1
  AMP PEAK 16(9Q34.3) MUTATED   33 15
  AMP PEAK 16(9Q34.3) WILD-TYPE 75 33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED     33   15
  AMP PEAK 16(9Q34.3) WILD-TYPE   75   33
    clus
vv   AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  M0                          33                            75
  MX                          15                            33
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(9Q34.3) MUTATED    39 100
  AMP PEAK 16(9Q34.3) WILD-TYPE  82 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED     39  100
  AMP PEAK 16(9Q34.3) WILD-TYPE   82  196
        clus
vv       AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  FEMALE                          39                            82
  MALE                           100                           196
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(9Q34.3) MUTATED                                     137
  AMP PEAK 16(9Q34.3) WILD-TYPE                                   273
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 16(9Q34.3) MUTATED                                                             0
  AMP PEAK 16(9Q34.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 16(9Q34.3) MUTATED                                                     2
  AMP PEAK 16(9Q34.3) WILD-TYPE                                                   4
D16V8, multiclass
                                                             clus
vv                                                            AMP PEAK 16(9Q34.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               137
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            AMP PEAK 16(9Q34.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 273
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                               cls
clus                              0   1
  AMP PEAK 16(9Q34.3) MUTATED    24 115
  AMP PEAK 16(9Q34.3) WILD-TYPE  55 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED     24  115
  AMP PEAK 16(9Q34.3) WILD-TYPE   55  223
     clus
vv    AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  NO                           24                            55
  YES                         115                           223
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(9Q34.3) MUTATED                                  0     2
  AMP PEAK 16(9Q34.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(9Q34.3) MUTATED                          14   120
  AMP PEAK 16(9Q34.3) WILD-TYPE                        19   241
D16V12, multiclass
                                  clus
vv                                 AMP PEAK 16(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    120
                                  clus
vv                                 AMP PEAK 16(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                               cls
clus                              0   1
  AMP PEAK 16(9Q34.3) MUTATED     8 127
  AMP PEAK 16(9Q34.3) WILD-TYPE  10 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED      8  127
  AMP PEAK 16(9Q34.3) WILD-TYPE   10  254
                        clus
vv                       AMP PEAK 16(9Q34.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         127
                        clus
vv                       AMP PEAK 16(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           254
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(11P13) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(11P13) MUTATED    50  15
  AMP PEAK 17(11P13) WILD-TYPE 207  83
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                          65                          290 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                          15                           83 
$`AMP PEAK 17(11P13) MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         283          725          190          384          113          236 
TCGA-BA-A6D8 TCGA-BB-4225 TCGA-BB-7861 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 
         513          140          310            5          721          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-6018 
         240         1960         1988          488         1977           45 
TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-5333 TCGA-CQ-5334 
         119          225         1466         1422          341          129 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1000         1461         1007          901          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 
         613          393          391          354          379         1191 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7382 TCGA-CR-7392 TCGA-CV-5430 TCGA-CV-5440 
        1440          105          796          946         1955         1978 
TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6942 TCGA-CV-7254 
         406         1840         1665          641         3835         1976 
TCGA-CV-7261 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6827 TCGA-D6-8569 TCGA-DQ-5624 
        1099          828          292          568          128         1778 
TCGA-DQ-7588 TCGA-F7-A50J TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A67D TCGA-P3-A5QA 
        1965          585          485          351           56         1652 
TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IJ 
        1120         1917         1968          218           64 

$`AMP PEAK 17(11P13) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          520          623         1636         1747 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB 
         644          451           63          895          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         182          187         2878          278          133          558 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         536          423          687          638         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
         436         1955          624            4          799          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142          452          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 
         642          369         1330          811         1268          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1980         1081         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          413          290          630          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         433          594          629          432           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202          424          224          318          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U 
         432          429           46          443          447          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 
         484          348          175          367         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 
        1660          896         1399          317          870         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 
         985         1959         1959          815         1378          509 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
        1309          877         1963          545          548          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
         514         1969          362          311          345          234 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1956         1435         1245         1960 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         907          913          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         156          181         1077          911         1472          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
        1950         3295         1438          584          546         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958         2437          519          701         2641 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1478          215         1315         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1969         1952         1959         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1967         1960         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1947         1937         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1958         1959         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          321          237 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 
         773          701           77          491          154          106 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         112          104         1081          516         1030          548 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         575          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          92            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
         407           58          133          414          403            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           5           25           37           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          25           11           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
        1057          122          441          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         440          360          224          210           14           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910          721 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1954          578          400          553          357          245 
TCGA-QK-A6IH TCGA-QK-A6II 
         228          225 

  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                           5                            2 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                        3835                         3837 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                         613                          629 
[1] "5.0 - 3835.0 (613.0)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.1"
D17V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 17(11P13) MUTATED         4       17        16        38         4
  AMP PEAK 17(11P13) WILD-TYPE      20       46        55       154         5
D17V3, multiclass
           clus
vv          AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  STAGE I                            4                           20
  STAGE II                          17                           46
  STAGE III                         16                           55
  STAGE IVA                         38                          154
  STAGE IVB                          4                            5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 17(11P13) MUTATED     6  26  18  31
  AMP PEAK 17(11P13) WILD-TYPE  34  82  67 100
D17V4, multiclass
    clus
vv   AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  T1                          6                           34
  T2                         26                           82
  T3                         18                           67
  T4                         31                          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                            N0  N1  N2  N3
  AMP PEAK 17(11P13) MUTATED    32  10  26   3
  AMP PEAK 17(11P13) WILD-TYPE 104  46 103   4
D17V5, multiclass
    clus
vv   AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  N0                         32                          104
  N1                         10                           46
  N2                         26                          103
  N3                          3                            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"
D17V6, binary
                              cls
clus                            0  1
  AMP PEAK 17(11P13) MUTATED   29  9
  AMP PEAK 17(11P13) WILD-TYPE 79 39
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED     29    9
  AMP PEAK 17(11P13) WILD-TYPE   79   39
    clus
vv   AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  M0                         29                           79
  MX                          9                           39
[1] 2 2
[1] FALSE
D17V7, binary
                              cls
clus                             0   1
  AMP PEAK 17(11P13) MUTATED    23  64
  AMP PEAK 17(11P13) WILD-TYPE  98 232
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED     23   64
  AMP PEAK 17(11P13) WILD-TYPE   98  232
        clus
vv       AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  FEMALE                         23                           98
  MALE                           64                          232
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(11P13) MUTATED                                      86
  AMP PEAK 17(11P13) WILD-TYPE                                   324
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 17(11P13) MUTATED                                                             0
  AMP PEAK 17(11P13) WILD-TYPE                                                           1
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 17(11P13) MUTATED                                                     1
  AMP PEAK 17(11P13) WILD-TYPE                                                   5
D17V8, multiclass
                                                             clus
vv                                                            AMP PEAK 17(11P13) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               86
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  1
                                                             clus
vv                                                            AMP PEAK 17(11P13) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                324
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                              cls
clus                             0   1
  AMP PEAK 17(11P13) MUTATED    16  71
  AMP PEAK 17(11P13) WILD-TYPE  63 267
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED     16   71
  AMP PEAK 17(11P13) WILD-TYPE   63  267
     clus
vv    AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  NO                          16                           63
  YES                         71                          267
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(11P13) MUTATED                                  0     4
  AMP PEAK 17(11P13) WILD-TYPE                                1     6
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(11P13) MUTATED                           8    70
  AMP PEAK 17(11P13) WILD-TYPE                        25   291
D17V12, multiclass
                                  clus
vv                                 AMP PEAK 17(11P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    70
                                  clus
vv                                 AMP PEAK 17(11P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     291
[1] 4 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(11P13) MUTATED     7  74
  AMP PEAK 17(11P13) WILD-TYPE  11 307
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED      7   74
  AMP PEAK 17(11P13) WILD-TYPE   11  307
                        clus
vv                       AMP PEAK 17(11P13) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         74
                        clus
vv                       AMP PEAK 17(11P13) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          307
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(11Q13.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(11Q13.3) MUTATED   108  52
  AMP PEAK 18(11Q13.3) WILD-TYPE 149  46
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           160                            195 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                            52                             46 
$`AMP PEAK 18(11Q13.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         520          725         1636          190          451           63 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 
         384          236          351          187          140          133 
TCGA-BB-7861 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4723 
         310         1153          428         1955            5          721 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
         452          613          993          369          240         1960 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1330         1988          488         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1966         1975          413          630          424          629 
TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         433           45           98          611          394          119 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CQ-5323 TCGA-CQ-5329 
         429          443          447          526         1466         1422 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         341          129         1000         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1461         1007          509          901          968         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5247 
        1963          545          548          393          391          358 
TCGA-CR-5248 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6491 
        1663         1971          514         1969          379          350 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1956         1191         1440         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 
         759         1968         1036         1954         1951          907 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5970 
         181         1955          522         1978         2886          406 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 
        1969         1952         1969         1969         1959         1970 
TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7261 TCGA-CV-7418 
        1970         1945         1724          954         1099         1955 
TCGA-CV-7422 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JE 
        1957         1937         1984         1959         1981          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         717          317          237          828          773          292 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          154          568          106          112          104 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-7848 TCGA-F7-8298 
        1081          548         1965          575          564          490 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 
          92          585          384          133            2            5 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         485          122          360          412          440          351 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6SX 
         210           14           34           56         1652         1954 
TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
        1968          218          228           64 

$`AMP PEAK 18(11Q13.3) WILD-TYPE`
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6869 
         722         1288         1762          623         1747          644 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4223 
         113          895          513          216          182         2878 
TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         278          558          536          423          687          638 
TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 
         436          624            4          799          485          142 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 
         392          462          642          395          811         1268 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6016 
         512          173         1980         1081          290          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         629          432         1970          202          424          224 
TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
         318          432           46          225          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 
         175          367         1207          654         1660          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7064 
        1399          317          870         1057          985         1378 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
        1309          877          613          303          608         2562 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1125          362          311          345          354          234 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         479         1435         1245          889           30          972 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         796          997         1430          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
         911         1472         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 
         546         2327         1958         2437          519          701 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 
         641         1899         1970         1948         1959         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7099 
        1948         1966         1957         1959         3837         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1959         1939         1987         1979         1444         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 
         797         1967         1960         1976         1974         1948 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-A45O 
        1947         1937         1973         1972         1958          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7085 TCGA-D6-6823 TCGA-D6-6824 
        1945         1954         1970          321          701           77 
TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         128         1778          516         1030          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 
         299          369          368          324          340          658 
TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
          15            3           14           13            6          407 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
          58          414          403           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61O 
         111           33         1057          441          588          360 
TCGA-KU-A66S TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         224          392          111          112          254          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
         721         1120          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II 
         357          245          225 

  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                             2                              3 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                          2886                           3837 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           580                            642 
[1] "2.0 - 2886.0 (580.0)" "3.0 - 3837.0 (642.0)"
[1] "hr=" "1.2"
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 18(11Q13.3) MUTATED        14       25        31        93         5
  AMP PEAK 18(11Q13.3) WILD-TYPE      10       38        40        99         4
D18V3, multiclass
           clus
vv          AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  STAGE I                             14                             10
  STAGE II                            25                             38
  STAGE III                           31                             40
  STAGE IVA                           93                             99
  STAGE IVB                            5                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 18(11Q13.3) MUTATED   18 44 41 66
  AMP PEAK 18(11Q13.3) WILD-TYPE 22 64 44 65
D18V4, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  T1                           18                             22
  T2                           44                             64
  T3                           41                             44
  T4                           66                             65
[1] 4 2
[1] TRUE
[1] "dimension 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(11Q13.3) MUTATED   62 23 70  3
  AMP PEAK 18(11Q13.3) WILD-TYPE 74 33 59  4
D18V5, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  N0                           62                             74
  N1                           23                             33
  N2                           70                             59
  N3                            3                              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"
D18V6, binary
                                cls
clus                              0  1
  AMP PEAK 18(11Q13.3) MUTATED   54 15
  AMP PEAK 18(11Q13.3) WILD-TYPE 54 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     54   15
  AMP PEAK 18(11Q13.3) WILD-TYPE   54   33
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  M0                           54                             54
  MX                           15                             33
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    53 137
  AMP PEAK 18(11Q13.3) WILD-TYPE  68 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     53  137
  AMP PEAK 18(11Q13.3) WILD-TYPE   68  159
        clus
vv       AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  FEMALE                           53                             68
  MALE                            137                            159
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                                     190
  AMP PEAK 18(11Q13.3) WILD-TYPE                                   220
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 18(11Q13.3) MUTATED                                                             0
  AMP PEAK 18(11Q13.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 18(11Q13.3) MUTATED                                                     0
  AMP PEAK 18(11Q13.3) WILD-TYPE                                                   6
D18V8, multiclass
                                                             clus
vv                                                            AMP PEAK 18(11Q13.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                190
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            AMP PEAK 18(11Q13.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  220
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    42 148
  AMP PEAK 18(11Q13.3) WILD-TYPE  37 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     42  148
  AMP PEAK 18(11Q13.3) WILD-TYPE   37  190
     clus
vv    AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  NO                            42                             37
  YES                          148                            190
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(11Q13.3) MUTATED                                  0     3
  AMP PEAK 18(11Q13.3) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11Q13.3) MUTATED                          18   163
  AMP PEAK 18(11Q13.3) WILD-TYPE                        15   198
D18V12, multiclass
                                  clus
vv                                 AMP PEAK 18(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     163
                                  clus
vv                                 AMP PEAK 18(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED     9 173
  AMP PEAK 18(11Q13.3) WILD-TYPE   9 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED      9  173
  AMP PEAK 18(11Q13.3) WILD-TYPE    9  208
                        clus
vv                       AMP PEAK 18(11Q13.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          173
                        clus
vv                       AMP PEAK 18(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            208
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(12P13.33) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(12P13.33) MUTATED    80  29
  AMP PEAK 19(12P13.33) WILD-TYPE 177  69
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                            109                             246 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                             29                              69 
$`AMP PEAK 19(12P13.33) MUTATED`
TCGA-BA-4077 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF 
        1983          520         1747           63          113          895 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7870 TCGA-C9-A47Z 
        2878          278          140          536         1153            5 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4738 
         485          142          613          392          240         1960 
TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6013 
        1330         1980         1977         1966          629          433 
TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
          45          424          224          318          611          119 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6221 
         447          225          526         1422          317         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-5247 
        1057          985          509          393         2562          358 
TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 
        1777          234          379         1435         1191          759 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
        1968         1036         1954          907          216          156 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 
         181         1955          522         1950         3295         1978 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7091 
        2641          215         1665         1959         1969         1959 
TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 
        1945         1095          954          797         1967         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7434 
        1099         1974         1955         1957         1972         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-DQ-5624 
        1959         1981          237          828          701         1778 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 
         516         1965          575          622          299          564 
TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-7774 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         585            3          407            5           25           37 
TCGA-HD-8314 TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
          44          111          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF 
          56          112         1917          400          553          245 
TCGA-QK-A6IG 
         218 

$`AMP PEAK 19(12P13.33) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          283          415          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
        1288         1762          725          623         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA 
         644          451          384          236          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
         216          182          187          133          558          310 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4730 
         624            4          799          721          452          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 
         993          642          369          395          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 
        1988          488          512          173         1081         1980 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          413          290          630          424 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         594          629          432           98         1970          202 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63V 
         394          432          429           46          443          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1660          896         1399          341          129          870 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959          815         1461         1378         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1963          545          548          391          303          608 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1663         1152          799         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 
         345          354          350          479         1956         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960          105         1979          889           30 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         972          796          997         1430         1951          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 
         913          946          908          898          930         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
         911         1472         1438          584          546         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1478         1840         1315          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1948         1969         1952         3835         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         1959         3837         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1939         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1444         1960         1948         1947         1937         1973 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1937         1984          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 
         750          717          317          321          773          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
         112          104         1081         1030          548          775 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         369          368          324          340          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          15           92          384           14           13            6 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-8224 
          58          133          414          403            2           55 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          24           25           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A67F 
         412          440          351          360          224          111 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          910         1652          721         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         578         1968          357          228          225           64 

  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                              3                               2 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                           3295                            3837 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                          611.0                           639.5 
[1] "3.0 - 3295.0 (611.0)" "2.0 - 3837.0 (639.5)"
[1] "hr=" "1.3"
D19V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 19(12P13.33) MUTATED         8       19        22        64
  AMP PEAK 19(12P13.33) WILD-TYPE      16       44        49       128
                                 vv
clus                              STAGE IVB
  AMP PEAK 19(12P13.33) MUTATED           3
  AMP PEAK 19(12P13.33) WILD-TYPE         6
D19V3, multiclass
           clus
vv          AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  STAGE I                               8                              16
  STAGE II                             19                              44
  STAGE III                            22                              49
  STAGE IVA                            64                             128
  STAGE IVB                             3                               6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 19(12P13.33) MUTATED   11 35 28 43
  AMP PEAK 19(12P13.33) WILD-TYPE 29 73 57 88
D19V4, multiclass
    clus
vv   AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  T1                            11                              29
  T2                            35                              73
  T3                            28                              57
  T4                            43                              88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  AMP PEAK 19(12P13.33) MUTATED   44 16 44  3
  AMP PEAK 19(12P13.33) WILD-TYPE 92 40 85  4
D19V5, multiclass
    clus
vv   AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  N0                            44                              92
  N1                            16                              40
  N2                            44                              85
  N3                             3                               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"
D19V6, binary
                                 cls
clus                               0  1
  AMP PEAK 19(12P13.33) MUTATED   29 12
  AMP PEAK 19(12P13.33) WILD-TYPE 79 36
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED     29   12
  AMP PEAK 19(12P13.33) WILD-TYPE   79   36
    clus
vv   AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  M0                            29                              79
  MX                            12                              36
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(12P13.33) MUTATED    34  97
  AMP PEAK 19(12P13.33) WILD-TYPE  87 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED     34   97
  AMP PEAK 19(12P13.33) WILD-TYPE   87  199
        clus
vv       AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  FEMALE                            34                              87
  MALE                              97                             199
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(12P13.33) MUTATED                                     130
  AMP PEAK 19(12P13.33) WILD-TYPE                                   280
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 19(12P13.33) MUTATED                                                             0
  AMP PEAK 19(12P13.33) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 19(12P13.33) MUTATED                                                     1
  AMP PEAK 19(12P13.33) WILD-TYPE                                                   5
D19V8, multiclass
                                                             clus
vv                                                            AMP PEAK 19(12P13.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 130
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
                                                             clus
vv                                                            AMP PEAK 19(12P13.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   280
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                                 cls
clus                                0   1
  AMP PEAK 19(12P13.33) MUTATED    25 106
  AMP PEAK 19(12P13.33) WILD-TYPE  54 232
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED     25  106
  AMP PEAK 19(12P13.33) WILD-TYPE   54  232
     clus
vv    AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  NO                             25                              54
  YES                           106                             232
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(12P13.33) MUTATED                                  1     1
  AMP PEAK 19(12P13.33) WILD-TYPE                                0     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(12P13.33) MUTATED                          11   115
  AMP PEAK 19(12P13.33) WILD-TYPE                        22   246
D19V12, multiclass
                                  clus
vv                                 AMP PEAK 19(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      115
                                  clus
vv                                 AMP PEAK 19(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                        246
[1] 4 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(12P13.33) MUTATED     5 123
  AMP PEAK 19(12P13.33) WILD-TYPE  13 258
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED      5  123
  AMP PEAK 19(12P13.33) WILD-TYPE   13  258
                        clus
vv                       AMP PEAK 19(12P13.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           123
                        clus
vv                       AMP PEAK 19(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             258
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(12Q15) MUTATION ANALYSIS
D20V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 20(12Q15) MUTATED    51  17
  AMP PEAK 20(12Q15) WILD-TYPE 206  81
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                          68                          287 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                          17                           81 
$`AMP PEAK 20(12Q15) MUTATED`
TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6D8 TCGA-BB-4223 TCGA-BB-4225 
        1747          451           63          513         2878          140 
TCGA-BB-7870 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 
        1153          436            5          485          452          613 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6023 
         240         1330          512          630          629          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A49B TCGA-CN-A63T TCGA-CQ-6224 
         224          318          611          447          225          985 
TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 
         509         1963          393          358         1777         1969 
TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5434 
        1191         1036         1954          907         1955         3295 
TCGA-CV-6935 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 
        1969         1959         1939         1945         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7422 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7440 
         797         1967         1957         1973         1972         1981 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-DQ-7588 TCGA-DQ-7589 
         773          701          154          104         1965          575 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-7774 TCGA-HD-7753 
         299          368          585            3          407            5 
TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
         111          210           14          392           56          112 
TCGA-P3-A6T4 TCGA-QK-A6IF 
        1968          245 

$`AMP PEAK 20(12Q15) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1636          190          644          384          113          236 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 
         895          351          216          182          187          278 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
         638          428         1955          624            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         721          142          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         369          395         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         488          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1966         1966         1975          413          290          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
        1970          202          394          119          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
          46          443          526          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1000         1057         1959         1959          815         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1378         1007         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1960          613          545          548          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
         608         2562         1663         1152          799         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
        1966         1050         1125         1971          514          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1435         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         105         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1968          796          997         1430         1951          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         156          181         1077          911         1472          522 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1950         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 
         641         1899         1970         1948         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         1970         1970         1936         1959 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 
        1987         1979         1724         1444         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 
        1099         1974         1948         1955         1947         1937 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1959          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         237          828          292           77          491          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         106          128          112         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 
        1030          548          775          622          369          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340          564          490          658           15           92 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 
         384           14           13            6           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         414          403            2           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         360          412          440          351          360          224 
TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          34          111          254          910         1652          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          218          228          225           64 

  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                           3                            2 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                        3295                         3837 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                         598                          641 
[1] "3.0 - 3295.0 (598.0)" "2.0 - 3837.0 (641.0)"
[1] "hr=" "1.2"
D20V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 20(12Q15) MUTATED         9       12        13        35         1
  AMP PEAK 20(12Q15) WILD-TYPE      15       51        58       157         8
D20V3, multiclass
           clus
vv          AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  STAGE I                            9                           15
  STAGE II                          12                           51
  STAGE III                         13                           58
  STAGE IVA                         35                          157
  STAGE IVB                          1                            8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 20(12Q15) MUTATED    10  20  15  25
  AMP PEAK 20(12Q15) WILD-TYPE  30  88  70 106
D20V4, multiclass
    clus
vv   AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  T1                         10                           30
  T2                         20                           88
  T3                         15                           70
  T4                         25                          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                            N0  N1  N2  N3
  AMP PEAK 20(12Q15) MUTATED    33   8  21   1
  AMP PEAK 20(12Q15) WILD-TYPE 103  48 108   6
D20V5, multiclass
    clus
vv   AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  N0                         33                          103
  N1                          8                           48
  N2                         21                          108
  N3                          1                            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"
D20V6, binary
                              cls
clus                            0  1
  AMP PEAK 20(12Q15) MUTATED   18  7
  AMP PEAK 20(12Q15) WILD-TYPE 90 41
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED     18    7
  AMP PEAK 20(12Q15) WILD-TYPE   90   41
    clus
vv   AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  M0                         18                           90
  MX                          7                           41
[1] 2 2
[1] FALSE
D20V7, binary
                              cls
clus                             0   1
  AMP PEAK 20(12Q15) MUTATED    25  56
  AMP PEAK 20(12Q15) WILD-TYPE  96 240
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED     25   56
  AMP PEAK 20(12Q15) WILD-TYPE   96  240
        clus
vv       AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  FEMALE                         25                           96
  MALE                           56                          240
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(12Q15) MUTATED                                      81
  AMP PEAK 20(12Q15) WILD-TYPE                                   329
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 20(12Q15) MUTATED                                                             0
  AMP PEAK 20(12Q15) WILD-TYPE                                                           1
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 20(12Q15) MUTATED                                                     0
  AMP PEAK 20(12Q15) WILD-TYPE                                                   6
D20V8, multiclass
                                                             clus
vv                                                            AMP PEAK 20(12Q15) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               81
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  0
                                                             clus
vv                                                            AMP PEAK 20(12Q15) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                329
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                              cls
clus                             0   1
  AMP PEAK 20(12Q15) MUTATED    19  62
  AMP PEAK 20(12Q15) WILD-TYPE  60 276
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED     19   62
  AMP PEAK 20(12Q15) WILD-TYPE   60  276
     clus
vv    AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  NO                          19                           60
  YES                         62                          276
[1] 2 2
[1] FALSE
D20V10, continuous
D20V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(12Q15) MUTATED                                  1     2
  AMP PEAK 20(12Q15) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(12Q15) MUTATED                           6    69
  AMP PEAK 20(12Q15) WILD-TYPE                        27   292
D20V12, multiclass
                                  clus
vv                                 AMP PEAK 20(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 6
  WHITE                                                    69
                                  clus
vv                                 AMP PEAK 20(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     292
[1] 4 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(12Q15) MUTATED     2  74
  AMP PEAK 20(12Q15) WILD-TYPE  16 307
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED      2   74
  AMP PEAK 20(12Q15) WILD-TYPE   16  307
                        clus
vv                       AMP PEAK 20(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         74
                        clus
vv                       AMP PEAK 20(12Q15) WILD-TYPE
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          307
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(13Q22.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(13Q22.1) MUTATED    47  25
  AMP PEAK 21(13Q22.1) WILD-TYPE 210  73
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                            72                            283 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                            25                             73 
$`AMP PEAK 21(13Q22.1) MUTATED`
TCGA-BA-4075 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BB-4224 TCGA-BB-4225 
         283          451           63          895          278          140 
TCGA-BB-4227 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4737 
         133          142          613          392          395          240 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6989 
         811         1268         1988         1975          433          611 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         432          429          447          526          484          348 
TCGA-CN-A63Y TCGA-CQ-6227 TCGA-CQ-7065 TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-6472 
         175         1959         1007          303          358         1050 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
         354          379         1191         1440         1960          105 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5440 
         759           30          907         1955          522         1978 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
        1665         1970         3837         1970         1970         1959 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7424 
        1945         1987          954         1967         1099         1947 
TCGA-CV-7440 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 
        1981          828          701          128          112         1778 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50J 
         516          548         1965          622          299          585 
TCGA-HD-7753 TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A6T4 TCGA-QK-A6IH 
           5          360           14           34         1968          228 

$`AMP PEAK 21(13Q22.1) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1747          190          644          384          113          236 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          187         2878 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4730 
           4          799          721          485          452          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5355 
         993          642          369         1960         1330          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         512          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966          413          290          630          424 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         629          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
        1970          202          424          224          318          394 
TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A641 TCGA-CQ-5323 
         119           46          443          225          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7067 
         985         1959          815         1461         1378          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
        1963          545          548          393          391          608 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1966         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         311          345          234          350          479         1956 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
        1435         1245         1979          889          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         392          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
        1950         3295         1438          584          546         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
        2641         1478         1840          215         1315          641 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1899         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1948         1969         1966         1957         1969         1959 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1936         1939         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 
        1095          797         1960         1976         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1984         1958         1959          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          321          237 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         773          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 
         106          104         1081         1030          575          775 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         658           15           92            3          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          407           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         403            2           25           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          210 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         392           56          111          112          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         1120         1954          578         1917 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
         400          553          357          245          218          225 
TCGA-QK-A6IJ 
          64 

  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                             5                              2 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                          3837                           3835 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                           598                            638 
[1] "5.0 - 3837.0 (598.0)" "2.0 - 3835.0 (638.0)"
[1] "hr=" "1.1"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 21(13Q22.1) MUTATED         3       13        15        41         2
  AMP PEAK 21(13Q22.1) WILD-TYPE      21       50        56       151         7
D21V3, multiclass
           clus
vv          AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  STAGE I                              3                             21
  STAGE II                            13                             50
  STAGE III                           15                             56
  STAGE IVA                           41                            151
  STAGE IVB                            2                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 21(13Q22.1) MUTATED     5  20  22  28
  AMP PEAK 21(13Q22.1) WILD-TYPE  35  88  63 103
D21V4, multiclass
    clus
vv   AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  T1                            5                             35
  T2                           20                             88
  T3                           22                             63
  T4                           28                            103
[1] 4 2
[1] TRUE
[1] "dimension 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(13Q22.1) MUTATED    26  10  30   0
  AMP PEAK 21(13Q22.1) WILD-TYPE 110  46  99   7
D21V5, multiclass
    clus
vv   AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  N0                           26                            110
  N1                           10                             46
  N2                           30                             99
  N3                            0                              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"
D21V6, binary
                                cls
clus                              0  1
  AMP PEAK 21(13Q22.1) MUTATED   19 10
  AMP PEAK 21(13Q22.1) WILD-TYPE 89 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED     19   10
  AMP PEAK 21(13Q22.1) WILD-TYPE   89   38
    clus
vv   AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  M0                           19                             89
  MX                           10                             38
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(13Q22.1) MUTATED    23  67
  AMP PEAK 21(13Q22.1) WILD-TYPE  98 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED     23   67
  AMP PEAK 21(13Q22.1) WILD-TYPE   98  229
        clus
vv       AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  FEMALE                           23                             98
  MALE                             67                            229
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(13Q22.1) MUTATED                                      90
  AMP PEAK 21(13Q22.1) WILD-TYPE                                   320
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 21(13Q22.1) MUTATED                                                             0
  AMP PEAK 21(13Q22.1) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 21(13Q22.1) MUTATED                                                     0
  AMP PEAK 21(13Q22.1) WILD-TYPE                                                   6
D21V8, multiclass
                                                             clus
vv                                                            AMP PEAK 21(13Q22.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 90
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            AMP PEAK 21(13Q22.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  320
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                                cls
clus                               0   1
  AMP PEAK 21(13Q22.1) MUTATED    22  68
  AMP PEAK 21(13Q22.1) WILD-TYPE  57 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED     22   68
  AMP PEAK 21(13Q22.1) WILD-TYPE   57  270
     clus
vv    AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  NO                            22                             57
  YES                           68                            270
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(13Q22.1) MUTATED                                  1     4
  AMP PEAK 21(13Q22.1) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(13Q22.1) MUTATED                           7    75
  AMP PEAK 21(13Q22.1) WILD-TYPE                        26   286
D21V12, multiclass
                                  clus
vv                                 AMP PEAK 21(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      75
                                  clus
vv                                 AMP PEAK 21(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                                cls
clus                               0   1
  AMP PEAK 21(13Q22.1) MUTATED     6  79
  AMP PEAK 21(13Q22.1) WILD-TYPE  12 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED      6   79
  AMP PEAK 21(13Q22.1) WILD-TYPE   12  302
                        clus
vv                       AMP PEAK 21(13Q22.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       AMP PEAK 21(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            302
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(13Q34) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(13Q34) MUTATED    45  22
  AMP PEAK 22(13Q34) WILD-TYPE 212  76
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                          67                          288 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                          22                           76 
$`AMP PEAK 22(13Q34) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BB-4224 TCGA-BB-4225 
         283         1747          451          895          278          140 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5358 
         142          613          392          240         1988          173 
TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6997 
        1975          433           98          611          432          429 
TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5329 TCGA-CQ-6228 
         447          484          348          175         1422         1959 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
        1960          613         1963          303          608          358 
TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 
        1663         1777          354          379         1191         1440 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7392 TCGA-CV-5431 
         105          759         1951          907          946          522 
TCGA-CV-5440 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 
        1978          519         1665         1959         3837         1970 
TCGA-CV-7097 TCGA-CV-7243 TCGA-CV-7424 TCGA-CV-7440 TCGA-CX-7219 TCGA-D6-6517 
        1970          954         1947         1981          828          292 
TCGA-D6-6823 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J 
         701          128          516          548         1965          585 
TCGA-HD-8314 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A6T4 
          44          485          360           14           34         1968 
TCGA-QK-A6IH 
         228 

$`AMP PEAK 22(13Q34) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         190          644           63          384          113          236 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          187         2878 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         638         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 
           5            4          799          721          485          452 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         462          993          642          369          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 
        1330          811         1268          488          512         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 
        1081         1977         1980         1966         1966          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 
         290          630          424          629          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
          45          432         1970          202          424          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T 
         318          394          119           46          443          225 
TCGA-CN-A63U TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         526          367         1466         1207          654         1660 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
        1000         1057          985         1959          815         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1378         1007          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 
         968          545          548          393          391         2562 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 
         234          350          479         1956         1435         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1960         1979          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
        1036          796         1954          997         1430          392 
TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         913          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
         181         1077          911         1472         1955         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
        3295         1438          584          546         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958         2437          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840          215         1315          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7099 
        1969         1966         1957         1969         1959         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444         1095          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 
        1099         1974         1948         1955         1957         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 
         317          321          237          773           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 
         154          568          106          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1081         1030          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         658           15           92            3          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          407           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         403            2            5           25           37           55 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H 
          33         1057          122          441          588          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A67A 
         440          351          360          224          210          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          56          111          112          254          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
         721         1120         1954          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          218          225           64 

  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                          14                            2 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                        3837                         3835 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                       585.0                        641.5 
[1] "14.0 - 3837.0 (585.0)" "2.0 - 3835.0 (641.5)" 
[1] "hr=" "1.2"
D22V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 22(13Q34) MUTATED         2       16        19        33         2
  AMP PEAK 22(13Q34) WILD-TYPE      22       47        52       159         7
D22V3, multiclass
           clus
vv          AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  STAGE I                            2                           22
  STAGE II                          16                           47
  STAGE III                         19                           52
  STAGE IVA                         33                          159
  STAGE IVB                          2                            7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 22(13Q34) MUTATED     5  25  21  21
  AMP PEAK 22(13Q34) WILD-TYPE  35  83  64 110
D22V4, multiclass
    clus
vv   AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  T1                          5                           35
  T2                         25                           83
  T3                         21                           64
  T4                         21                          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                            N0  N1  N2  N3
  AMP PEAK 22(13Q34) MUTATED    24  16  25   0
  AMP PEAK 22(13Q34) WILD-TYPE 112  40 104   7
D22V5, multiclass
    clus
vv   AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  N0                         24                          112
  N1                         16                           40
  N2                         25                          104
  N3                          0                            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"
D22V6, binary
                              cls
clus                            0  1
  AMP PEAK 22(13Q34) MUTATED   21 10
  AMP PEAK 22(13Q34) WILD-TYPE 87 38
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED     21   10
  AMP PEAK 22(13Q34) WILD-TYPE   87   38
    clus
vv   AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  M0                         21                           87
  MX                         10                           38
[1] 2 2
[1] FALSE
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(13Q34) MUTATED    20  64
  AMP PEAK 22(13Q34) WILD-TYPE 101 232
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED     20   64
  AMP PEAK 22(13Q34) WILD-TYPE  101  232
        clus
vv       AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  FEMALE                         20                          101
  MALE                           64                          232
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(13Q34) MUTATED                                      82
  AMP PEAK 22(13Q34) WILD-TYPE                                   328
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 22(13Q34) MUTATED                                                             0
  AMP PEAK 22(13Q34) WILD-TYPE                                                           1
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 22(13Q34) MUTATED                                                     2
  AMP PEAK 22(13Q34) WILD-TYPE                                                   4
D22V8, multiclass
                                                             clus
vv                                                            AMP PEAK 22(13Q34) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               82
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  2
                                                             clus
vv                                                            AMP PEAK 22(13Q34) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                328
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                              cls
clus                             0   1
  AMP PEAK 22(13Q34) MUTATED    19  65
  AMP PEAK 22(13Q34) WILD-TYPE  60 273
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED     19   65
  AMP PEAK 22(13Q34) WILD-TYPE   60  273
     clus
vv    AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  NO                          19                           60
  YES                         65                          273
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(13Q34) MUTATED                                  0     3
  AMP PEAK 22(13Q34) WILD-TYPE                                1     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(13Q34) MUTATED                           5    71
  AMP PEAK 22(13Q34) WILD-TYPE                        28   290
D22V12, multiclass
                                  clus
vv                                 AMP PEAK 22(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 5
  WHITE                                                    71
                                  clus
vv                                 AMP PEAK 22(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     290
[1] 4 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(13Q34) MUTATED     5  76
  AMP PEAK 22(13Q34) WILD-TYPE  13 305
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED      5   76
  AMP PEAK 22(13Q34) WILD-TYPE   13  305
                        clus
vv                       AMP PEAK 22(13Q34) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         76
                        clus
vv                       AMP PEAK 22(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          305
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(15Q26.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(15Q26.3) MUTATED    48  23
  AMP PEAK 23(15Q26.3) WILD-TYPE 209  75
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                            71                            284 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                            23                             75 
$`AMP PEAK 23(15Q26.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A6D8 
         283         1983          451           63          113          513 
TCGA-BB-7861 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 
         310         1955            5          613          392          240 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 
        1330          811          512         1980         1980         1966 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6022 TCGA-CN-6992 TCGA-CQ-6228 TCGA-CQ-7067 
         630          433          202          394         1959          509 
TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 
         901          613          608          358         1971          514 
TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 
         354          350         1435         1191          105           30 
TCGA-CR-7379 TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-7090 TCGA-CV-7101 
        1036          907         1665         1948         3837         1939 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7424 
        1724         1095         1976         1099         1955         1947 
TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-A6JD TCGA-D6-6516 TCGA-D6-8569 TCGA-DQ-5629 
        1937         1984         1970          773          128          516 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-7848 TCGA-H7-8501 TCGA-HD-7753 
         548         1965          575          564           58            5 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7632 
          37           55           49          111           33          441 
TCGA-IQ-A61H TCGA-MT-A67A TCGA-MT-A67G TCGA-P3-A5QA TCGA-QK-A6IH 
         412          392          112         1652          228 

$`AMP PEAK 23(15Q26.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415          276          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA 
         190          644          384          236          895          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
        1153          428          436          624            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 
         721          485          142          452          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
         642          369          395         1960         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5370 
         488          173         1081         1977         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 
         413          290          424          629          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
          45          432           98         1970          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         318          611          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         443          447          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
         870         1000         1057          985         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1461         1378         1007         1309          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1960         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         303         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 
        1521         1966         1050         1125         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
         311          345          234          379          479         1956 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960         1979          759          889 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1968          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1951          392          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840          215         1315          641         1899         1970 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1966         1957         1969         1959         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1945         1987         1979 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 
        1444          954          797         1967         1960         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
        1948         1957         1973         1972         1937         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JE 
        1959         1981          851         1945         1954          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 
         717          317          321          237          828          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 
         112          104         1778         1081         1030          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 
         384           14           13            6          407          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 
         414          403            2           25           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          25           11           10         1057          485          122 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         588          360          440          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 
         210           14           34           56          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910          721         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                             5                              2 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                          3837                           3835 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                           564                            643 
[1] "5.0 - 3837.0 (564.0)" "2.0 - 3835.0 (643.0)"
[1] "hr=" "1.2"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 23(15Q26.3) MUTATED         5       13        13        43         3
  AMP PEAK 23(15Q26.3) WILD-TYPE      19       50        58       149         6
D23V3, multiclass
           clus
vv          AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  STAGE I                              5                             19
  STAGE II                            13                             50
  STAGE III                           13                             58
  STAGE IVA                           43                            149
  STAGE IVB                            3                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 23(15Q26.3) MUTATED    8 22 12 35
  AMP PEAK 23(15Q26.3) WILD-TYPE 32 86 73 96
D23V4, multiclass
    clus
vv   AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  T1                            8                             32
  T2                           22                             86
  T3                           12                             73
  T4                           35                             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                              N0  N1  N2  N3
  AMP PEAK 23(15Q26.3) MUTATED    28  12  25   1
  AMP PEAK 23(15Q26.3) WILD-TYPE 108  44 104   6
D23V5, multiclass
    clus
vv   AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  N0                           28                            108
  N1                           12                             44
  N2                           25                            104
  N3                            1                              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"
D23V6, binary
                                cls
clus                              0  1
  AMP PEAK 23(15Q26.3) MUTATED   23 11
  AMP PEAK 23(15Q26.3) WILD-TYPE 85 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED     23   11
  AMP PEAK 23(15Q26.3) WILD-TYPE   85   37
    clus
vv   AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  M0                           23                             85
  MX                           11                             37
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(15Q26.3) MUTATED    28  61
  AMP PEAK 23(15Q26.3) WILD-TYPE  93 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED     28   61
  AMP PEAK 23(15Q26.3) WILD-TYPE   93  235
        clus
vv       AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  FEMALE                           28                             93
  MALE                             61                            235
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(15Q26.3) MUTATED                                      88
  AMP PEAK 23(15Q26.3) WILD-TYPE                                   322
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 23(15Q26.3) MUTATED                                                             0
  AMP PEAK 23(15Q26.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 23(15Q26.3) MUTATED                                                     1
  AMP PEAK 23(15Q26.3) WILD-TYPE                                                   5
D23V8, multiclass
                                                             clus
vv                                                            AMP PEAK 23(15Q26.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 88
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
                                                             clus
vv                                                            AMP PEAK 23(15Q26.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  322
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                                cls
clus                               0   1
  AMP PEAK 23(15Q26.3) MUTATED    17  72
  AMP PEAK 23(15Q26.3) WILD-TYPE  62 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED     17   72
  AMP PEAK 23(15Q26.3) WILD-TYPE   62  266
     clus
vv    AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  NO                            17                             62
  YES                           72                            266
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(15Q26.3) MUTATED                                  0     3
  AMP PEAK 23(15Q26.3) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(15Q26.3) MUTATED                           7    74
  AMP PEAK 23(15Q26.3) WILD-TYPE                        26   287
D23V12, multiclass
                                  clus
vv                                 AMP PEAK 23(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      74
                                  clus
vv                                 AMP PEAK 23(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       287
[1] 4 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(15Q26.3) MUTATED     4  79
  AMP PEAK 23(15Q26.3) WILD-TYPE  14 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED      4   79
  AMP PEAK 23(15Q26.3) WILD-TYPE   14  302
                        clus
vv                       AMP PEAK 23(15Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       AMP PEAK 23(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            302
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(17Q12) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(17Q12) MUTATED    39  17
  AMP PEAK 24(17Q12) WILD-TYPE 218  81
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          56                          299 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          17                           81 
$`AMP PEAK 24(17Q12) MUTATED`
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-8601 
         384          236          895          140          133          624 
TCGA-C9-A47Z TCGA-CN-5356 TCGA-CN-5366 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
           5          512         1966          424          318          611 
TCGA-CN-6994 TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-A4C9 
         119          526          348         1959          901          613 
TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-7365 
         393          358         1777         1969          379         1191 
TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
         105         1954          907          181         1955          522 
TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6941 
        1950         1978          406         1840         1665         1959 
TCGA-CV-6945 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1969         1939         1945         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7424 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
        1099         1947          128          516         1965          575 
TCGA-F7-8298 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-IQ-A61O 
         490            5           37          111          351          360 
TCGA-MT-A67D TCGA-QK-A6IG 
          56          218 

$`AMP PEAK 24(17Q12) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6873 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         113          513          351          216          182          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        2878          278          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1988          488          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1980         1966         1975          413          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         424          629          433          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
         432           98         1970          202          224          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         484          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877          968         1960         1963          545          548 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
         799         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
         514          362          311          345          354          234 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
         350          479         1956         1435         1440         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1960         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968         1036          796          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         392          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5434 
         216          156         1077          911         1472         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
        1438          584          546         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
        2437          519          701         2641         1478          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1315          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1952         3835         1948         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1959         1987         1979         1724         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
         954          797         1974         1948         1955         1957 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         568          106          112          104         1778         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1030          548          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          340          564          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
           2           25           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          11           49           10           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         224          210           14           34          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          228          225           64 

  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                           5                            2 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                        1978                         3837 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                       550.5                        641.0 
[1] "5.0 - 1978.0 (550.5)" "2.0 - 3837.0 (641.0)"
[1] "hr=" "1.4"
D24V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 24(17Q12) MUTATED         3        9        15        31         0
  AMP PEAK 24(17Q12) WILD-TYPE      21       54        56       161         9
D24V3, multiclass
           clus
vv          AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  STAGE I                            3                           21
  STAGE II                           9                           54
  STAGE III                         15                           56
  STAGE IVA                         31                          161
  STAGE IVB                          0                            9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 24(17Q12) MUTATED     4  18  17  19
  AMP PEAK 24(17Q12) WILD-TYPE  36  90  68 112
D24V4, multiclass
    clus
vv   AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  T1                          4                           36
  T2                         18                           90
  T3                         17                           68
  T4                         19                          112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 24(17Q12) MUTATED    21  10  24   0
  AMP PEAK 24(17Q12) WILD-TYPE 115  46 105   7
D24V5, multiclass
    clus
vv   AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  N0                         21                          115
  N1                         10                           46
  N2                         24                          105
  N3                          0                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                              cls
clus                            0  1
  AMP PEAK 24(17Q12) MUTATED   16  7
  AMP PEAK 24(17Q12) WILD-TYPE 92 41
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED     16    7
  AMP PEAK 24(17Q12) WILD-TYPE   92   41
    clus
vv   AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  M0                         16                           92
  MX                          7                           41
[1] 2 2
[1] FALSE
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(17Q12) MUTATED    16  52
  AMP PEAK 24(17Q12) WILD-TYPE 105 244
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED     16   52
  AMP PEAK 24(17Q12) WILD-TYPE  105  244
        clus
vv       AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  FEMALE                         16                          105
  MALE                           52                          244
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(17Q12) MUTATED                                      67
  AMP PEAK 24(17Q12) WILD-TYPE                                   343
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 24(17Q12) MUTATED                                                             1
  AMP PEAK 24(17Q12) WILD-TYPE                                                           0
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 24(17Q12) MUTATED                                                     0
  AMP PEAK 24(17Q12) WILD-TYPE                                                   6
D24V8, multiclass
                                                             clus
vv                                                            AMP PEAK 24(17Q12) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               67
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  0
                                                             clus
vv                                                            AMP PEAK 24(17Q12) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                343
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                              cls
clus                             0   1
  AMP PEAK 24(17Q12) MUTATED    12  56
  AMP PEAK 24(17Q12) WILD-TYPE  67 282
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED     12   56
  AMP PEAK 24(17Q12) WILD-TYPE   67  282
     clus
vv    AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  NO                          12                           67
  YES                         56                          282
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(17Q12) MUTATED                                  0     2
  AMP PEAK 24(17Q12) WILD-TYPE                                1     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(17Q12) MUTATED                           4    60
  AMP PEAK 24(17Q12) WILD-TYPE                        29   301
D24V12, multiclass
                                  clus
vv                                 AMP PEAK 24(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 4
  WHITE                                                    60
                                  clus
vv                                 AMP PEAK 24(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  29
  WHITE                                                     301
[1] 4 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(17Q12) MUTATED     6  60
  AMP PEAK 24(17Q12) WILD-TYPE  12 321
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED      6   60
  AMP PEAK 24(17Q12) WILD-TYPE   12  321
                        clus
vv                       AMP PEAK 24(17Q12) MUTATED
  HISPANIC OR LATINO                              6
  NOT HISPANIC OR LATINO                         60
                        clus
vv                       AMP PEAK 24(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          321
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(18P11.31) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(18P11.31) MUTATED    70  33
  AMP PEAK 25(18P11.31) WILD-TYPE 187  65
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                            103                             252 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                             33                              65 
$`AMP PEAK 25(18P11.31) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 
         283          415          722          520         1636         1747 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4223 TCGA-BB-4224 
         644           63          384          113         2878          278 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-8601 
         140          558          310          536         1153          624 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
           5          485          452          613          392          462 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6012 
         395          240         1977         1966         1966          629 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-A63T TCGA-CN-A63U 
          98          202          224          318          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-7067 TCGA-CQ-A4C9 
         348          367          317         1959          509          613 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6482 
         391          358         1777         1971         1969          345 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7390 
        1956         1435         1191          105          759          907 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
         181         1077          911         1472         1950         3295 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5977 
         546         1978         2886          519         2641         1840 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 
        1315          641         1970         1969         1959         1969 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 
        1939         1945         1987         1724          954          797 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 
        1955         1957         1958         1959         1981         1954 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5631 TCGA-DQ-7588 
         237          701          106          128          548         1965 
TCGA-DQ-7590 TCGA-DQ-7595 TCGA-F7-8298 TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C5 
         775          324          490            6          133          403 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-KU-A66S 
          25           44           10          111          360          224 
TCGA-KU-A66T 
         210 

$`AMP PEAK 25(18P11.31) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 
         462         1983          276          248         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A4IF 
         725          623          190          451          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4227 
         513          351          216          182          187          133 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4731 TCGA-CN-4733 
           4          799          721          142          993          642 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         369         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
         488          512          173         1980         1081         1980 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1975          413          290          630          424          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
         594          629           45          432         1970          424 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         443          447          484          175         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
         129          870         1000         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
         815         1461         1378         1007         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877          968         1960         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         393          303          608         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
         799         1521         1966         1050         1125          514 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          311          354          234          379          350 
TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 
         479         1440         1245         1960         1979          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 
         908          898          930          216          156         1955 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         522         1438          584         2327         1958         2437 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6436 
         406          701         1478          215         1665         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1948         1952         3835         1948         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 
        1936         1959         1979         1444         1095         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7424 
        1960         1976         1099         1974         1948         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A45O 
        1937         1973         1972         1937         1984          851 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1945         1970          750          717          317          321 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         828          773          292           77          491          154 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         568          112          104         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1030          575          622          299          369          368 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         340          564          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 
           3          384           14           13          407           58 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 
         414            2            5           37           55           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          25           11           49           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         122          441          588          412          440          351 
TCGA-IQ-A61O TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         360           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225           64 

  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                              5                               2 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                           3295                            3837 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                            613                             640 
[1] "5.0 - 3295.0 (613.0)" "2.0 - 3837.0 (640.0)"
[1] "hr=" "1"  
D25V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 25(18P11.31) MUTATED         4       12        25        60
  AMP PEAK 25(18P11.31) WILD-TYPE      20       51        46       132
                                 vv
clus                              STAGE IVB
  AMP PEAK 25(18P11.31) MUTATED           2
  AMP PEAK 25(18P11.31) WILD-TYPE         7
D25V3, multiclass
           clus
vv          AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  STAGE I                               4                              20
  STAGE II                             12                              51
  STAGE III                            25                              46
  STAGE IVA                            60                             132
  STAGE IVB                             2                               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 25(18P11.31) MUTATED    9 26 33 36
  AMP PEAK 25(18P11.31) WILD-TYPE 31 82 52 95
D25V4, multiclass
    clus
vv   AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  T1                             9                              31
  T2                            26                              82
  T3                            33                              52
  T4                            36                              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                               N0  N1  N2  N3
  AMP PEAK 25(18P11.31) MUTATED    33  18  43   2
  AMP PEAK 25(18P11.31) WILD-TYPE 103  38  86   5
D25V5, multiclass
    clus
vv   AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  N0                            33                             103
  N1                            18                              38
  N2                            43                              86
  N3                             2                               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"
D25V6, binary
                                 cls
clus                               0  1
  AMP PEAK 25(18P11.31) MUTATED   22 15
  AMP PEAK 25(18P11.31) WILD-TYPE 86 33
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED     22   15
  AMP PEAK 25(18P11.31) WILD-TYPE   86   33
    clus
vv   AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  M0                            22                              86
  MX                            15                              33
[1] 2 2
[1] FALSE
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(18P11.31) MUTATED    20 102
  AMP PEAK 25(18P11.31) WILD-TYPE 101 194
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED     20  102
  AMP PEAK 25(18P11.31) WILD-TYPE  101  194
        clus
vv       AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  FEMALE                            20                             101
  MALE                             102                             194
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(18P11.31) MUTATED                                     120
  AMP PEAK 25(18P11.31) WILD-TYPE                                   290
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 25(18P11.31) MUTATED                                                             0
  AMP PEAK 25(18P11.31) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 25(18P11.31) MUTATED                                                     2
  AMP PEAK 25(18P11.31) WILD-TYPE                                                   4
D25V8, multiclass
                                                             clus
vv                                                            AMP PEAK 25(18P11.31) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 120
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     2
                                                             clus
vv                                                            AMP PEAK 25(18P11.31) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   290
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                                 cls
clus                                0   1
  AMP PEAK 25(18P11.31) MUTATED    21 101
  AMP PEAK 25(18P11.31) WILD-TYPE  58 237
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED     21  101
  AMP PEAK 25(18P11.31) WILD-TYPE   58  237
     clus
vv    AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  NO                             21                              58
  YES                           101                             237
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(18P11.31) MUTATED                                  0     1
  AMP PEAK 25(18P11.31) WILD-TYPE                                1     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(18P11.31) MUTATED                          13   105
  AMP PEAK 25(18P11.31) WILD-TYPE                        20   256
D25V12, multiclass
                                  clus
vv                                 AMP PEAK 25(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      105
                                  clus
vv                                 AMP PEAK 25(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                        256
[1] 4 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(18P11.31) MUTATED     5 114
  AMP PEAK 25(18P11.31) WILD-TYPE  13 267
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED      5  114
  AMP PEAK 25(18P11.31) WILD-TYPE   13  267
                        clus
vv                       AMP PEAK 25(18P11.31) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           114
                        clus
vv                       AMP PEAK 25(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             267
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(18Q11.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(18Q11.2) MUTATED    48  20
  AMP PEAK 26(18Q11.2) WILD-TYPE 209  78
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                            68                            287 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                            20                             78 
$`AMP PEAK 26(18Q11.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 
         462          283          415          722          520         1636 
TCGA-BA-5559 TCGA-BA-A4IF TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
        1747          895         2878          278          140          558 
TCGA-BB-7861 TCGA-CN-4723 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5367 
         310          721          462          395          240         1966 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-A63W TCGA-CN-A641 
         629           98          202          224          348          367 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6482 
        1378         1007          509          358         1777          345 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7390 
        1440          105          759           30         1954          907 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
         156          181         1077         1472         1950         3295 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6941 
         546         1978         1840         1315          641         1959 
TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7406 
        1957         3837         1970         1939         1987         1974 
TCGA-CV-7418 TCGA-CV-A461 TCGA-CX-7219 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-HD-7917 
        1955         1954          828          575          775           37 
TCGA-HD-A634 TCGA-IQ-7630 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X 
          10          485          360          224          210           34 
TCGA-QK-A64Z TCGA-QK-A6IG 
         553          218 

$`AMP PEAK 26(18Q11.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
        1983          276          248         1288         1762          725 
TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
         623          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         113          236          513          351          216          182 
TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         187          133          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          799          485          142          452          613 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 
         392          993          642          369         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988          488          512          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 
        1980         1081         1977         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
         413          290          630          424          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 
         629           45          432         1970          424          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         443          447          225          526          484          175 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959          815         1461 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
         608         2562         1663         1152          799         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1966         1050         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          311          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1435         1191         1245         1960 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1979          889          972         1968         1036          796 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7402 TCGA-CV-5430 
         908          898          930          216          911         1955 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         522         1438          584         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
         215         1665         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 
        1952         3835         1948         1969         1966         1969 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1959         1959         1970         1936         1959         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 
        1967         1960         1976         1099         1948         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1947         1937         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD 
        1958         1959         1981          851         1945         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
         750          717          317          321          237          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 
         516         1030          548         1965          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 
         414          403            2            5           25           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
          44           24           25           11           49          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
          33         1057          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         412          440          351           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1652          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          228          225           64 

  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                            10                              2 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                          3837                           3835 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                           602                            629 
[1] "10.0 - 3837.0 (602.0)" "2.0 - 3835.0 (629.0)" 
[1] "hr=" "1"  
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 26(18Q11.2) MUTATED         4       12        10        41         0
  AMP PEAK 26(18Q11.2) WILD-TYPE      20       51        61       151         9
D26V3, multiclass
           clus
vv          AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  STAGE I                              4                             20
  STAGE II                            12                             51
  STAGE III                           10                             61
  STAGE IVA                           41                            151
  STAGE IVB                            0                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 26(18Q11.2) MUTATED     8  23  12  25
  AMP PEAK 26(18Q11.2) WILD-TYPE  32  85  73 106
D26V4, multiclass
    clus
vv   AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  T1                            8                             32
  T2                           23                             85
  T3                           12                             73
  T4                           25                            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                              N0  N1  N2  N3
  AMP PEAK 26(18Q11.2) MUTATED    21   9  27   0
  AMP PEAK 26(18Q11.2) WILD-TYPE 115  47 102   7
D26V5, multiclass
    clus
vv   AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  N0                           21                            115
  N1                            9                             47
  N2                           27                            102
  N3                            0                              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"
D26V6, binary
                                cls
clus                              0  1
  AMP PEAK 26(18Q11.2) MUTATED   16  8
  AMP PEAK 26(18Q11.2) WILD-TYPE 92 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED     16    8
  AMP PEAK 26(18Q11.2) WILD-TYPE   92   40
    clus
vv   AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  M0                           16                             92
  MX                            8                             40
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(18Q11.2) MUTATED    16  66
  AMP PEAK 26(18Q11.2) WILD-TYPE 105 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED     16   66
  AMP PEAK 26(18Q11.2) WILD-TYPE  105  230
        clus
vv       AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  FEMALE                           16                            105
  MALE                             66                            230
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(18Q11.2) MUTATED                                      80
  AMP PEAK 26(18Q11.2) WILD-TYPE                                   330
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 26(18Q11.2) MUTATED                                                             1
  AMP PEAK 26(18Q11.2) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 26(18Q11.2) MUTATED                                                     1
  AMP PEAK 26(18Q11.2) WILD-TYPE                                                   5
D26V8, multiclass
                                                             clus
vv                                                            AMP PEAK 26(18Q11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 80
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
                                                             clus
vv                                                            AMP PEAK 26(18Q11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  330
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                                cls
clus                               0   1
  AMP PEAK 26(18Q11.2) MUTATED    14  68
  AMP PEAK 26(18Q11.2) WILD-TYPE  65 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED     14   68
  AMP PEAK 26(18Q11.2) WILD-TYPE   65  270
     clus
vv    AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  NO                            14                             65
  YES                           68                            270
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(18Q11.2) MUTATED                                  0     1
  AMP PEAK 26(18Q11.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(18Q11.2) MUTATED                          10    70
  AMP PEAK 26(18Q11.2) WILD-TYPE                        23   291
D26V12, multiclass
                                  clus
vv                                 AMP PEAK 26(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      70
                                  clus
vv                                 AMP PEAK 26(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    23
  WHITE                                                       291
[1] 4 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(18Q11.2) MUTATED     3  77
  AMP PEAK 26(18Q11.2) WILD-TYPE  15 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED      3   77
  AMP PEAK 26(18Q11.2) WILD-TYPE   15  304
                        clus
vv                       AMP PEAK 26(18Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       AMP PEAK 26(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            304
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20P12.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(20P12.2) MUTATED    99  32
  AMP PEAK 27(20P12.2) WILD-TYPE 158  66
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           131                            224 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                            32                             66 
$`AMP PEAK 27(20P12.2) MUTATED`
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 
         276          248          722          725         1747          190 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DB TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 
         384          236          216          278          140          310 
TCGA-BB-7862 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
         536          436            5          613          462          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1268         1988          512         1980         1081         1977 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 
        1966          290          629          433           98          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A63T TCGA-CQ-5329 
         424          224          318          611          225         1422 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 
         896         1057          985          815         1378          509 
TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
         901          968         1960          613          545          393 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 
         608         2562          358         1777          354          379 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7389 
        1191         1440          105          759         1968          392 
TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5434 
         946          216          181         1077          522         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1438          584         2327         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6936 
         701         2641         1840          215         1665         1952 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7180 TCGA-CV-7235 
        1969         1957         3837         1970         1987         1724 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7430 TCGA-CV-7435 
        1095          954          797         1967         1972         1959 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6825 
         750          717          317          773          292          491 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-A50J 
         128          104         1778         1965          299          585 
TCGA-F7-A61S TCGA-H7-8501 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 
           3           58           44           10          111          485 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A67A 
         441          588          360          351          210          392 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 
          56          112          254         1652          578         1968 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          225           64 

$`AMP PEAK 27(20P12.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5153 
         462          283          415         1983         1288         1762 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         520          623         1636          644          451           63 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 
         113          895          513          351          182          187 
TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        2878          133          558          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
        1153          428         1955          624            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 
         721          485          142          452          392          369 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
         488          173         1980         1966         1975          413 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         630          424          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
        1970          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         443          447          526          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 
         367         1466         1207          654         1660         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 
         317          341          129          870         1000         1959 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CA 
        1959         1461         1007         1309          877         1963 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         548          391          303         1663         1152          799 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 
        1969          362          311          345          234          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
         479         1956         1435         1245         1960         1979 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         889           30          972         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 
         997         1430         1951          907          913          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         898          930          156          911         1472         1955 
TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5976 
        1950          546         1978         2886         1958         1478 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1315          641         1899         1970         1948         1969 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 
        1959         3835         1948         1966         1969         1959 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         1970         1936         1959         1939         1945 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
        1979         1444         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 
        1954         1970          321          237          828          701 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5625 
          77          154          568          106          112         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030          548          575          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658           15           92          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
           6          407          133          414          403            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 
           5           25           37           55           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61H 
          11           49           33         1057          122          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67F 
         440          360          224           14           34          111 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 
         910          721         1120         1954         1917          400 
TCGA-QK-A64Z TCGA-QK-A6IH 
         553          228 

  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                             3                              2 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                          3837                           3835 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           585                            656 
[1] "3.0 - 3837.0 (585.0)" "2.0 - 3835.0 (656.0)"
[1] "hr=" "1.4"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 27(20P12.2) MUTATED         9       22        31        73         4
  AMP PEAK 27(20P12.2) WILD-TYPE      15       41        40       119         5
D27V3, multiclass
           clus
vv          AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  STAGE I                              9                             15
  STAGE II                            22                             41
  STAGE III                           31                             40
  STAGE IVA                           73                            119
  STAGE IVB                            4                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 27(20P12.2) MUTATED   17 40 32 51
  AMP PEAK 27(20P12.2) WILD-TYPE 23 68 53 80
D27V4, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  T1                           17                             23
  T2                           40                             68
  T3                           32                             53
  T4                           51                             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                             N0 N1 N2 N3
  AMP PEAK 27(20P12.2) MUTATED   47 29 49  3
  AMP PEAK 27(20P12.2) WILD-TYPE 89 27 80  4
D27V5, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  N0                           47                             89
  N1                           29                             27
  N2                           49                             80
  N3                            3                              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(20P12.2) MUTATED   47 15
  AMP PEAK 27(20P12.2) WILD-TYPE 61 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     47   15
  AMP PEAK 27(20P12.2) WILD-TYPE   61   33
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  M0                           47                             61
  MX                           15                             33
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    47 109
  AMP PEAK 27(20P12.2) WILD-TYPE  74 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     47  109
  AMP PEAK 27(20P12.2) WILD-TYPE   74  187
        clus
vv       AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  FEMALE                           47                             74
  MALE                            109                            187
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                     154
  AMP PEAK 27(20P12.2) WILD-TYPE                                   256
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 27(20P12.2) MUTATED                                                             0
  AMP PEAK 27(20P12.2) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 27(20P12.2) MUTATED                                                     2
  AMP PEAK 27(20P12.2) WILD-TYPE                                                   4
D27V8, multiclass
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                154
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    2
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  256
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    33 123
  AMP PEAK 27(20P12.2) WILD-TYPE  46 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     33  123
  AMP PEAK 27(20P12.2) WILD-TYPE   46  215
     clus
vv    AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  NO                            33                             46
  YES                          123                            215
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(20P12.2) MUTATED                                  1     4
  AMP PEAK 27(20P12.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20P12.2) MUTATED                          12   131
  AMP PEAK 27(20P12.2) WILD-TYPE                        21   230
D27V12, multiclass
                                  clus
vv                                 AMP PEAK 27(20P12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     131
                                  clus
vv                                 AMP PEAK 27(20P12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       230
[1] 4 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(20P12.2) MUTATED    10 136
  AMP PEAK 27(20P12.2) WILD-TYPE   8 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     10  136
  AMP PEAK 27(20P12.2) WILD-TYPE    8  245
                        clus
vv                       AMP PEAK 27(20P12.2) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       AMP PEAK 27(20P12.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            245
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(20Q11.22) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 28(20Q11.22) MUTATED   116  36
  AMP PEAK 28(20Q11.22) WILD-TYPE 141  62
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            152                             203 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                             36                              62 
$`AMP PEAK 28(20Q11.22) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5559 
         283          276          248          722          725         1747 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         190          451          384          113          236          895 
TCGA-BA-A6DB TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
         216         2878          278          140          558          310 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4725 
         536          687          638          436            5          485 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
         613          462          993          642          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988          512 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 
        1980         1977         1966          290          424          433 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         202          424          318          611          394          119 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 
         225          526         1422          896         1057          985 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         815         1378          509          901          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 
         613          393          391         2562          358         1777 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6488 
        1125         1971          514         1969          354          379 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 
        1956         1435         1191         1440          105          759 
TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 
         889         1968         1036         1954          392          946 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
         216         1077          911         1955         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
        1438          584         2327         1958         2437          406 
TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6936 
         701         1840          215         1665          641         1952 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7180 
        1969         1957         1969         3837         1970         1987 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-A6JE 
        1095          954          797         1967         1976          750 
TCGA-CV-A6JN TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8569 
         717          237          773          701          491          128 
TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
        1778          548         1965          575          622          299 
TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8501 TCGA-HD-7753 
         490          585            3            6           58            5 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7632 
          37           44           10          111          485          441 
TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         588          351          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 
          56          112         1652          578         1968          357 
TCGA-QK-A6IG TCGA-QK-A6IJ 
         218           64 

$`AMP PEAK 28(20Q11.22) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         462          415         1983         1288         1762          520 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A6D8 TCGA-BA-A6DA 
         623         1636          644           63          513          351 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 
         182          187          133          423         1153          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
        1955          624            4          799          721          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
         452          392          369          488          173         1081 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6012 
        1980         1966         1975          413          630          629 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         594          629           45          432           98         1970 
TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         224          432          429           46          443          447 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 
         870         1000         1959         1959         1461         1007 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
        1309          877         1963          545          548          303 
TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
         608         1663         1152          799         1521         1966 
TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 
        1050          362          311          345          234          350 
TCGA-CR-6492 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 
         479         1245         1960         1979           30          972 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
         796          997         1430         1951          907          913 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 
         908          898          930          156          181         1472 
TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 
         522          546         1978         2886          519         2641 
TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1478         1315         1899         1970         1948         1969 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7091 
        1959         3835         1948         1966         1959         1959 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 
        1970         1936         1959         1939         1945         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1724         1444         1960         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 
        1945         1954         1970          317          321          828 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
         292           77          154          568          106          112 
TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7593 
         104         1081          516         1030          775          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          340          564          658           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8502 
          92          384           14           13          407          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8634 
         414          403            2           25           55           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          25           11           49           33         1057          122 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A67F 
         360          412          440          360          224          111 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
         254          910          721         1120         1954         1917 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          245          228          225 

  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                              3                               2 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                           3837                            3835 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            613                             630 
[1] "3.0 - 3837.0 (613.0)" "2.0 - 3835.0 (630.0)"
[1] "hr=" "1.4"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 28(20Q11.22) MUTATED        14       26        33        80
  AMP PEAK 28(20Q11.22) WILD-TYPE      10       37        38       112
                                 vv
clus                              STAGE IVB
  AMP PEAK 28(20Q11.22) MUTATED           5
  AMP PEAK 28(20Q11.22) WILD-TYPE         4
D28V3, multiclass
           clus
vv          AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  STAGE I                              14                              10
  STAGE II                             26                              37
  STAGE III                            33                              38
  STAGE IVA                            80                             112
  STAGE IVB                             5                               4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 28(20Q11.22) MUTATED   23 44 36 56
  AMP PEAK 28(20Q11.22) WILD-TYPE 17 64 49 75
D28V4, multiclass
    clus
vv   AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  T1                            23                              17
  T2                            44                              64
  T3                            36                              49
  T4                            56                              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                              N0 N1 N2 N3
  AMP PEAK 28(20Q11.22) MUTATED   60 26 54  4
  AMP PEAK 28(20Q11.22) WILD-TYPE 76 30 75  3
D28V5, multiclass
    clus
vv   AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  N0                            60                              76
  N1                            26                              30
  N2                            54                              75
  N3                             4                               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"
D28V6, binary
                                 cls
clus                               0  1
  AMP PEAK 28(20Q11.22) MUTATED   51 17
  AMP PEAK 28(20Q11.22) WILD-TYPE 57 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     51   17
  AMP PEAK 28(20Q11.22) WILD-TYPE   57   31
    clus
vv   AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  M0                            51                              57
  MX                            17                              31
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.22) MUTATED    51 132
  AMP PEAK 28(20Q11.22) WILD-TYPE  70 164
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     51  132
  AMP PEAK 28(20Q11.22) WILD-TYPE   70  164
        clus
vv       AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  FEMALE                            51                              70
  MALE                             132                             164
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.22) MUTATED                                     182
  AMP PEAK 28(20Q11.22) WILD-TYPE                                   228
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 28(20Q11.22) MUTATED                                                             0
  AMP PEAK 28(20Q11.22) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 28(20Q11.22) MUTATED                                                     1
  AMP PEAK 28(20Q11.22) WILD-TYPE                                                   5
D28V8, multiclass
                                                             clus
vv                                                            AMP PEAK 28(20Q11.22) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 182
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
                                                             clus
vv                                                            AMP PEAK 28(20Q11.22) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   228
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.22) MUTATED    39 144
  AMP PEAK 28(20Q11.22) WILD-TYPE  40 194
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     39  144
  AMP PEAK 28(20Q11.22) WILD-TYPE   40  194
     clus
vv    AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  NO                             39                              40
  YES                           144                             194
[1] 2 2
[1] FALSE
D28V10, continuous
D28V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(20Q11.22) MUTATED                                  1     4
  AMP PEAK 28(20Q11.22) WILD-TYPE                                0     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q11.22) MUTATED                          19   151
  AMP PEAK 28(20Q11.22) WILD-TYPE                        14   210
D28V12, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      151
                                  clus
vv                                 AMP PEAK 28(20Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     14
  WHITE                                                        210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.22) MUTATED    10 163
  AMP PEAK 28(20Q11.22) WILD-TYPE   8 218
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     10  163
  AMP PEAK 28(20Q11.22) WILD-TYPE    8  218
                        clus
vv                       AMP PEAK 28(20Q11.22) MUTATED
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           163
                        clus
vv                       AMP PEAK 28(20Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             218
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(XQ28) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 29(XQ28) MUTATED    63  31
  AMP PEAK 29(XQ28) WILD-TYPE 194  67
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         94                         261 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         31                          67 
$`AMP PEAK 29(XQ28) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6872 TCGA-BA-7269 
         283         1983          248         1636          384          236 
TCGA-BA-A6DA TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-8596 TCGA-CN-4725 
         351         2878          140          133         1955          485 
TCGA-CN-4728 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5367 
         613          395          240         1960         1988         1966 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
         630          629          433          424          318          611 
TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63Y TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-6218 
         432          447          175         1660         1422          870 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CG TCGA-CR-5247 
        1959          815          509         1960          391          358 
TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7383 
        1663         1777          514          234         1956         1954 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         907          216          181         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 
        3295         1438          546         2327         2437          406 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-7095 
        1478         1840          641         1969         1952         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 
        1939         1945         1724          954          797         1960 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-A45Q TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-6516 
        1947         1937         1945          750          237          773 
TCGA-D6-6823 TCGA-D6-6827 TCGA-D6-8568 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 
         701          568          106         1081          516          548 
TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50G TCGA-H7-A6C5 TCGA-HD-7754 
        1965          299          564           15          403           25 
TCGA-HD-7917 TCGA-HD-8635 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-KU-A66T 
          37           25           33          485          360          210 
TCGA-MT-A51X TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-P3-A6T4 
          34          254          721         1968 

$`AMP PEAK 29(XQ28) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462          415          276          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         520          725          623         1747          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
         451           63          113          895          513          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         182          187          278          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
         624            5            4          799          721          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         452          392          462          993          642          369 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268          488          512          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 
        1980         1081         1977         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         413          290          424          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
         432           98         1970          202          224          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U 
         119          429           46          443          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         484          348          367         1466         1207          654 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 
         896         1399          317          341          129         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1057          985         1959         1461         1378         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          901          877          968          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         545          548          393          303          608         2562 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971         1969          362          311          345          354 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         379          350          479         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245         1960          105         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
          30          972         1968         1036          796          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         898          930          156         1077          911         1472 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 
         584         1978         2886         1958          519          701 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 
        2641          215         1315         1665         1899         1970 
TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1948         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1936         1959         1987         1979         1444         1095 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
        1957         1937         1973         1972         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN 
        1959         1981          851         1954         1970          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         317          321          828          292           77          491 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 
         154          128          112          104         1778         1030 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         340          490          658           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8314 
         133          414            2            5           55           44 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 
          24           11           49           10          111         1057 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         122          441          588          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         360          224           14          392           56          111 
TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         112          910         1652         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1917          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         15                           2 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                       3295                        3837 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                      629.5                       624.0 
[1] "15.0 - 3295.0 (629.5)" "2.0 - 3837.0 (624.0)" 
[1] "hr=" "1.2"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 29(XQ28) MUTATED         6       16        18        59         2
  AMP PEAK 29(XQ28) WILD-TYPE      18       47        53       133         7
D29V3, multiclass
           clus
vv          AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  STAGE I                           6                          18
  STAGE II                         16                          47
  STAGE III                        18                          53
  STAGE IVA                        59                         133
  STAGE IVB                         2                           7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  AMP PEAK 29(XQ28) MUTATED    9 24 33 36
  AMP PEAK 29(XQ28) WILD-TYPE 31 84 52 95
D29V4, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T1                         9                          31
  T2                        24                          84
  T3                        33                          52
  T4                        36                          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                           N0  N1  N2  N3
  AMP PEAK 29(XQ28) MUTATED    33  15  44   1
  AMP PEAK 29(XQ28) WILD-TYPE 103  41  85   6
D29V5, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  N0                        33                         103
  N1                        15                          41
  N2                        44                          85
  N3                         1                           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"
D29V6, binary
                             cls
clus                           0  1
  AMP PEAK 29(XQ28) MUTATED   21 14
  AMP PEAK 29(XQ28) WILD-TYPE 87 34
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     21   14
  AMP PEAK 29(XQ28) WILD-TYPE   87   34
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  M0                        21                          87
  MX                        14                          34
[1] 2 2
[1] FALSE
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    32  85
  AMP PEAK 29(XQ28) WILD-TYPE  89 211
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     32   85
  AMP PEAK 29(XQ28) WILD-TYPE   89  211
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        32                          89
  MALE                          85                         211
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                     116
  AMP PEAK 29(XQ28) WILD-TYPE                                   294
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 29(XQ28) MUTATED                                                             0
  AMP PEAK 29(XQ28) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 29(XQ28) MUTATED                                                     1
  AMP PEAK 29(XQ28) WILD-TYPE                                                   5
D29V8, multiclass
                                                             clus
vv                                                            AMP PEAK 29(XQ28) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             116
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 1
                                                             clus
vv                                                            AMP PEAK 29(XQ28) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               294
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    29  88
  AMP PEAK 29(XQ28) WILD-TYPE  50 250
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     29   88
  AMP PEAK 29(XQ28) WILD-TYPE   50  250
     clus
vv    AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  NO                         29                          50
  YES                        88                         250
[1] 2 2
[1] FALSE
D29V10, continuous
D29V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 29(XQ28) MUTATED                                  1     2
  AMP PEAK 29(XQ28) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(XQ28) MUTATED                           7   105
  AMP PEAK 29(XQ28) WILD-TYPE                        26   256
D29V12, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                  105
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    256
[1] 4 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(XQ28) MUTATED     7 109
  AMP PEAK 29(XQ28) WILD-TYPE  11 272
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      7  109
  AMP PEAK 29(XQ28) WILD-TYPE   11  272
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             7                          11
  NOT HISPANIC OR LATINO                       109                         272
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  1(1P36.21) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.21) MUTATED    44  27
  DEL PEAK  1(1P36.21) WILD-TYPE 213  71
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            71                            284 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            27                             71 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         462          283          276          190          451           63 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8601 
         236          513          558          536          428          624 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
         488          512         1081          629           45          432 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
        1970          224          611          394          119          429 
TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
         225          317         1000         1959          613          608 
TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 
        1521         1050          354         1191          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         759          889           30         1950         3295         1438 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-7095 
         546         1978          215         1665         1969         1970 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 
        1970         1939         1976         1099         1974         1955 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7440 TCGA-CV-A6JE TCGA-D6-6516 TCGA-DQ-5629 
        1947         1972         1981          750          773          516 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-8489 TCGA-HD-8314 TCGA-HD-8634 
         575          622          299          658           44           24 
TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W 
         111          360          351          224           14 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         415         1983          248          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
         520          725          623         1636         1747          644 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         384          113          895          351          216          182 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 
         187         2878          278          140          133          310 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638         1153          436         1955 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
        1268         1988          173         1980         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          413          290          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 
         424          433          594          629           98          202 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         424          318          432           46          443          447 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         526          484          348          175          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         341          129          870         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         901          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 
         548          393          391          303         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 
        1663         1152          799         1777         1966         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1440         1245         1960          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
        1955          522          584         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1840         1315          641         1899         1970         1948 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 
        1957         1969         1959         3837         1959         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1945         1987         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7410 
        1095          954          797         1967         1960         1948 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1957         1937         1973         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN 
        1959          851         1945         1954         1970          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
         317          321          237          828          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         112          104         1778         1081         1030          548 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
        1965          775          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         564          490           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          403            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          37           55           25           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67A 
         412          440          360          210           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          56          111          112          254          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         721         1120         1954          578         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
         400          553          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            14                              2 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          3295                           3837 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                           575                            649 
[1] "14.0 - 3295.0 (575.0)" "2.0 - 3837.0 (649.0)" 
[1] "hr=" "1.4"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.21) MUTATED         4        9        17        31         3
  DEL PEAK  1(1P36.21) WILD-TYPE      20       54        54       161         6
D30V3, multiclass
           clus
vv          DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  STAGE I                              4                             20
  STAGE II                             9                             54
  STAGE III                           17                             54
  STAGE IVA                           31                            161
  STAGE IVB                            3                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.21) MUTATED     7  16  19  23
  DEL PEAK  1(1P36.21) WILD-TYPE  33  92  66 108
D30V4, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  T1                            7                             33
  T2                           16                             92
  T3                           19                             66
  T4                           23                            108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.21) MUTATED    22  11  21   2
  DEL PEAK  1(1P36.21) WILD-TYPE 114  45 108   5
D30V5, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  N0                           22                            114
  N1                           11                             45
  N2                           21                            108
  N3                            2                              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
  DEL PEAK  1(1P36.21) MUTATED   16  6
  DEL PEAK  1(1P36.21) WILD-TYPE 92 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     16    6
  DEL PEAK  1(1P36.21) WILD-TYPE   92   42
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  M0                           16                             92
  MX                            6                             42
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    19  59
  DEL PEAK  1(1P36.21) WILD-TYPE 102 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     19   59
  DEL PEAK  1(1P36.21) WILD-TYPE  102  237
        clus
vv       DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           19                            102
  MALE                             59                            237
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                      75
  DEL PEAK  1(1P36.21) WILD-TYPE                                   335
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  1(1P36.21) MUTATED                                                             0
  DEL PEAK  1(1P36.21) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  1(1P36.21) MUTATED                                                     3
  DEL PEAK  1(1P36.21) WILD-TYPE                                                   3
D30V8, multiclass
                                                             clus
vv                                                            DEL PEAK  1(1P36.21) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 75
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            DEL PEAK  1(1P36.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  335
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    22  56
  DEL PEAK  1(1P36.21) WILD-TYPE  57 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     22   56
  DEL PEAK  1(1P36.21) WILD-TYPE   57  282
     clus
vv    DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  NO                            22                             57
  YES                           56                            282
[1] 2 2
[1] FALSE
D30V10, continuous
D30V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.21) MUTATED                                  1     2
  DEL PEAK  1(1P36.21) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.21) MUTATED                           9    64
  DEL PEAK  1(1P36.21) WILD-TYPE                        24   297
D30V12, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      64
                                  clus
vv                                 DEL PEAK  1(1P36.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       297
[1] 4 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
  DEL PEAK  1(1P36.21) MUTATED     4  71
  DEL PEAK  1(1P36.21) WILD-TYPE  14 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED      4   71
  DEL PEAK  1(1P36.21) WILD-TYPE   14  310
                        clus
vv                       DEL PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           71
                        clus
vv                       DEL PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            310
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    58  30
  DEL PEAK  2(1P13.2) WILD-TYPE 199  68
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           88                           267 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           30                            68 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 
         283          415         1288          451           63          236 
TCGA-BA-A6DE TCGA-BB-7862 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4729 
         182          536          624            5          721          392 
TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-6010 
         993          240          488         1980         1081          630 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
         629           45         1970          202          224          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5332 
         119          429           46          225          348          317 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CI TCGA-CR-6478 TCGA-CR-6481 
        1378          509         1963          608         1969          311 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7399 
        1191          105         1979          759           30          181 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1955         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
        1978         2437         2641         1840          215         1665 
TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-7091 TCGA-CV-7095 
         641         1969         1952         1959         1959         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7254 
        1939         1945         1987         1095          797         1976 
TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A461 TCGA-CX-7082 
        1099         1955         1947         1959         1954          317 
TCGA-D6-6516 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S 
         773          104          516          658           92            3 
TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-IQ-A61H 
           6            5           44           24           25          412 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-P3-A5QE TCGA-P3-A6T8 
         351          210          721          400 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         462         1983          276          248          722         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
         520          725          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
         644          384          113          895          513          351 
TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         216          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         558          310          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
         428          436         1955            4          799          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 
         142          452          613          462          642          369 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         395         1960         1330          811         1268         1988 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         512          173         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        1975          413          290          424          433          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
         629          432           98          424          318          611 
TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         432          443          447          526          484          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
         896         1399          341          129          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
         613          545          548          393          391          303 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1435         1440         1245         1960 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         889          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         997         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5441 TCGA-CV-5442 
        1077          911         1472          522         2886         2327 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 
        1958          519          406          701         1478         1315 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1899         1970         1948         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1966         1957         1969         1959         3837         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 
        1936         1959         1979         1724         1444          954 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 
        1967         1960         1974         1948         1957         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1973         1972         1937         1984         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 
         851         1945         1970          750          717          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          828          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 
         154          568          106          128          112         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
        1081         1030          548         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
         564          490           15          585          384           14 
TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          13          407           58          133          414          403 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 
           2           25           37           55           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          10          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         441          588          360          440          360          224 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
          14           34          392           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         254          910         1652         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1917         1968          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            3                             2 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         3295                          3837 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          616                           638 
[1] "3.0 - 3295.0 (616.0)" "2.0 - 3837.0 (638.0)"
[1] "hr=" "1.1"
D31V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  2(1P13.2) MUTATED         6       13        20        51         2
  DEL PEAK  2(1P13.2) WILD-TYPE      18       50        51       141         7
D31V3, multiclass
           clus
vv          DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                             6                            18
  STAGE II                           13                            50
  STAGE III                          20                            51
  STAGE IVA                          51                           141
  STAGE IVB                           2                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  2(1P13.2) MUTATED    9 24 25 34
  DEL PEAK  2(1P13.2) WILD-TYPE 31 84 60 97
D31V4, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T1                           9                            31
  T2                          24                            84
  T3                          25                            60
  T4                          34                            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                             N0  N1  N2  N3
  DEL PEAK  2(1P13.2) MUTATED    34  15  34   2
  DEL PEAK  2(1P13.2) WILD-TYPE 102  41  95   5
D31V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          34                           102
  N1                          15                            41
  N2                          34                            95
  N3                           2                             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"
D31V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.2) MUTATED   21 11
  DEL PEAK  2(1P13.2) WILD-TYPE 87 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     21   11
  DEL PEAK  2(1P13.2) WILD-TYPE   87   37
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                          21                            87
  MX                          11                            37
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    30  72
  DEL PEAK  2(1P13.2) WILD-TYPE  91 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     30   72
  DEL PEAK  2(1P13.2) WILD-TYPE   91  224
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          30                            91
  MALE                            72                           224
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED                                      99
  DEL PEAK  2(1P13.2) WILD-TYPE                                   311
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  2(1P13.2) MUTATED                                                             0
  DEL PEAK  2(1P13.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                     3
  DEL PEAK  2(1P13.2) WILD-TYPE                                                   3
D31V8, multiclass
                                                             clus
vv                                                            DEL PEAK  2(1P13.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                99
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
                                                             clus
vv                                                            DEL PEAK  2(1P13.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 311
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    17  85
  DEL PEAK  2(1P13.2) WILD-TYPE  62 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     17   85
  DEL PEAK  2(1P13.2) WILD-TYPE   62  253
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                           17                            62
  YES                          85                           253
[1] 2 2
[1] FALSE
D31V10, continuous
D31V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P13.2) MUTATED                                  0     2
  DEL PEAK  2(1P13.2) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.2) MUTATED                           9    88
  DEL PEAK  2(1P13.2) WILD-TYPE                        24   273
D31V12, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     88
                                  clus
vv                                 DEL PEAK  2(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      273
[1] 4 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
  DEL PEAK  2(1P13.2) MUTATED     7  92
  DEL PEAK  2(1P13.2) WILD-TYPE  11 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7   92
  DEL PEAK  2(1P13.2) WILD-TYPE   11  289
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           289
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D32V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED    23  11
  DEL PEAK  3(1Q44) WILD-TYPE 234  87
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         34                         321 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         11                          87 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-BA-4074 TCGA-BA-5152 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-5355 
         462         1288          624            5          395          488 
TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5330 TCGA-CQ-5333 
          45          119          225          348          896          341 
TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7372 
         870         1959         1960         1969         1191          759 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-6945 TCGA-CV-7095 TCGA-CV-A6JN 
         546         2886         1665         1969         1970          717 
TCGA-D6-6517 TCGA-D6-A4Z9 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-8489 TCGA-F7-A61S 
         292          112         1965          575          658            3 
TCGA-F7-A61W TCGA-HD-8634 TCGA-IQ-A61L TCGA-P3-A6T8 
          14           24          351          400 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         283          415         1983          276          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          513          351          216          182 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         428          436         1955            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          642          369          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988          512          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1081         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         413          290          630          424          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         594          629          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
         424          224          318          611          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V 
         429           46          443          447          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 
        1422         1399          317          129         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
         985         1959          815         1461         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
         509         1309          901          877          968          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
         514          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
         379          350          479         1956         1435         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960          105         1979          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
        3295         1438          584         1978         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840          215         1315          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7085 
        1945         1954         1970          750          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          828          773          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 
         154          568          106          128          104         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
        1081          516         1030          548          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340          564 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A620 
         490           15           92          585          384           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           2            5           25           37           55           44 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          25           11           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         412          440          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          34          392           56          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1652          721         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1917         1968          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                          3                           2 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       2886                        3837 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      560.5                       630.0 
[1] "3.0 - 2886.0 (560.5)" "2.0 - 3837.0 (630.0)"
[1] "hr=" "1.3"
D32V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  3(1Q44) MUTATED         2        4         8        19         0
  DEL PEAK  3(1Q44) WILD-TYPE      22       59        63       173         9
D32V3, multiclass
           clus
vv          DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                           2                          22
  STAGE II                          4                          59
  STAGE III                         8                          63
  STAGE IVA                        19                         173
  STAGE IVB                         0                           9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  3(1Q44) MUTATED     3   9  11  11
  DEL PEAK  3(1Q44) WILD-TYPE  37  99  74 120
D32V4, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T1                         3                          37
  T2                         9                          99
  T3                        11                          74
  T4                        11                         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                           N0  N1  N2  N3
  DEL PEAK  3(1Q44) MUTATED    13   4  14   0
  DEL PEAK  3(1Q44) WILD-TYPE 123  52 115   7
D32V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                        13                         123
  N1                         4                          52
  N2                        14                         115
  N3                         0                           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"
D32V6, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q44) MUTATED   11  5
  DEL PEAK  3(1Q44) WILD-TYPE 97 43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     11    5
  DEL PEAK  3(1Q44) WILD-TYPE   97   43
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  M0                        11                          97
  MX                         5                          43
[1] 2 2
[1] FALSE
D32V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    12  26
  DEL PEAK  3(1Q44) WILD-TYPE 109 270
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     12   26
  DEL PEAK  3(1Q44) WILD-TYPE  109  270
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        12                         109
  MALE                          26                         270
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(1Q44) MUTATED                                      38
  DEL PEAK  3(1Q44) WILD-TYPE                                   372
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  3(1Q44) MUTATED                                                             0
  DEL PEAK  3(1Q44) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  3(1Q44) MUTATED                                                     0
  DEL PEAK  3(1Q44) WILD-TYPE                                                   6
D32V8, multiclass
                                                             clus
vv                                                            DEL PEAK  3(1Q44) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                              38
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 0
                                                             clus
vv                                                            DEL PEAK  3(1Q44) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               372
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     7  31
  DEL PEAK  3(1Q44) WILD-TYPE  72 307
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      7   31
  DEL PEAK  3(1Q44) WILD-TYPE   72  307
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                          7                          72
  YES                        31                         307
[1] 2 2
[1] FALSE
D32V10, continuous
D32V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1Q44) MUTATED                                  0     2
  DEL PEAK  3(1Q44) WILD-TYPE                                1     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q44) MUTATED                           2    33
  DEL PEAK  3(1Q44) WILD-TYPE                        31   328
D32V12, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   33
                                  clus
vv                                 DEL PEAK  3(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 31
  WHITE                                                    328
[1] 4 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
  DEL PEAK  3(1Q44) MUTATED     2  36
  DEL PEAK  3(1Q44) WILD-TYPE  16 345
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      2   36
  DEL PEAK  3(1Q44) WILD-TYPE   16  345
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             2                          16
  NOT HISPANIC OR LATINO                        36                         345
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  4(2Q21.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q21.2) MUTATED    40  11
  DEL PEAK  4(2Q21.2) WILD-TYPE 217  87
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           51                           304 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           11                            87 
$`DEL PEAK  4(2Q21.2) MUTATED`
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-6873 TCGA-BB-7861 
         415          722         1288          190          113          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-5359 
         536          423            5          721          395         1980 
TCGA-CN-5363 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6024 
        1977          413          290          424           45          224 
TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63V TCGA-CQ-5331 TCGA-CQ-5334 
         119          443          447          484         1399          129 
TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4CB TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7395 
        1378          901          545         1050          354          930 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-7091 
         181          911         2641         1665         1899         1959 
TCGA-CV-7095 TCGA-CV-7235 TCGA-D6-6826 TCGA-DQ-7593 TCGA-F7-A50J TCGA-F7-A620 
        1970         1724          154          369          585           13 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T 
           5           37          111          588          351          210 
TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IH 
        1968          218          228 

$`DEL PEAK  4(2Q21.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5153 
         462          283         1983          276          248         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
         520          725          623         1636         1747          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         451           63          384          236          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         351          216          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         140          133          558          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
         428          436         1955          624            4          799 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          642          369          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988          488          512          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6010 
        1081         1980         1966         1966         1975          630 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         629          433          594          629          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970          202          424          318          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
         432          429           46          225          526          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 
        1422          896          317          341          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007          509         1309          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
         613         1963          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1777         1521         1966         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1969          362          311          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479         1956         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245         1960          105         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         997         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         946          908          898          216          156         1077 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 
        2437          519          406          701         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
         215         1315          641         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
        1957         1969         1959         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1959         1939         1945         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         773          292          701           77          491          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         622          299          368          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
         490          658           15           92            3          384 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14            6          407           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
         403            2           25           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
          25           11           49           10           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         485          122          441          360          412          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         360          224           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1652          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          225           64 

  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                            5                             2 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                         2641                          3837 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                          424                           656 
[1] "5.0 - 2641.0 (424.0)" "2.0 - 3837.0 (656.0)"
[1] "hr=" "1"  
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  4(2Q21.2) MUTATED         3        7        15        24         2
  DEL PEAK  4(2Q21.2) WILD-TYPE      21       56        56       168         7
D33V3, multiclass
           clus
vv          DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  STAGE I                             3                            21
  STAGE II                            7                            56
  STAGE III                          15                            56
  STAGE IVA                          24                           168
  STAGE IVB                           2                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  4(2Q21.2) MUTATED     6  13  12  22
  DEL PEAK  4(2Q21.2) WILD-TYPE  34  95  73 109
D33V4, multiclass
    clus
vv   DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  T1                           6                            34
  T2                          13                            95
  T3                          12                            73
  T4                          22                           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                             N0  N1  N2  N3
  DEL PEAK  4(2Q21.2) MUTATED    24  11  12   1
  DEL PEAK  4(2Q21.2) WILD-TYPE 112  45 117   6
D33V5, multiclass
    clus
vv   DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  N0                          24                           112
  N1                          11                            45
  N2                          12                           117
  N3                           1                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q21.2) MUTATED   18  8
  DEL PEAK  4(2Q21.2) WILD-TYPE 90 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     18    8
  DEL PEAK  4(2Q21.2) WILD-TYPE   90   40
    clus
vv   DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  M0                          18                            90
  MX                           8                            40
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED    27  31
  DEL PEAK  4(2Q21.2) WILD-TYPE  94 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     27   31
  DEL PEAK  4(2Q21.2) WILD-TYPE   94  265
        clus
vv       DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  FEMALE                          27                            94
  MALE                            31                           265
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q21.2) MUTATED                                      58
  DEL PEAK  4(2Q21.2) WILD-TYPE                                   352
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  4(2Q21.2) MUTATED                                                             0
  DEL PEAK  4(2Q21.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  4(2Q21.2) MUTATED                                                     0
  DEL PEAK  4(2Q21.2) WILD-TYPE                                                   6
D33V8, multiclass
                                                             clus
vv                                                            DEL PEAK  4(2Q21.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                58
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   0
                                                             clus
vv                                                            DEL PEAK  4(2Q21.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 352
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED     7  51
  DEL PEAK  4(2Q21.2) WILD-TYPE  72 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED      7   51
  DEL PEAK  4(2Q21.2) WILD-TYPE   72  287
     clus
vv    DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  NO                            7                            72
  YES                          51                           287
[1] 2 2
[1] FALSE
D33V10, continuous
D33V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q21.2) MUTATED                                  0     2
  DEL PEAK  4(2Q21.2) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q21.2) MUTATED                           4    49
  DEL PEAK  4(2Q21.2) WILD-TYPE                        29   312
D33V12, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     49
                                  clus
vv                                 DEL PEAK  4(2Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      312
[1] 4 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
  DEL PEAK  4(2Q21.2) MUTATED     4  52
  DEL PEAK  4(2Q21.2) WILD-TYPE  14 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED      4   52
  DEL PEAK  4(2Q21.2) WILD-TYPE   14  329
                        clus
vv                       DEL PEAK  4(2Q21.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       DEL PEAK  4(2Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           329
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    52  20
  DEL PEAK  5(2Q22.1) WILD-TYPE 205  78
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           72                           283 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           20                            78 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5558 TCGA-BA-6871 TCGA-BA-6873 
         415         1983         1288         1636           63          113 
TCGA-BA-7269 TCGA-BB-7861 TCGA-BB-7862 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 
         236          310          536            5          721          395 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
         512         1980         1977          290          630          424 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A49B 
          45           98          424          119          429          447 
TCGA-CN-A641 TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4CD TCGA-CR-5247 
         367         1660         1378          901          548          358 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7386 
        1050         1971          354         1440         1979         1430 
TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 
         907          181          911         1438          584         2886 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7235 TCGA-CV-7424 
        2641          215         1969         1959         1724         1947 
TCGA-CV-7427 TCGA-CV-A45Q TCGA-CV-A6JN TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-8568 
        1937         1945          717          773          154          106 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-F7-A50J 
         112          104         1778          516          369          585 
TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-HD-8224 TCGA-HD-A6HZ 
         384           13            6          407           55          111 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-KU-A66T TCGA-P3-A6T8 TCGA-QK-A6IH 
         588          412          351          210          400          228 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         462          283          276          248          722         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         520          725          623         1747          190          644 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         451          384          895          513          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         182          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         558          423          687          638         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
         436         1955          624            4          799          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142          452          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642          369          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 
        1268         1988          488          173         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 
        1966         1966         1975          413          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
         594          629          432         1970          202          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
         318          611          394          432           46          443 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 
         225          526          484          348          175         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        1207          654         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1959          815         1461         1007          509 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         545          393          391          303          608         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125          514         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
        1191         1245         1960          105          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1951          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 
         898          930          216          156         1077         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 
        1955          522         1950         3295          546         1978 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1966         1957         1969         1959         3837 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1970         1970         1936         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1987         1979         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1955         1957         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A461 TCGA-CV-A6JD 
        1958         1959         1981          851         1954         1970 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 
         750          317          321          237          828          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 TCGA-DQ-5625 
         701           77          491          568          128         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         299          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61W TCGA-H7-8501 
         658           15           92            3           14           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          403            2            5           25 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10           33         1057          485          122          441 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X 
         360          440          360          224           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         392           56          111          112          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
        1968          553          357          245          218          225 
TCGA-QK-A6IJ 
          64 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                            5                             2 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         2886                          3837 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                        479.5                         658.0 
[1] "5.0 - 2886.0 (479.5)" "2.0 - 3837.0 (658.0)"
[1] "hr=" "1.1"
D34V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  5(2Q22.1) MUTATED         2       11        16        43         4
  DEL PEAK  5(2Q22.1) WILD-TYPE      22       52        55       149         5
D34V3, multiclass
           clus
vv          DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                             2                            22
  STAGE II                           11                            52
  STAGE III                          16                            55
  STAGE IVA                          43                           149
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  5(2Q22.1) MUTATED    5 18 18 36
  DEL PEAK  5(2Q22.1) WILD-TYPE 35 90 67 95
D34V4, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T1                           5                            35
  T2                          18                            90
  T3                          18                            67
  T4                          36                            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                             N0  N1  N2  N3
  DEL PEAK  5(2Q22.1) MUTATED    28  11  28   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 108  45 101   4
D34V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          28                           108
  N1                          11                            45
  N2                          28                           101
  N3                           3                             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"
D34V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q22.1) MUTATED   29  8
  DEL PEAK  5(2Q22.1) WILD-TYPE 79 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     29    8
  DEL PEAK  5(2Q22.1) WILD-TYPE   79   40
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  M0                          29                            79
  MX                           8                            40
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    32  56
  DEL PEAK  5(2Q22.1) WILD-TYPE  89 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     32   56
  DEL PEAK  5(2Q22.1) WILD-TYPE   89  240
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          32                            89
  MALE                            56                           240
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                                      88
  DEL PEAK  5(2Q22.1) WILD-TYPE                                   322
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  5(2Q22.1) MUTATED                                                             0
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  5(2Q22.1) MUTATED                                                     0
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                   6
D34V8, multiclass
                                                             clus
vv                                                            DEL PEAK  5(2Q22.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                88
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   0
                                                             clus
vv                                                            DEL PEAK  5(2Q22.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 322
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    17  71
  DEL PEAK  5(2Q22.1) WILD-TYPE  62 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     17   71
  DEL PEAK  5(2Q22.1) WILD-TYPE   62  267
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           17                            62
  YES                          71                           267
[1] 2 2
[1] FALSE
D34V10, continuous
D34V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q22.1) MUTATED                                  0     4
  DEL PEAK  5(2Q22.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q22.1) MUTATED                           6    75
  DEL PEAK  5(2Q22.1) WILD-TYPE                        27   286
D34V12, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     75
                                  clus
vv                                 DEL PEAK  5(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     5  80
  DEL PEAK  5(2Q22.1) WILD-TYPE  13 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      5   80
  DEL PEAK  5(2Q22.1) WILD-TYPE   13  301
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           301
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  6(2Q36.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q36.2) MUTATED    74  38
  DEL PEAK  6(2Q36.2) WILD-TYPE 183  60
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          112                           243 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                           38                            60 
$`DEL PEAK  6(2Q36.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5558 
         283          415         1983         1288          520         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A6D8 TCGA-BA-A6DE 
        1747          190           63          113          513          182 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-8601 
         133          310          536          423          687          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4736 TCGA-CN-4740 
           5            4          721          452          395          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5370 
        1268         1988          512         1081         1977         1975 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6024 
         290          424          629           45         1970          224 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5327 
         119          429          447          348         1466         1660 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-7064 TCGA-CQ-A4CI TCGA-CR-6472 TCGA-CR-6477 
         317          870         1378          608         1050          514 
TCGA-CR-6484 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
         354         1956         1435         1440         1960          105 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 
        1979          889           30          181          911         1472 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5966 TCGA-CV-5973 
         522         3295          584         1978          519         2641 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 
         215         1665          641         1969         1959         3835 
TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7248 
        1969         1959         1959         1970         1970         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1976         1099         1974         1955         1957         1947 
TCGA-CV-7440 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-D6-6826 TCGA-D6-A4ZB TCGA-DQ-5629 
        1981          750          717          154          104          516 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-A50G TCGA-F7-A50J 
         575          299          369          368           15          585 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-A633 
          13            6          403            5           55           49 
TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-KU-A66T 
         111          588          360          412          351          210 
TCGA-MZ-A6I9 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6IJ 
         254          400          218           64 

$`DEL PEAK  6(2Q36.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
         462          276          248          722         1762          725 
TCGA-BA-5557 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         623          644          451          384          236          895 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         351          216          187         2878          278          140 
TCGA-BB-4228 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         558          638         1153          428          436         1955 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         799          485          142          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          642          369          240         1960         1330 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         488          173         1980         1980         1966         1966 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         413          630          433          594          629          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
          98          202          424          318          611          394 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         432           46          443          225          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
         175          367         1207          654         1422          896 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        1399          341          129         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1959          815         1461         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 
        1521         1966         1125         1971         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          345          234          379          350          479 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1191         1245          759          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 
         216          156         1077         1955         1950         1438 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
         546         2886         2327         1958         2437          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 
         701         1478         1840         1315         1899         1970 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1948         1952         1948         1966         1957         1969 
TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        3837         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7250 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1960         1948         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1984         1958         1959          851         1945         1954 
TCGA-CV-A6JD TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1970          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
         292          701           77          491          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         128          112         1778         1081         1030          548 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        1965          775          622          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         490          658           92            3          384           14 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7754 
         407           58          133          414            2           25 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
          37           44           24           25           11           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61J 
          33         1057          485          122          441          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         360          224           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          910         1652          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 
        1954          578         1917         1968          553          357 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
         245          228          225 

  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                            4                             2 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                         3835                          3837 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                        555.5                         658.0 
[1] "4.0 - 3835.0 (555.5)" "2.0 - 3837.0 (658.0)"
[1] "hr=" "1.1"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  6(2Q36.2) MUTATED         3       14        27        57         4
  DEL PEAK  6(2Q36.2) WILD-TYPE      21       49        44       135         5
D35V3, multiclass
           clus
vv          DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  STAGE I                             3                            21
  STAGE II                           14                            49
  STAGE III                          27                            44
  STAGE IVA                          57                           135
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  6(2Q36.2) MUTATED    6 23 33 44
  DEL PEAK  6(2Q36.2) WILD-TYPE 34 85 52 87
D35V4, multiclass
    clus
vv   DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  T1                           6                            34
  T2                          23                            85
  T3                          33                            52
  T4                          44                            87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  6(2Q36.2) MUTATED   38 20 35  3
  DEL PEAK  6(2Q36.2) WILD-TYPE 98 36 94  4
D35V5, multiclass
    clus
vv   DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  N0                          38                            98
  N1                          20                            36
  N2                          35                            94
  N3                           3                             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
  DEL PEAK  6(2Q36.2) MUTATED   33 13
  DEL PEAK  6(2Q36.2) WILD-TYPE 75 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     33   13
  DEL PEAK  6(2Q36.2) WILD-TYPE   75   35
    clus
vv   DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  M0                          33                            75
  MX                          13                            35
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    39  87
  DEL PEAK  6(2Q36.2) WILD-TYPE  82 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     39   87
  DEL PEAK  6(2Q36.2) WILD-TYPE   82  209
        clus
vv       DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  FEMALE                          39                            82
  MALE                            87                           209
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(2Q36.2) MUTATED                                     125
  DEL PEAK  6(2Q36.2) WILD-TYPE                                   285
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  6(2Q36.2) MUTATED                                                             0
  DEL PEAK  6(2Q36.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  6(2Q36.2) MUTATED                                                     1
  DEL PEAK  6(2Q36.2) WILD-TYPE                                                   5
D35V8, multiclass
                                                             clus
vv                                                            DEL PEAK  6(2Q36.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               125
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK  6(2Q36.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 285
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    21 105
  DEL PEAK  6(2Q36.2) WILD-TYPE  58 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     21  105
  DEL PEAK  6(2Q36.2) WILD-TYPE   58  233
     clus
vv    DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  NO                           21                            58
  YES                         105                           233
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(2Q36.2) MUTATED                                  1     5
  DEL PEAK  6(2Q36.2) WILD-TYPE                                0     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q36.2) MUTATED                          15   101
  DEL PEAK  6(2Q36.2) WILD-TYPE                        18   260
D35V12, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q36.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    101
                                  clus
vv                                 DEL PEAK  6(2Q36.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    10 112
  DEL PEAK  6(2Q36.2) WILD-TYPE   8 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     10  112
  DEL PEAK  6(2Q36.2) WILD-TYPE    8  269
                        clus
vv                       DEL PEAK  6(2Q36.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         112
                        clus
vv                       DEL PEAK  6(2Q36.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           269
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  7(3P24.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P24.1) MUTATED   169  86
  DEL PEAK  7(3P24.1) WILD-TYPE  88  12
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                          255                           100 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                           86                            12 
$`DEL PEAK  7(3P24.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         520         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
          63          384          236          895          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
         216          182          278          133          558          536 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
           5          721          485          142          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         462          993          369          395          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1988          488          512          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1975          413          630          424          629          433 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         594           45          432           98         1970          202 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          119          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
         429           46          443          447          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 
         348          367          896          317          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
        1057          985         1959         1959          815         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1007          509          901          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 
        1963          545          548          393          608         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
         358         1663          799         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
        1969          362          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479         1956         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245         1960          105         1979          759          889 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1968         1036         1954         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
         907          216          156         1077          911         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 
        1978         2886         2437          519          406         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        1478         1840          215         1315         1665         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6952 
        1948         1969         1952         1959         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 
        1444         1095          954          797         1967         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7428 
        1099         1948         1955         1957         1947         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A461 
        1972         1937         1984         1958         1959         1954 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         750          717          317          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
         292          701          491          154          106          128 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         104         1778          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         575          622          299          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
         384           14           13          133          414          403 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 
           2            5           37           55           24           25 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
          49          111          485          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         440          351          360          210           14           34 
TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
          56         1652         1954         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ 
         357          228           64 

$`DEL PEAK  7(3P24.1) WILD-TYPE`
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6873 
         722         1288         1762          725          623          113 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 
         187         2878          140          310          423          638 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-5374 
           4          799          452          642         1268          290 
TCGA-CN-6017 TCGA-CN-6023 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         629          424          484          175         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1422         1399          341          129 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 
        1461         1309          877          391          303         1152 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6481 TCGA-CR-7374 
        1777         1521         1966         1050          311           30 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         972          796          997          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5442 TCGA-CV-5443 
         898          930          181         1472         2327         1958 
TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-7183 
         701          641         1899         3835         1948         1979 
TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7427 TCGA-CV-7440 TCGA-CV-A45O 
        1724         1960         1974         1937         1981          851 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 
        1945         1970          321           77          568          112 
TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-A623 TCGA-H7-7774 
        1081          775          369          368            6          407 
TCGA-H7-8501 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
          58           25           44           11           10           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A66S TCGA-MT-A67A TCGA-MT-A67F 
        1057          122          441          224          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         112          254          910          721         1120          578 
TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
        1917          245          218          225 

  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                            2                             4 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                         3837                          3835 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                          608                           711 
[1] "2.0 - 3837.0 (608.0)" "4.0 - 3835.0 (711.0)"
[1] "hr=" "2.1"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  7(3P24.1) MUTATED        16       40        51       149         7
  DEL PEAK  7(3P24.1) WILD-TYPE       8       23        20        43         2
D36V3, multiclass
           clus
vv          DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  STAGE I                            16                             8
  STAGE II                           40                            23
  STAGE III                          51                            20
  STAGE IVA                         149                            43
  STAGE IVB                           7                             2
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  7(3P24.1) MUTATED    23  72  68 102
  DEL PEAK  7(3P24.1) WILD-TYPE  17  36  17  29
D36V4, multiclass
    clus
vv   DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  T1                          23                            17
  T2                          72                            36
  T3                          68                            17
  T4                         102                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  7(3P24.1) MUTATED    92  42 105   5
  DEL PEAK  7(3P24.1) WILD-TYPE  44  14  24   2
D36V5, multiclass
    clus
vv   DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  N0                          92                            44
  N1                          42                            14
  N2                         105                            24
  N3                           5                             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"
D36V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P24.1) MUTATED   76 31
  DEL PEAK  7(3P24.1) WILD-TYPE 32 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P24.1) MUTATED     76   31
  DEL PEAK  7(3P24.1) WILD-TYPE   32   17
    clus
vv   DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  M0                          76                            32
  MX                          31                            17
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P24.1) MUTATED    76 225
  DEL PEAK  7(3P24.1) WILD-TYPE  45  71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P24.1) MUTATED     76  225
  DEL PEAK  7(3P24.1) WILD-TYPE   45   71
        clus
vv       DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  FEMALE                          76                            45
  MALE                           225                            71
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P24.1) MUTATED                                     299
  DEL PEAK  7(3P24.1) WILD-TYPE                                   111
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  7(3P24.1) MUTATED                                                             1
  DEL PEAK  7(3P24.1) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  7(3P24.1) MUTATED                                                     1
  DEL PEAK  7(3P24.1) WILD-TYPE                                                   5
D36V8, multiclass
                                                             clus
vv                                                            DEL PEAK  7(3P24.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               299
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK  7(3P24.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 111
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P24.1) MUTATED    58 243
  DEL PEAK  7(3P24.1) WILD-TYPE  21  95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P24.1) MUTATED     58  243
  DEL PEAK  7(3P24.1) WILD-TYPE   21   95
     clus
vv    DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  NO                           58                            21
  YES                         243                            95
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P24.1) MUTATED                                  1     7
  DEL PEAK  7(3P24.1) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P24.1) MUTATED                          30   255
  DEL PEAK  7(3P24.1) WILD-TYPE                         3   106
D36V12, multiclass
                                  clus
vv                                 DEL PEAK  7(3P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 30
  WHITE                                                    255
                                  clus
vv                                 DEL PEAK  7(3P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                      106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P24.1) MUTATED    14 272
  DEL PEAK  7(3P24.1) WILD-TYPE   4 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P24.1) MUTATED     14  272
  DEL PEAK  7(3P24.1) WILD-TYPE    4  109
                        clus
vv                       DEL PEAK  7(3P24.1) MUTATED
  HISPANIC OR LATINO                              14
  NOT HISPANIC OR LATINO                         272
                        clus
vv                       DEL PEAK  7(3P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           109
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  8(3P12.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P12.1) MUTATED   156  81
  DEL PEAK  8(3P12.1) WILD-TYPE 101  17
  DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE 
                          237                           118 
  DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE 
                           81                            17 
$`DEL PEAK  8(3P12.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1762          520          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451           63          384          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
         513          182          278          687         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 
         436         1955          624            5          721          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 
         142          452          392          462          993          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 
         395          240         1960         1330          811          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         512          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1966         1966          413          630          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         433          594           45          432           98         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         424          224          611          394          119          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
         429           46          443          447          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 
         348          367         1466          896          317          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959          815 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1378         1007          509          901          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI 
         613         1963          545          548          393          608 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        2562          358         1777         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1968         1036         1954         1951          392          907 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
         216          156         1077          911         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1950         3295         1438          584          546         1978 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2437          519          406         2641         1478         1840 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1315         1665         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
        1959         1969         1957         1969         1959         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1970         1970         1936         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1987         1444         1095          954          797         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1976         1099         1948         1955         1957         1947 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1973         1972         1937         1958         1959         1981 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        1954          750          717          317          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         773          292          154          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
         104         1778          516         1030         1965          575 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         299          324          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          92          585            3           14           13            6 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 
         133          414          403           37           55           25 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
          49          111          485          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         440          351          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
          34           56         1652         1954         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IJ 
         553          357           64 

$`DEL PEAK  8(3P12.1) WILD-TYPE`
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DB 
         722         1288          725          113          351          216 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
         187         2878          140          133          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4728 
         536          423          638            4          799          613 
TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6017 
         642         1268         1988         1975          290          629 
TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5324 TCGA-CQ-5325 
         202          318          484          175         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 
        1660         1422         1399          341          129         1461 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
        1309          877          391          303         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6481 
         799         1521         1966         1050         1125          311 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
         972          796          997         1430          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5441 
         908          898          930          181         1472         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
        2327         1958          701          215          641         1899 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7183 TCGA-CV-7235 
        3835         1948         1966         3837         1979         1724 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q 
        1960         1974         1937         1984          851         1945 
TCGA-CV-A6JD TCGA-CX-7085 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
        1970          321          701           77          491          568 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
        1081          548          775          622          369          368 
TCGA-DQ-7596 TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7753 
         340          384          407           58            2            5 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
          25           44           24           11           10           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
        1057          122          441          392          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         254          910          721         1120          578         1917 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         245          218          228          225 

  DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE 
                            3                             2 
  DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE 
                         3295                          3837 
  DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE 
                          611                           648 
[1] "3.0 - 3295.0 (611.0)" "2.0 - 3837.0 (648.0)"
[1] "hr=" "2.4"
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  8(3P12.1) MUTATED        13       38        52       139         5
  DEL PEAK  8(3P12.1) WILD-TYPE      11       25        19        53         4
D37V3, multiclass
           clus
vv          DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE
  STAGE I                            13                            11
  STAGE II                           38                            25
  STAGE III                          52                            19
  STAGE IVA                         139                            53
  STAGE IVB                           5                             4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  8(3P12.1) MUTATED   23 73 62 92
  DEL PEAK  8(3P12.1) WILD-TYPE 17 35 23 39
D37V4, multiclass
    clus
vv   DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE
  T1                          23                            17
  T2                          73                            35
  T3                          62                            23
  T4                          92                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK  8(3P12.1) MUTATED   87 43 96  4
  DEL PEAK  8(3P12.1) WILD-TYPE 49 13 33  3
D37V5, multiclass
    clus
vv   DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE
  N0                          87                            49
  N1                          43                            13
  N2                          96                            33
  N3                           4                             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"
D37V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(3P12.1) MUTATED   70 32
  DEL PEAK  8(3P12.1) WILD-TYPE 38 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.1) MUTATED     70   32
  DEL PEAK  8(3P12.1) WILD-TYPE   38   16
    clus
vv   DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE
  M0                          70                            38
  MX                          32                            16
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.1) MUTATED    71 210
  DEL PEAK  8(3P12.1) WILD-TYPE  50  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.1) MUTATED     71  210
  DEL PEAK  8(3P12.1) WILD-TYPE   50   86
        clus
vv       DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE
  FEMALE                          71                            50
  MALE                           210                            86
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P12.1) MUTATED                                     278
  DEL PEAK  8(3P12.1) WILD-TYPE                                   132
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  8(3P12.1) MUTATED                                                             1
  DEL PEAK  8(3P12.1) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  8(3P12.1) MUTATED                                                     2
  DEL PEAK  8(3P12.1) WILD-TYPE                                                   4
D37V8, multiclass
                                                             clus
vv                                                            DEL PEAK  8(3P12.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               278
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            DEL PEAK  8(3P12.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 132
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.1) MUTATED    57 224
  DEL PEAK  8(3P12.1) WILD-TYPE  22 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.1) MUTATED     57  224
  DEL PEAK  8(3P12.1) WILD-TYPE   22  114
     clus
vv    DEL PEAK  8(3P12.1) MUTATED DEL PEAK  8(3P12.1) WILD-TYPE
  NO                           57                            22
  YES                         224                           114
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3P12.1) MUTATED                                  1     7
  DEL PEAK  8(3P12.1) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P12.1) MUTATED                          28   236
  DEL PEAK  8(3P12.1) WILD-TYPE                         5   125
D37V12, multiclass
                                  clus
vv                                 DEL PEAK  8(3P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    236
                                  clus
vv                                 DEL PEAK  8(3P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                      125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.1) MUTATED    15 252
  DEL PEAK  8(3P12.1) WILD-TYPE   3 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.1) MUTATED     15  252
  DEL PEAK  8(3P12.1) WILD-TYPE    3  129
                        clus
vv                       DEL PEAK  8(3P12.1) MUTATED
  HISPANIC OR LATINO                              15
  NOT HISPANIC OR LATINO                         252
                        clus
vv                       DEL PEAK  8(3P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           129
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  9(4P15.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4P15.2) MUTATED    99  50
  DEL PEAK  9(4P15.2) WILD-TYPE 158  48
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                          149                           206 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           50                            48 
$`DEL PEAK  9(4P15.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
         722          520          623         1636          190          451 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BB-4223 TCGA-BB-4224 
          63          895          513          216         2878          278 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         133          310          428         1955          624            5 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
           4          721          485          142          613          462 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
         369         1330         1988          488          173         1081 
TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
        1977          290          630          424          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 
         432         1970          424          224          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63T 
         119          432          429           46          447          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6223 
         526          348          367         1466          317         1057 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI 
        1959         1378          509          613          548          608 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6487 TCGA-CR-6488 
         358         1663         1050         1971          234          379 
TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
         350         1191         1440         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 
         759          889           30         1954         1951          907 
TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         156         1472          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6934 TCGA-CV-6935 
         584         1978         2437          215         1948         1969 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        1959         3835         1959         1959         1970         1939 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 
        1724         1444         1095          797         1967         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7432 
        1099         1974         1955         1957         1972         1937 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-D6-6516 TCGA-D6-6823 
        1984         1959         1981          317          773          701 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 
         112          104          516         1965          575          324 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-8502 TCGA-H7-A6C5 
         490           15          384           14          133          403 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ 
           5           37           55           44           49          111 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-MZ-A6I9 
         588          360          412          440          112          254 
TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
        1652         1120         1954         1968          400 

$`DEL PEAK  9(4P15.2) WILD-TYPE`
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6872 
        1288         1762          725         1747          644          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4225 
         113          236          351          182          187          140 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         558          536          423          687          638         1153 
TCGA-BB-7872 TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
         436          799          452          392          993          642 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 
         395          240         1960          811         1268          512 
TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1980         1980         1966         1966         1975          413 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6988 
         433          594          629           98          202          318 
TCGA-CN-A498 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         443          484          175         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422          896         1399          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
        1000          985         1959          815         1461         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
        1309          901          877          968         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 
         545          393          391          303         2562         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 
         799         1777         1521         1966         1125          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6492 
        1969          362          311          345          354          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1956         1435         1245          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         796          997         1430          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
         908          898          930          216          181         1077 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         911         1955          546         2886         2327         1958 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6936 
        1315         1665          641         1899         1970         1952 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 
        1948         1969         1966         1957         1969         3837 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1945         1987         1979 
TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
         954         1960         1948         1947         1937         1973 
TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1958          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 
         717          321          237          828          292           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5624 
         491          154          568          106          128         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1081         1030          548          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I 
         369          368          340          564          658           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         585            3           13            6          407           58 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
         414            2           25           24           25           11 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10           33         1057          485          122          441 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         351          360          224          210           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6T0 
         392           56          111          910          721          578 
TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
        1917          553          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                            4                             2 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                         3835                          3837 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                          575                           709 
[1] "4.0 - 3835.0 (575.0)" "2.0 - 3837.0 (709.0)"
[1] "hr=" "1.2"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  9(4P15.2) MUTATED        12       25        27        83         4
  DEL PEAK  9(4P15.2) WILD-TYPE      12       38        44       109         5
D38V3, multiclass
           clus
vv          DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  STAGE I                            12                            12
  STAGE II                           25                            38
  STAGE III                          27                            44
  STAGE IVA                          83                           109
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  9(4P15.2) MUTATED   17 40 40 54
  DEL PEAK  9(4P15.2) WILD-TYPE 23 68 45 77
D38V4, multiclass
    clus
vv   DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  T1                          17                            23
  T2                          40                            68
  T3                          40                            45
  T4                          54                            77
[1] 4 2
[1] TRUE
[1] "dimension 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(4P15.2) MUTATED   55 22 59  4
  DEL PEAK  9(4P15.2) WILD-TYPE 81 34 70  3
D38V5, multiclass
    clus
vv   DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  N0                          55                            81
  N1                          22                            34
  N2                          59                            70
  N3                           4                             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"
D38V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(4P15.2) MUTATED   37 22
  DEL PEAK  9(4P15.2) WILD-TYPE 71 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED     37   22
  DEL PEAK  9(4P15.2) WILD-TYPE   71   26
    clus
vv   DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  M0                          37                            71
  MX                          22                            26
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P15.2) MUTATED    41 130
  DEL PEAK  9(4P15.2) WILD-TYPE  80 166
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED     41  130
  DEL PEAK  9(4P15.2) WILD-TYPE   80  166
        clus
vv       DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  FEMALE                          41                            80
  MALE                           130                           166
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(4P15.2) MUTATED                                     168
  DEL PEAK  9(4P15.2) WILD-TYPE                                   242
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  9(4P15.2) MUTATED                                                             0
  DEL PEAK  9(4P15.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  9(4P15.2) MUTATED                                                     3
  DEL PEAK  9(4P15.2) WILD-TYPE                                                   3
D38V8, multiclass
                                                             clus
vv                                                            DEL PEAK  9(4P15.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               168
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
                                                             clus
vv                                                            DEL PEAK  9(4P15.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 242
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P15.2) MUTATED    36 135
  DEL PEAK  9(4P15.2) WILD-TYPE  43 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED     36  135
  DEL PEAK  9(4P15.2) WILD-TYPE   43  203
     clus
vv    DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  NO                           36                            43
  YES                         135                           203
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4P15.2) MUTATED                                  0     3
  DEL PEAK  9(4P15.2) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4P15.2) MUTATED                          16   146
  DEL PEAK  9(4P15.2) WILD-TYPE                        17   215
D38V12, multiclass
                                  clus
vv                                 DEL PEAK  9(4P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    146
                                  clus
vv                                 DEL PEAK  9(4P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P15.2) MUTATED     9 157
  DEL PEAK  9(4P15.2) WILD-TYPE   9 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED      9  157
  DEL PEAK  9(4P15.2) WILD-TYPE    9  224
                        clus
vv                       DEL PEAK  9(4P15.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         157
                        clus
vv                       DEL PEAK  9(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           224
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED    81  37
  DEL PEAK 10(4Q22.1) WILD-TYPE 176  61
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          118                           237 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           37                            61 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF 
         283          276          520          451          113          895 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         513          216          133         1153          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 
         624            5            4          485          392          369 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 
         240         1330         1081         1966          630          424 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 
         629           45          432           98         1970          224 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         611          119          429           46          443          447 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6228 
         225          348         1466         1000          985         1959 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1378          509         1960          613          303          608 
TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 
        1663         1050          354          234          379         1956 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1191         1440          105         1979          759          889 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 
          30         1954          946          156         1472          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 
        1950         3295         1438          546         1978         2437 
TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 
        1478         1665         1970         1969         1959         3835 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 
        1969         1957         1959         1970         1939         1987 
TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
         797         1099         1974         1955         1957         1947 
TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CX-7086 TCGA-D6-6516 
        1972         1959         1981         1945          237          773 
TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
         701          112          104          516         1965          575 
TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-A6HZ 
         299          585            3          403           24          111 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-P3-A5QA 
         588          360          412          440          112         1652 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A6IG 
        1954         1968          245          218 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1762          725          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DE 
         644           63          384          236          351          182 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
         187         2878          278          140          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-CN-4722 
         536          423          687          638          436          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
         721          142          452          613          462          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         642          395         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
         488          512          173         1980         1977         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 
        1966         1975          413          290          433          594 
TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 
         629          202          424          318          394          432 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 
         526          484          175          367         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
         129          870         1057         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA 
        1007         1309          901          877          968         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 
         545          548          393          391         2562          358 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
        1152          799         1777         1521         1966         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 
         350          479         1435         1245         1960          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968         1036          796          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         392          907          913          908          898          930 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 
         216          181         1077          911         1955          584 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2886         2327         1958          519          406          701 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        2641         1840          215         1315          641         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 
        1948         1952         1948         1966         1969         1959 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 
        3837         1970         1936         1959         1945         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        1724         1444         1095          954         1967         1960 
TCGA-CV-7254 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 
        1976         1948         1937         1973         1937         1984 
TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1958          851         1954         1970          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         317          321          828          292           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5625 
         154          568          106          128         1778         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
        1030          548          775          622          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
          92          384           14           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
          58          133          414            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           55           44           25           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10           33         1057          485          122          441 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         351          360          224          210           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392           56          111          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1120          578         1917          400          553          357 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                            3                             2 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                         3835                          3837 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        626.5                         629.0 
[1] "3.0 - 3835.0 (626.5)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1"  
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 10(4Q22.1) MUTATED        10       17        29        61         1
  DEL PEAK 10(4Q22.1) WILD-TYPE      14       46        42       131         8
D39V3, multiclass
           clus
vv          DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  STAGE I                            10                            14
  STAGE II                           17                            46
  STAGE III                          29                            42
  STAGE IVA                          61                           131
  STAGE IVB                           1                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 10(4Q22.1) MUTATED   12 34 33 40
  DEL PEAK 10(4Q22.1) WILD-TYPE 28 74 52 91
D39V4, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  T1                          12                            28
  T2                          34                            74
  T3                          33                            52
  T4                          40                            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                            N0 N1 N2 N3
  DEL PEAK 10(4Q22.1) MUTATED   42 21 42  1
  DEL PEAK 10(4Q22.1) WILD-TYPE 94 35 87  6
D39V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  N0                          42                            94
  N1                          21                            35
  N2                          42                            87
  N3                           1                             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"
D39V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(4Q22.1) MUTATED   29 18
  DEL PEAK 10(4Q22.1) WILD-TYPE 79 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     29   18
  DEL PEAK 10(4Q22.1) WILD-TYPE   79   30
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  M0                          29                            79
  MX                          18                            30
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    37  97
  DEL PEAK 10(4Q22.1) WILD-TYPE  84 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     37   97
  DEL PEAK 10(4Q22.1) WILD-TYPE   84  199
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  FEMALE                          37                            84
  MALE                            97                           199
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                     133
  DEL PEAK 10(4Q22.1) WILD-TYPE                                   277
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 10(4Q22.1) MUTATED                                                             0
  DEL PEAK 10(4Q22.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 10(4Q22.1) MUTATED                                                     1
  DEL PEAK 10(4Q22.1) WILD-TYPE                                                   5
D39V8, multiclass
                                                             clus
vv                                                            DEL PEAK 10(4Q22.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               133
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 10(4Q22.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 277
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    27 107
  DEL PEAK 10(4Q22.1) WILD-TYPE  52 231
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     27  107
  DEL PEAK 10(4Q22.1) WILD-TYPE   52  231
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                           27                            52
  YES                         107                           231
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4Q22.1) MUTATED                                  1     5
  DEL PEAK 10(4Q22.1) WILD-TYPE                                0     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q22.1) MUTATED                          12   110
  DEL PEAK 10(4Q22.1) WILD-TYPE                        21   251
D39V12, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    110
                                  clus
vv                                 DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      251
[1] 4 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 10(4Q22.1) MUTATED     9 120
  DEL PEAK 10(4Q22.1) WILD-TYPE   9 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      9  120
  DEL PEAK 10(4Q22.1) WILD-TYPE    9  261
                        clus
vv                       DEL PEAK 10(4Q22.1) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         120
                        clus
vv                       DEL PEAK 10(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           261
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 11(4Q35.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q35.2) MUTATED   103  43
  DEL PEAK 11(4Q35.2) WILD-TYPE 154  55
  DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE 
                          146                           209 
  DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE 
                           43                            55 
$`DEL PEAK 11(4Q35.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 
         283          276          520          623         1636          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BB-7870 
         384          113          895          513          216         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4737 
         799          721          485          392          395          240 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5367 
        1330         1988          488         1980         1081         1966 
TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
        1975          630          424          629           45          432 
TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         202          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5329 
         443          447          225          526          348         1422 
TCGA-CQ-5330 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
         896         1959         1378          509         1960          613 
TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6487 
         608         1663         1050         1971          354          234 
TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
         379         1435         1191          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7399 
         889           30          392          946          156          181 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1077         1472          522         1950         3295         1438 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         1978         2327         1958         2437          519 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 
        2641         1478          215         1665         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-7091 
        1969         1952         1959         3835         1957         1959 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 
        1970         1939         1987         1095          954         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 
        1976         1099         1957         1972         1984         1959 
TCGA-CV-A45Q TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
        1945          237          828          701          112          104 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 
         516          548         1965          575          299          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-A6C4 
         658           15           92          585            3          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A634 
         403            2           24           25           49           10 
TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-MT-A67G 
         111          588          412          440          351          112 
TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF 
         254         1652         1954          400          553          245 
TCGA-QK-A6IG TCGA-QK-A6IH 
         218          228 

$`DEL PEAK 11(4Q35.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 
        1762          725         1747          190          644           63 
TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         236          351          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 
         687          638          142          452          613          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         993          642          369         1960          811         1268 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5373 
         512          173         1977         1980         1966          413 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6021 
         290          433          594          629           98         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A63V TCGA-CN-A63Y 
         424          224          318          611          484          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 
         367         1466         1207          654         1660         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 
         985         1959          815         1461         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         901          877          968         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
         393          391          303         2562          358         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 
         799         1777         1521         1966         1125          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6492 
        1969          362          311          345          350          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 
        1956         1440         1245         1960          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         907          913          908          898          930          216 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5970 TCGA-CV-5971 
         911         1955          584         2886          406          701 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6943 TCGA-CV-6945 
        1840         1315          641         1899         1948         1969 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 
        1966         1969         1959         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7245 
        1959         1945         1979         1724         1444          797 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 
        1960         1974         1948         1955         1947         1937 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A461 
        1973         1937         1958         1981          851         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 
        1970          750          717          317          321          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         292           77          491          154          568          106 
TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         128         1778         1081         1030          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A61V 
         369          368          324          340          564          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
           5           25           37           55           44           11 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
          33         1057          485          122          441          360 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
          56          111          910          721         1120          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ 
        1917         1968          357          225           64 

  DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE 
                            2                             5 
  DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE 
                         3835                          3837 
  DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE 
                          580                           687 
[1] "2.0 - 3835.0 (580.0)" "5.0 - 3837.0 (687.0)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 11(4Q35.2) MUTATED        11       20        40        76         4
  DEL PEAK 11(4Q35.2) WILD-TYPE      13       43        31       116         5
D40V3, multiclass
           clus
vv          DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE
  STAGE I                            11                            13
  STAGE II                           20                            43
  STAGE III                          40                            31
  STAGE IVA                          76                           116
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 11(4Q35.2) MUTATED   16 37 46 53
  DEL PEAK 11(4Q35.2) WILD-TYPE 24 71 39 78
D40V4, multiclass
    clus
vv   DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE
  T1                          16                            24
  T2                          37                            71
  T3                          46                            39
  T4                          53                            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                            N0 N1 N2 N3
  DEL PEAK 11(4Q35.2) MUTATED   54 27 53  2
  DEL PEAK 11(4Q35.2) WILD-TYPE 82 29 76  5
D40V5, multiclass
    clus
vv   DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE
  N0                          54                            82
  N1                          27                            29
  N2                          53                            76
  N3                           2                             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 11(4Q35.2) MUTATED   40 23
  DEL PEAK 11(4Q35.2) WILD-TYPE 68 25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.2) MUTATED     40   23
  DEL PEAK 11(4Q35.2) WILD-TYPE   68   25
    clus
vv   DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE
  M0                          40                            68
  MX                          23                            25
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.2) MUTATED    58 113
  DEL PEAK 11(4Q35.2) WILD-TYPE  63 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.2) MUTATED     58  113
  DEL PEAK 11(4Q35.2) WILD-TYPE   63  183
        clus
vv       DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE
  FEMALE                          58                            63
  MALE                           113                           183
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4Q35.2) MUTATED                                     170
  DEL PEAK 11(4Q35.2) WILD-TYPE                                   240
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 11(4Q35.2) MUTATED                                                             0
  DEL PEAK 11(4Q35.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 11(4Q35.2) MUTATED                                                     1
  DEL PEAK 11(4Q35.2) WILD-TYPE                                                   5
D40V8, multiclass
                                                             clus
vv                                                            DEL PEAK 11(4Q35.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               170
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 11(4Q35.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 240
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.2) MUTATED    32 139
  DEL PEAK 11(4Q35.2) WILD-TYPE  47 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.2) MUTATED     32  139
  DEL PEAK 11(4Q35.2) WILD-TYPE   47  199
     clus
vv    DEL PEAK 11(4Q35.2) MUTATED DEL PEAK 11(4Q35.2) WILD-TYPE
  NO                           32                            47
  YES                         139                           199
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4Q35.2) MUTATED                                  1     4
  DEL PEAK 11(4Q35.2) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4Q35.2) MUTATED                          15   144
  DEL PEAK 11(4Q35.2) WILD-TYPE                        18   217
D40V12, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    144
                                  clus
vv                                 DEL PEAK 11(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      217
[1] 4 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 11(4Q35.2) MUTATED     9 156
  DEL PEAK 11(4Q35.2) WILD-TYPE   9 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.2) MUTATED      9  156
  DEL PEAK 11(4Q35.2) WILD-TYPE    9  225
                        clus
vv                       DEL PEAK 11(4Q35.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         156
                        clus
vv                       DEL PEAK 11(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           225
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 12(5Q11.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q11.2) MUTATED   105  41
  DEL PEAK 12(5Q11.2) WILD-TYPE 152  57
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                          146                           209 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                           41                            57 
$`DEL PEAK 12(5Q11.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 
         462          283          276          520          190          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA 
          63          384          113          236          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 
         216          182          187          278          133          536 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 
         428         1955          624            5          485          452 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 
         392          462          993          240         1330         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 
         488          512         1980         1081         1966          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         424          629          432          224          318          394 
TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6224 
         429          526          348          367          317          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
        1959          815         1378         1007          509          901 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 
         613          393          608          358         1971          514 
TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
        1969          379          350         1956         1435         1191 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7377 
        1245         1960          105         1979          759         1968 
TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
        1036          907          156          181         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 
        1950         3295         1438         1978         2886         2437 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         406         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1665         1957         1969         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 
        1970         1939         1987         1724         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 
         797         1967         1976         1099         1974         1955 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1947         1972         1959          750          717          317 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6825 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         237          701          491          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
        1965          575          299          368          324          564 
TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6I0 
          15          384          403            5           37           33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67D 
         360          412          440          360          210           56 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG 
        1652         1954         1968          400          357          218 
TCGA-QK-A6IH TCGA-QK-A6IJ 
         228           64 

$`DEL PEAK 12(5Q11.2) WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         415         1983          248          722         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-A4IF 
         725          623         1636         1747          644          895 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
        2878          140          558          310          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         638         1153          436            4          799          721 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         142          613          642          369          395         1960 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
         811         1268          173         1977         1980         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        1975          413          290          433          594          629 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 
          45           98         1970          202          424          611 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         119          432           46          443          447          225 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         484          175         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422          896         1399          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 
        1000         1057         1959         1461         1309          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
         968         1960         1963          545          548          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         303         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
        1521         1966         1050         1125          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 
         345          354          234          479         1440          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
          30          972          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1951          392          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 
         930          216         1077          911         1472          584 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-6433 
         546         2327         1958          519          701          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1899         1970         1948         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7099 
        3835         1948         1969         1966         1959         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7410 
        1959         1945         1979         1444         1960         1948 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1957         1937         1973         1937         1984         1958 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7085 
        1981          851         1945         1954         1970          321 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
         828          773          292           77          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         1778         1081 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         775          622          369          340          490          658 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          92          585            3           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7754 
         407           58          133          414            2           25 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10          111         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         588          351          224           14           34          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910          721         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6II 
         578         1917          553          245          225 

  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                            5                             2 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                         3837                          3835 
  DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE 
                          542                           658 
[1] "5.0 - 3837.0 (542.0)" "2.0 - 3835.0 (658.0)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 12(5Q11.2) MUTATED         8       27        28        86         3
  DEL PEAK 12(5Q11.2) WILD-TYPE      16       36        43       106         6
D41V3, multiclass
           clus
vv          DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  STAGE I                             8                            16
  STAGE II                           27                            36
  STAGE III                          28                            43
  STAGE IVA                          86                           106
  STAGE IVB                           3                             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 12(5Q11.2) MUTATED    9 49 31 63
  DEL PEAK 12(5Q11.2) WILD-TYPE 31 59 54 68
D41V4, multiclass
    clus
vv   DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  T1                           9                            31
  T2                          49                            59
  T3                          31                            54
  T4                          63                            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                            N0 N1 N2 N3
  DEL PEAK 12(5Q11.2) MUTATED   46 26 62  2
  DEL PEAK 12(5Q11.2) WILD-TYPE 90 30 67  5
D41V5, multiclass
    clus
vv   DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  N0                          46                            90
  N1                          26                            30
  N2                          62                            67
  N3                           2                             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"
D41V6, binary
                               cls
clus                             0  1
  DEL PEAK 12(5Q11.2) MUTATED   37 20
  DEL PEAK 12(5Q11.2) WILD-TYPE 71 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q11.2) MUTATED     37   20
  DEL PEAK 12(5Q11.2) WILD-TYPE   71   28
    clus
vv   DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  M0                          37                            71
  MX                          20                            28
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q11.2) MUTATED    40 131
  DEL PEAK 12(5Q11.2) WILD-TYPE  81 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q11.2) MUTATED     40  131
  DEL PEAK 12(5Q11.2) WILD-TYPE   81  165
        clus
vv       DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  FEMALE                          40                            81
  MALE                           131                           165
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(5Q11.2) MUTATED                                     169
  DEL PEAK 12(5Q11.2) WILD-TYPE                                   241
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 12(5Q11.2) MUTATED                                                             1
  DEL PEAK 12(5Q11.2) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 12(5Q11.2) MUTATED                                                     1
  DEL PEAK 12(5Q11.2) WILD-TYPE                                                   5
D41V8, multiclass
                                                             clus
vv                                                            DEL PEAK 12(5Q11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               169
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 12(5Q11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 241
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q11.2) MUTATED    37 134
  DEL PEAK 12(5Q11.2) WILD-TYPE  42 204
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q11.2) MUTATED     37  134
  DEL PEAK 12(5Q11.2) WILD-TYPE   42  204
     clus
vv    DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
  NO                           37                            42
  YES                         134                           204
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(5Q11.2) MUTATED                                  1     3
  DEL PEAK 12(5Q11.2) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(5Q11.2) MUTATED                          21   140
  DEL PEAK 12(5Q11.2) WILD-TYPE                        12   221
D41V12, multiclass
                                  clus
vv                                 DEL PEAK 12(5Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                    140
                                  clus
vv                                 DEL PEAK 12(5Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q11.2) MUTATED    11 152
  DEL PEAK 12(5Q11.2) WILD-TYPE   7 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q11.2) MUTATED     11  152
  DEL PEAK 12(5Q11.2) WILD-TYPE    7  229
                        clus
vv                       DEL PEAK 12(5Q11.2) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         152
                        clus
vv                       DEL PEAK 12(5Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           229
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 13(5Q15) MUTATION ANALYSIS
D42V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(5Q15) MUTATED   113  40
  DEL PEAK 13(5Q15) WILD-TYPE 144  58
  DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE 
                        153                         202 
  DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE 
                         40                          58 
$`DEL PEAK 13(5Q15) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 
         462          283          276          520          190          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA 
          63          384          113          236          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7863 
         216          182          187          278          133          423 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 
        1153          428         1955          624            5          485 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
         452          392          462          993          395          240 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 
        1330         1988          488          512         1081         1966 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6019 TCGA-CN-6021 
         630          424          629          433          432         1970 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63W 
         224          318          394          429          526          348 
TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 
         367          317          341         1959          815         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH 
        1007          509          901          613          393          303 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 
         608          358         1971          514          379          350 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        1956         1435         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7390 
         105         1979          759         1968         1036          907 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         156          181         1472         1955          522         1950 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5973 
        1438          546         1978         2886         2437         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6954 
        1478         1840          215         1315         1665         1957 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
        1969         3837         1959         1970         1970         1939 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1987         1724         1095          954          797         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7435 
        1976         1099         1955         1947         1972         1959 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6825 
         750          717          317          237          701          491 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         106          104         1778          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
        1965          575          299          368          324          564 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 
          92          384           14          414          403            5 
TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T 
          37           33          360          412          360          210 
TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 
          56         1652         1954         1968          400          357 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
         218          228           64 

$`DEL PEAK 13(5Q15) WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         415         1983          248          722         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-A4IF 
         725          623         1636         1747          644          895 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
        2878          140          558          310          536          687 
TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
         638          436            4          799          721          142 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         613          642          369         1960          811         1268 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 
         173         1980         1977         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
         413          290          594          629           45           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
         202          424          611          119          432           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 
         443          447          225          484          175         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
         129          870         1000         1057          985         1959 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
        1461         1309          877          968         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         545          548          391         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6492 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7383 
         479          889           30          972          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
         908          898          930          216         1077          911 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
        3295          584         2327         1958          519          406 
TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
         701          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 
        1959         1936         1959         1945         1979         1444 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 
        1960         1974         1948         1957         1937         1973 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
        1954         1970          321          828          773          292 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5625 
          77          154          568          128          112         1081 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         775          622          369          340          490          658 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
          15          585            3           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 
          58          133            2           25           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J 
        1057          485          122          441          588          440 
TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         351          224           14           34          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         112          254          910          721         1120          578 
TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6II 
        1917          553          245          225 

  DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE 
                          5                           2 
  DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE 
                       3837                        3835 
  DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE 
                        520                         721 
[1] "5.0 - 3837.0 (520.0)" "2.0 - 3835.0 (721.0)"
[1] "hr=" "1.1"
D42V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 13(5Q15) MUTATED         8       28        30        90         3
  DEL PEAK 13(5Q15) WILD-TYPE      16       35        41       102         6
D42V3, multiclass
           clus
vv          DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE
  STAGE I                           8                          16
  STAGE II                         28                          35
  STAGE III                        30                          41
  STAGE IVA                        90                         102
  STAGE IVB                         3                           6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK 13(5Q15) MUTATED   10 50 33 67
  DEL PEAK 13(5Q15) WILD-TYPE 30 58 52 64
D42V4, multiclass
    clus
vv   DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE
  T1                        10                          30
  T2                        50                          58
  T3                        33                          52
  T4                        67                          64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 13(5Q15) MUTATED   53 26 61  2
  DEL PEAK 13(5Q15) WILD-TYPE 83 30 68  5
D42V5, multiclass
    clus
vv   DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE
  N0                        53                          83
  N1                        26                          30
  N2                        61                          68
  N3                         2                           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"
D42V6, binary
                             cls
clus                           0  1
  DEL PEAK 13(5Q15) MUTATED   42 22
  DEL PEAK 13(5Q15) WILD-TYPE 66 26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(5Q15) MUTATED     42   22
  DEL PEAK 13(5Q15) WILD-TYPE   66   26
    clus
vv   DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE
  M0                        42                          66
  MX                        22                          26
[1] 2 2
[1] FALSE
D42V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(5Q15) MUTATED    45 136
  DEL PEAK 13(5Q15) WILD-TYPE  76 160
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(5Q15) MUTATED     45  136
  DEL PEAK 13(5Q15) WILD-TYPE   76  160
        clus
vv       DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE
  FEMALE                        45                          76
  MALE                         136                         160
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(5Q15) MUTATED                                     179
  DEL PEAK 13(5Q15) WILD-TYPE                                   231
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 13(5Q15) MUTATED                                                             1
  DEL PEAK 13(5Q15) WILD-TYPE                                                           0
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 13(5Q15) MUTATED                                                     1
  DEL PEAK 13(5Q15) WILD-TYPE                                                   5
D42V8, multiclass
                                                             clus
vv                                                            DEL PEAK 13(5Q15) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             179
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 1
                                                             clus
vv                                                            DEL PEAK 13(5Q15) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               231
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                             cls
clus                            0   1
  DEL PEAK 13(5Q15) MUTATED    38 143
  DEL PEAK 13(5Q15) WILD-TYPE  41 195
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(5Q15) MUTATED     38  143
  DEL PEAK 13(5Q15) WILD-TYPE   41  195
     clus
vv    DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE
  NO                         38                          41
  YES                       143                         195
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q15) MUTATED                                  1     5
  DEL PEAK 13(5Q15) WILD-TYPE                                0     5
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q15) MUTATED                          20   149
  DEL PEAK 13(5Q15) WILD-TYPE                        13   212
D42V12, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               20
  WHITE                                                  149
                                  clus
vv                                 DEL PEAK 13(5Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                             cls
clus                            0   1
  DEL PEAK 13(5Q15) MUTATED    11 161
  DEL PEAK 13(5Q15) WILD-TYPE   7 220
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(5Q15) MUTATED     11  161
  DEL PEAK 13(5Q15) WILD-TYPE    7  220
                        clus
vv                       DEL PEAK 13(5Q15) MUTATED DEL PEAK 13(5Q15) WILD-TYPE
  HISPANIC OR LATINO                            11                           7
  NOT HISPANIC OR LATINO                       161                         220
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 14(5Q35.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q35.3) MUTATED   101  37
  DEL PEAK 14(5Q35.3) WILD-TYPE 156  61
  DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE 
                          138                           217 
  DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE 
                           37                            61 
$`DEL PEAK 14(5Q35.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 
         462          283          276          520          451          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         113          236          513          351          216          182 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 
         187          278          536          687         1153         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
         624            5          485          452          392          462 
TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
         993          240         1330         1988          488          512 
TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6021 
        1081         1966          630          629          432         1970 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         224          318          394          119          432          429 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-6229 
         526          348          367          317         1959          815 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
        1378         1007          509          901          613          393 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 
         303          608          358         1971          514          379 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1956         1435         1191         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 
        1979          759           30         1036          907          156 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         181         1472          522         1950         3295         1438 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
        1978         2886         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 
        1315         1665         1970         1959         1957         1969 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7242 
        3837         1959         1970         1939         1987         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 
         954          797         1967         1976         1099         1957 
TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 
        1947         1959          750          317          237          701 
TCGA-D6-6826 TCGA-D6-8568 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         154          106          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G 
         575          299          368          324          564           15 
TCGA-F7-A61V TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         384          414            5           25           37           55 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A6I9 
         360          412          360          210           56          254 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
        1652         1954          357          218          228           64 

$`DEL PEAK 14(5Q35.3) WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         415         1983          248          722         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         725          623         1636         1747          190          644 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
          63          895         2878          140          133          558 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 
         310          423          638          428          436            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 
         799          721          142          613          642          369 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 
         395         1960          811         1268          173         1980 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1977         1980         1966         1975          413          290 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
         424          433          594          629           45           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         202          424          611           46          443          447 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         225          484          175         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 
         870         1000         1057          985         1959         1461 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         548          391         2562         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 
        1777         1521         1966         1050         1125         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 
         362          311          345          354          234          350 
TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
         479         1440          889          972         1968          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
        1954          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 
         946          908          898          930          216         1077 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 
         911         1955          584          546         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 
        2437          519          406          701          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1948         1969         1952         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1966         1959         1970         1936         1959         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 
        1979         1724         1444         1960         1974         1948 
TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1955         1937         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1958         1981          851         1945         1954         1970 
TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
         717          321          828          773          292           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 
         491          568          128          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 
        1081          775          622          369          340          490 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 
         658           92          585            3           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 
           6          407           58          133          403            2 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         111           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X 
         588          440          351          224           14           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         392          111          112          910          721         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF 
         578         1917         1968          400          553          245 
TCGA-QK-A6II 
         225 

  DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE 
                            5                             2 
  DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE 
                         3837                          3835 
  DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE 
                          524                           717 
[1] "5.0 - 3837.0 (524.0)" "2.0 - 3835.0 (717.0)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 14(5Q35.3) MUTATED         7       23        31        78         2
  DEL PEAK 14(5Q35.3) WILD-TYPE      17       40        40       114         7
D43V3, multiclass
           clus
vv          DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE
  STAGE I                             7                            17
  STAGE II                           23                            40
  STAGE III                          31                            40
  STAGE IVA                          78                           114
  STAGE IVB                           2                             7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 14(5Q35.3) MUTATED    8 45 36 52
  DEL PEAK 14(5Q35.3) WILD-TYPE 32 63 49 79
D43V4, multiclass
    clus
vv   DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE
  T1                           8                            32
  T2                          45                            63
  T3                          36                            49
  T4                          52                            79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 14(5Q35.3) MUTATED   45 24 58  1
  DEL PEAK 14(5Q35.3) WILD-TYPE 91 32 71  6
D43V5, multiclass
    clus
vv   DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE
  N0                          45                            91
  N1                          24                            32
  N2                          58                            71
  N3                           1                             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"
D43V6, binary
                               cls
clus                             0  1
  DEL PEAK 14(5Q35.3) MUTATED   39 17
  DEL PEAK 14(5Q35.3) WILD-TYPE 69 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q35.3) MUTATED     39   17
  DEL PEAK 14(5Q35.3) WILD-TYPE   69   31
    clus
vv   DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE
  M0                          39                            69
  MX                          17                            31
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q35.3) MUTATED    40 120
  DEL PEAK 14(5Q35.3) WILD-TYPE  81 176
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q35.3) MUTATED     40  120
  DEL PEAK 14(5Q35.3) WILD-TYPE   81  176
        clus
vv       DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE
  FEMALE                          40                            81
  MALE                           120                           176
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(5Q35.3) MUTATED                                     158
  DEL PEAK 14(5Q35.3) WILD-TYPE                                   252
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 14(5Q35.3) MUTATED                                                             1
  DEL PEAK 14(5Q35.3) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 14(5Q35.3) MUTATED                                                     1
  DEL PEAK 14(5Q35.3) WILD-TYPE                                                   5
D43V8, multiclass
                                                             clus
vv                                                            DEL PEAK 14(5Q35.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               158
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 14(5Q35.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 252
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q35.3) MUTATED    34 126
  DEL PEAK 14(5Q35.3) WILD-TYPE  45 212
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q35.3) MUTATED     34  126
  DEL PEAK 14(5Q35.3) WILD-TYPE   45  212
     clus
vv    DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE
  NO                           34                            45
  YES                         126                           212
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(5Q35.3) MUTATED                                  1     4
  DEL PEAK 14(5Q35.3) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q35.3) MUTATED                          17   132
  DEL PEAK 14(5Q35.3) WILD-TYPE                        16   229
D43V12, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    132
                                  clus
vv                                 DEL PEAK 14(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      229
[1] 4 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 14(5Q35.3) MUTATED     9 144
  DEL PEAK 14(5Q35.3) WILD-TYPE   9 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q35.3) MUTATED      9  144
  DEL PEAK 14(5Q35.3) WILD-TYPE    9  237
                        clus
vv                       DEL PEAK 14(5Q35.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         144
                        clus
vv                       DEL PEAK 14(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           237
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6P25.3) MUTATED    44  25
  DEL PEAK 15(6P25.3) WILD-TYPE 213  73
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           69                           286 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           25                            73 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-BA-5152 TCGA-BA-5559 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7862 TCGA-CN-4723 
        1288         1747          140          133          536          721 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5359 TCGA-CN-5370 
         485          613          369          811         1980         1975 
TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 
         630          594          202          224          611          119 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6221 
         429          443          225          367          317         1000 
TCGA-CQ-6223 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-6473 TCGA-CR-6478 
        1057          613          548          608         1125         1969 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7388 
         379         1956         1191         1979          889         1951 
TCGA-CR-7399 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
         181         1950         3295         1438          584         1978 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6934 TCGA-CV-6945 TCGA-CV-6960 
        1958         2437          215         1948         1969         1969 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7418 TCGA-CV-7430 
        1970         1939         1967         1976         1955         1972 
TCGA-D6-6823 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-F7-A50I 
         701          154         1778          575          622           92 
TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-MT-A67G 
           6            5           37           55          111          112 
TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T8 
        1652          578          400 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1762          520          725          623         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          513          351          216          182 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
         187         2878          278          558          310          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 
         624            5            4          799          142          452 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
         392          462          993          642          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1960         1330         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1081         1977         1980         1966         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6017 
         413          290          424          629          433          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 
          45          432           98         1970          424          318 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V 
         394          432           46          447          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         348          175         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422          896         1399          341          129          870 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1007          509         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1960         1963          545          393          391          303 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
        1521         1966         1050         1971          514          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
         311          345          354          234          350          479 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
        1435         1440         1245         1960          105          759 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         997         1430          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5441 
         911         1472         1955          522          546         2886 
TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2327          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840         1315         1665          641         1899         1970 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1969         1952         1959         3835         1948         1966 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        1957         1959         3837         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1945         1987         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 
        1095          954          797         1960         1099         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
        1948         1957         1947         1937         1973         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1984         1958         1959         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         237          828          773          292           77          491 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 
         568          106          128          112          104         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7592 
         516         1030          548         1965          775          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         658           15          585            3          384           14 
TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          13          407           58          133          414          403 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
           2           25           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         441          588          360          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
          56          111          254          910          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1954         1917         1968          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         218          228          225           64 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                            5                             2 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         3295                          3837 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                          622                           629 
[1] "5.0 - 3295.0 (622.0)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 15(6P25.3) MUTATED         2        9        12        45         1
  DEL PEAK 15(6P25.3) WILD-TYPE      22       54        59       147         8
D44V3, multiclass
           clus
vv          DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                             2                            22
  STAGE II                            9                            54
  STAGE III                          12                            59
  STAGE IVA                          45                           147
  STAGE IVB                           1                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 15(6P25.3) MUTATED    5 14 19 32
  DEL PEAK 15(6P25.3) WILD-TYPE 35 94 66 99
D44V4, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T1                           5                            35
  T2                          14                            94
  T3                          19                            66
  T4                          32                            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                             N0  N1  N2  N3
  DEL PEAK 15(6P25.3) MUTATED    22  10  29   1
  DEL PEAK 15(6P25.3) WILD-TYPE 114  46 100   6
D44V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          22                           114
  N1                          10                            46
  N2                          29                           100
  N3                           1                             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"
D44V6, binary
                               cls
clus                             0  1
  DEL PEAK 15(6P25.3) MUTATED   18  9
  DEL PEAK 15(6P25.3) WILD-TYPE 90 39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     18    9
  DEL PEAK 15(6P25.3) WILD-TYPE   90   39
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  M0                          18                            90
  MX                           9                            39
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    18  60
  DEL PEAK 15(6P25.3) WILD-TYPE 103 236
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     18   60
  DEL PEAK 15(6P25.3) WILD-TYPE  103  236
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          18                           103
  MALE                            60                           236
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                                      77
  DEL PEAK 15(6P25.3) WILD-TYPE                                   333
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 15(6P25.3) MUTATED                                                             0
  DEL PEAK 15(6P25.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 15(6P25.3) MUTATED                                                     1
  DEL PEAK 15(6P25.3) WILD-TYPE                                                   5
D44V8, multiclass
                                                             clus
vv                                                            DEL PEAK 15(6P25.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                77
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 15(6P25.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 333
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    17  61
  DEL PEAK 15(6P25.3) WILD-TYPE  62 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     17   61
  DEL PEAK 15(6P25.3) WILD-TYPE   62  277
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                           17                            62
  YES                          61                           277
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(6P25.3) MUTATED                                  0     0
  DEL PEAK 15(6P25.3) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6P25.3) MUTATED                          12    62
  DEL PEAK 15(6P25.3) WILD-TYPE                        21   299
D44V12, multiclass
                                  clus
vv                                 DEL PEAK 15(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     62
                                  clus
vv                                 DEL PEAK 15(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      299
[1] 4 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 15(6P25.3) MUTATED     3  69
  DEL PEAK 15(6P25.3) WILD-TYPE  15 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      3   69
  DEL PEAK 15(6P25.3) WILD-TYPE   15  312
                        clus
vv                       DEL PEAK 15(6P25.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          69
                        clus
vv                       DEL PEAK 15(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           312
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 16(7Q31.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(7Q31.1) MUTATED    40  19
  DEL PEAK 16(7Q31.1) WILD-TYPE 217  79
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           59                           296 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           19                            79 
$`DEL PEAK 16(7Q31.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 
         462          415          248         1288         1747          190 
TCGA-BA-6872 TCGA-BA-A6DE TCGA-BB-7861 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 
         384          182          310          436            5            4 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5374 
         462          993          369          240         1980          290 
TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6998 TCGA-CN-A49B TCGA-CQ-6218 
         424           45          318           46          447          870 
TCGA-CQ-A4CA TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
        1963          358         1971         1191         1440         1245 
TCGA-CR-7374 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-6003 
          30          156          181         2437         2641         1665 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7433 
        1957         1969         1959         1959         1987         1984 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JE TCGA-CX-7082 TCGA-D6-6823 TCGA-D6-6826 
        1959         1981          750          317          701          154 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A623 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
         658           15            6          441          360          412 
TCGA-KU-A66T TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A64Z 
         210          721         1954         1968          553 

$`DEL PEAK 16(7Q31.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
         283         1983          276          722         1762          520 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         725          623         1636          644          451           63 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         113          236          895          513          351          216 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         536          423          687          638         1153          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        1955          624          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 
         452          613          392          642          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1975          413          630          629          433          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
         629          432           98         1970          202          424 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         224          611          394          119          432          429 
TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         443          225          526          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 
         896         1399          317          341          129         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959          815         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1378         1007          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         968         1960          613          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
        1960          105         1979          759          889          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         898          930          216         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1955          522         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
         546         1978         2886         2327         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         406          701         1478         1840          215         1315 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-7090 
        1959         3835         1948         1969         1966         3837 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1970         1970         1936         1959         1939         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1937         1958          851         1945         1954         1970 
TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         717          321          237          828          773          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
          77          491          568          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         104         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1965          575          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I 
         368          324          340          564          490           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
          25           37           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          11           49           10          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         485          122          588          440          351          360 
TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         224           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6T0 
         112          254          910         1652         1120          578 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
        1917          400          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                            4                             2 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                         2641                          3837 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                          462                           634 
[1] "4.0 - 2641.0 (462.0)" "2.0 - 3837.0 (634.0)"
[1] "hr=" "1.1"
D45V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 16(7Q31.1) MUTATED         3        9        12        34         0
  DEL PEAK 16(7Q31.1) WILD-TYPE      21       54        59       158         9
D45V3, multiclass
           clus
vv          DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  STAGE I                             3                            21
  STAGE II                            9                            54
  STAGE III                          12                            59
  STAGE IVA                          34                           158
  STAGE IVB                           0                             9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 16(7Q31.1) MUTATED     5  19  13  21
  DEL PEAK 16(7Q31.1) WILD-TYPE  35  89  72 110
D45V4, multiclass
    clus
vv   DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  T1                           5                            35
  T2                          19                            89
  T3                          13                            72
  T4                          21                           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                             N0  N1  N2  N3
  DEL PEAK 16(7Q31.1) MUTATED    17  14  22   0
  DEL PEAK 16(7Q31.1) WILD-TYPE 119  42 107   7
D45V5, multiclass
    clus
vv   DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  N0                          17                           119
  N1                          14                            42
  N2                          22                           107
  N3                           0                             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 16(7Q31.1) MUTATED   17  8
  DEL PEAK 16(7Q31.1) WILD-TYPE 91 40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED     17    8
  DEL PEAK 16(7Q31.1) WILD-TYPE   91   40
    clus
vv   DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  M0                          17                            91
  MX                           8                            40
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(7Q31.1) MUTATED    18  47
  DEL PEAK 16(7Q31.1) WILD-TYPE 103 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED     18   47
  DEL PEAK 16(7Q31.1) WILD-TYPE  103  249
        clus
vv       DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  FEMALE                          18                           103
  MALE                            47                           249
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(7Q31.1) MUTATED                                      64
  DEL PEAK 16(7Q31.1) WILD-TYPE                                   346
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 16(7Q31.1) MUTATED                                                             0
  DEL PEAK 16(7Q31.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 16(7Q31.1) MUTATED                                                     1
  DEL PEAK 16(7Q31.1) WILD-TYPE                                                   5
D45V8, multiclass
                                                             clus
vv                                                            DEL PEAK 16(7Q31.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                64
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 16(7Q31.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 346
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(7Q31.1) MUTATED    15  50
  DEL PEAK 16(7Q31.1) WILD-TYPE  64 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED     15   50
  DEL PEAK 16(7Q31.1) WILD-TYPE   64  288
     clus
vv    DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  NO                           15                            64
  YES                          50                           288
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(7Q31.1) MUTATED                                  0     3
  DEL PEAK 16(7Q31.1) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(7Q31.1) MUTATED                           5    56
  DEL PEAK 16(7Q31.1) WILD-TYPE                        28   305
D45V12, multiclass
                                  clus
vv                                 DEL PEAK 16(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     56
                                  clus
vv                                 DEL PEAK 16(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      305
[1] 4 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 16(7Q31.1) MUTATED     2  60
  DEL PEAK 16(7Q31.1) WILD-TYPE  16 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED      2   60
  DEL PEAK 16(7Q31.1) WILD-TYPE   16  321
                        clus
vv                       DEL PEAK 16(7Q31.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       DEL PEAK 16(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           321
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 17(7Q36.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(7Q36.1) MUTATED    59  31
  DEL PEAK 17(7Q36.1) WILD-TYPE 198  67
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           90                           265 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           31                            67 
$`DEL PEAK 17(7Q36.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6871 
         462          415         1288         1747          190           63 
TCGA-BA-7269 TCGA-BA-A6DE TCGA-BB-7863 TCGA-BB-7872 TCGA-CN-4729 TCGA-CN-4730 
         236          182          423          436          392          462 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-5355 
         993          369          395          240         1960          488 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
         173         1980         1977          290          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6997 TCGA-CN-6998 
         433          594           45          318          429           46 
TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5331 TCGA-CQ-6221 
         447          526          348          175         1399         1000 
TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CR-5247 
        1959          509         1960         1963          545          358 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
        1971         1969          350         1191         1245         1960 
TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5444 TCGA-CV-6003 
          30          997          156          522         2437         1665 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1970         1969         1959         1957         1969         1959 
TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7254 TCGA-CV-7424 TCGA-CV-7433 TCGA-CV-7435 
        1959         1987         1976         1947         1984         1959 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6826 TCGA-DQ-7588 
         750          317          828          701          154         1965 
TCGA-DQ-7594 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-8502 
         368          658           15           14            6          133 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T 
         111         1057          441          412          440          210 
TCGA-MT-A51W TCGA-MT-A67A TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
          14          392          721         1954         1968          400 

$`DEL PEAK 17(7Q36.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         283         1983          276          248          722         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
         520          725          623         1636          644          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         384          113          895          513          351          216 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         310          536          687          638         1153          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
        1955          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4739 
         485          142          452          613          642         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5365 
         811         1268         1988          512         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6017 
        1966         1966         1975          413          630          629 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202          424          224 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A63T 
         611          394          119          432          443          225 
TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         484          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422          896          317          341          129          870 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        1057          985         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
        1007         1309          901          877          968          613 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1050         1125          514          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         354          234          379          479         1956         1435 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
        1440          105         1979          759          889          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 
        1968         1036          796         1954         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         930          216          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1955         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
        1978         2886         2327         1958          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
         641         1899         1948         1952         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1969         1966         3837         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1945         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1095          954          797         1967         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 
        1974         1948         1955         1957         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1972         1937         1958         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
        1954         1970          717          321          237          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         292           77          491          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
         548          575          775          622          299          369 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J 
         324          340          564          490           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
           3          384           13          407           58          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         403            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L 
          33          485          122          588          360          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         360          224           34           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         254          910         1652         1120          578         1917 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ 
          64 

  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                            6                             2 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                         2437                          3837 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                        515.5                         642.0 
[1] "6.0 - 2437.0 (515.5)" "2.0 - 3837.0 (642.0)"
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 17(7Q36.1) MUTATED         6       12        18        50         3
  DEL PEAK 17(7Q36.1) WILD-TYPE      18       51        53       142         6
D46V3, multiclass
           clus
vv          DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  STAGE I                             6                            18
  STAGE II                           12                            51
  STAGE III                          18                            53
  STAGE IVA                          50                           142
  STAGE IVB                           3                             6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 17(7Q36.1) MUTATED   11 28 20 34
  DEL PEAK 17(7Q36.1) WILD-TYPE 29 80 65 97
D46V4, multiclass
    clus
vv   DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  T1                          11                            29
  T2                          28                            80
  T3                          20                            65
  T4                          34                            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                             N0  N1  N2  N3
  DEL PEAK 17(7Q36.1) MUTATED    29  16  36   3
  DEL PEAK 17(7Q36.1) WILD-TYPE 107  40  93   4
D46V5, multiclass
    clus
vv   DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  N0                          29                           107
  N1                          16                            40
  N2                          36                            93
  N3                           3                             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"
D46V6, binary
                               cls
clus                             0  1
  DEL PEAK 17(7Q36.1) MUTATED   23 13
  DEL PEAK 17(7Q36.1) WILD-TYPE 85 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED     23   13
  DEL PEAK 17(7Q36.1) WILD-TYPE   85   35
    clus
vv   DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  M0                          23                            85
  MX                          13                            35
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED    24  81
  DEL PEAK 17(7Q36.1) WILD-TYPE  97 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED     24   81
  DEL PEAK 17(7Q36.1) WILD-TYPE   97  215
        clus
vv       DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  FEMALE                          24                            97
  MALE                            81                           215
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(7Q36.1) MUTATED                                     104
  DEL PEAK 17(7Q36.1) WILD-TYPE                                   306
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 17(7Q36.1) MUTATED                                                             0
  DEL PEAK 17(7Q36.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 17(7Q36.1) MUTATED                                                     1
  DEL PEAK 17(7Q36.1) WILD-TYPE                                                   5
D46V8, multiclass
                                                             clus
vv                                                            DEL PEAK 17(7Q36.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               104
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 17(7Q36.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 306
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED    21  84
  DEL PEAK 17(7Q36.1) WILD-TYPE  58 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED     21   84
  DEL PEAK 17(7Q36.1) WILD-TYPE   58  254
     clus
vv    DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  NO                           21                            58
  YES                          84                           254
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(7Q36.1) MUTATED                                  0     3
  DEL PEAK 17(7Q36.1) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(7Q36.1) MUTATED                          10    90
  DEL PEAK 17(7Q36.1) WILD-TYPE                        23   271
D46V12, multiclass
                                  clus
vv                                 DEL PEAK 17(7Q36.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     90
                                  clus
vv                                 DEL PEAK 17(7Q36.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED     4  96
  DEL PEAK 17(7Q36.1) WILD-TYPE  14 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED      4   96
  DEL PEAK 17(7Q36.1) WILD-TYPE   14  285
                        clus
vv                       DEL PEAK 17(7Q36.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          96
                        clus
vv                       DEL PEAK 17(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           285
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 18(8P23.2) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED   132  68
  DEL PEAK 18(8P23.2) WILD-TYPE 125  30
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          200                           155 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           68                            30 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 
         462         1983          248          722          725          623 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1636          190          451          384          113          236 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 
         513          216          182          278          133          536 
TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 
         423         1153          428          436            5            4 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 
         721          485          142          452          392          369 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 
         395         1960          811         1988          512         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          413 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
         290          424          629          433          594           45 
TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
          98          224          611          394          432          429 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5329 
         443          447          348          367          654         1422 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         896          317          129         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
        1309          901          877          968         1960          545 
TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6471 TCGA-CR-6474 
         548          608         2562          358         1966         1971 
TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7369 
        1969          354          379         1435         1440         1960 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7383 
         759          889           30          972         1968         1954 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 
        1430         1951          907          930          181         1077 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1955          522         1950         3295         1438          584 
TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2886         2437          519         2641         1478         1840 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
        1899         1970         1969         1952         3835         1948 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        1966         1957         1969         3837         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 
        1936         1959         1945         1724         1444          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 
         797         1967         1976         1099         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1937         1973         1972         1984         1958         1981 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6517 
        1945         1970          750          317          828          292 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5624 
         701          491          154          106          112         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 
        1081         1030          548          575          299          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13            6           58          133          414 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6I0 
           2            5           55           25           49           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
        1057          485          588          360          412          440 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A6I9 TCGA-P3-A5QA 
         351          210           34           56          254         1652 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG 
        1954         1968          400          553          357          218 
TCGA-QK-A6IH TCGA-QK-A6IJ 
         228           64 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         283          415          276         1288         1762          520 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BB-4217 
        1747          644           63          895          351          187 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 
        2878          140          558          310          687          638 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
        1955          624          799          613          462          993 
TCGA-CN-4733 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 
         642          240         1330         1268          488          173 
TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
        1980          630          629          432         1970          202 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63U 
         424          318          119           46          225          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 
         484          175         1466         1207         1660         1399 
TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CE 
         341          870         1000          613         1963          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         391          303         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
        1521         1050         1125          514          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 
         345          234          350          479         1956         1191 
TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
        1245          105         1979         1036          796          997 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 
         392          913          946          908          898          216 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
         156          911         1472          546         1978         2327 
TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        1958          406          701          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-7091 
         641         1948         1959         1969         1959         1959 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7406 
        1939         1987         1979         1095         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A461 
        1948         1955         1937         1959          851         1954 
TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6827 
         717          321          237          773           77          568 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 
         128          104          516         1965          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A61V TCGA-H7-7774 
         369          368          324          340          384          407 
TCGA-H7-A6C5 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
         403           25           37           44           24           11 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S 
          10          111          122          441          360          224 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QE 
          14          392          111          112          910          721 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6II 
        1120          578         1917          245          225 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                            2                            10 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         3837                          2878 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        641.5                         624.0 
[1] "2.0 - 3837.0 (641.5)"  "10.0 - 2878.0 (624.0)"
[1] "hr=" "1.2"
D47V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 18(8P23.2) MUTATED        14       35        45       120         6
  DEL PEAK 18(8P23.2) WILD-TYPE      10       28        26        72         3
D47V3, multiclass
           clus
vv          DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  STAGE I                            14                            10
  STAGE II                           35                            28
  STAGE III                          45                            26
  STAGE IVA                         120                            72
  STAGE IVB                           6                             3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 18(8P23.2) MUTATED   23 61 52 85
  DEL PEAK 18(8P23.2) WILD-TYPE 17 47 33 46
D47V4, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  T1                          23                            17
  T2                          61                            47
  T3                          52                            33
  T4                          85                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 18(8P23.2) MUTATED   75 38 81  4
  DEL PEAK 18(8P23.2) WILD-TYPE 61 18 48  3
D47V5, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  N0                          75                            61
  N1                          38                            18
  N2                          81                            48
  N3                           4                             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"
D47V6, binary
                               cls
clus                             0  1
  DEL PEAK 18(8P23.2) MUTATED   70 25
  DEL PEAK 18(8P23.2) WILD-TYPE 38 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     70   25
  DEL PEAK 18(8P23.2) WILD-TYPE   38   23
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  M0                          70                            38
  MX                          25                            23
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    75 166
  DEL PEAK 18(8P23.2) WILD-TYPE  46 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     75  166
  DEL PEAK 18(8P23.2) WILD-TYPE   46  130
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                          75                            46
  MALE                           166                           130
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                     240
  DEL PEAK 18(8P23.2) WILD-TYPE                                   170
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 18(8P23.2) MUTATED                                                             0
  DEL PEAK 18(8P23.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 18(8P23.2) MUTATED                                                     1
  DEL PEAK 18(8P23.2) WILD-TYPE                                                   5
D47V8, multiclass
                                                             clus
vv                                                            DEL PEAK 18(8P23.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               240
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 18(8P23.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 170
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    47 194
  DEL PEAK 18(8P23.2) WILD-TYPE  32 144
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     47  194
  DEL PEAK 18(8P23.2) WILD-TYPE   32  144
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                           47                            32
  YES                         194                           144
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(8P23.2) MUTATED                                  1     8
  DEL PEAK 18(8P23.2) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P23.2) MUTATED                          16   207
  DEL PEAK 18(8P23.2) WILD-TYPE                        17   154
D47V12, multiclass
                                  clus
vv                                 DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    207
                                  clus
vv                                 DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    16 214
  DEL PEAK 18(8P23.2) WILD-TYPE   2 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     16  214
  DEL PEAK 18(8P23.2) WILD-TYPE    2  167
                        clus
vv                       DEL PEAK 18(8P23.2) MUTATED
  HISPANIC OR LATINO                              16
  NOT HISPANIC OR LATINO                         214
                        clus
vv                       DEL PEAK 18(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           167
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 19(9P23) MUTATION ANALYSIS
D48V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(9P23) MUTATED   111  51
  DEL PEAK 19(9P23) WILD-TYPE 146  47
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                        162                         193 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                         51                          47 
$`DEL PEAK 19(9P23) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 
         462          283          415          276          248          520 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
         190          644          451           63          384          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7863 
         895          513          182          278          536          423 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4723 
        1153          428          436         1955          624          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 
         142          452          392          462          993          369 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5365 
         240          811         1988          512         1081         1980 
TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
        1966          629           98         1970          202          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63V 
         318          611          394          429          526          484 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5327 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 
         348          367         1660          317         1000          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1959         1461         1378         1007          509 
TCGA-CQ-7069 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6472 
         901         1963          545          608          358         1050 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 
        1971          514          354          379          350         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1191         1440         1245          759          889           30 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
        1954         1951          392          907          216          156 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1077         1955         1950         1438          584          546 
TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 
        2437         2641         1478         1315         1970         1948 
TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 
        1969         3835         1969         1969         3837         1959 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 
        1970         1939         1945         1987         1724         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 
        1095          954          797         1099         1955         1957 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q 
        1972         1937         1984         1959         1981         1945 
TCGA-CV-A461 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
        1954          317          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         701          154          106          128          112          104 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-7848 
         516          548         1965          575          324          564 
TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C5 TCGA-HD-7229 
          92           14            6           58          403            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 
           5           25           25           49          111          485 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA 
         360          440          210           34           56         1652 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
        1954         1968          400          553          228           64 

$`DEL PEAK 19(9P23) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 
        1983          722         1288         1762          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 
        1636         1747          113          351          216          187 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 
        2878          140          133          558          310          687 
TCGA-BB-7866 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4728 
         638            5            4          799          485          613 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 
         642          395         1960         1330         1268          488 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 
         173         1980         1977         1966         1975          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          630          424          433          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
          45          432          424          119          432           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         443          447          225          175         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1422          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
         870         1057          815         1309          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1960          613          548          393          391          303 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1966         1125         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
         234          479         1956         1960          105         1979 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
         972         1968         1036          796          997         1430 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 
         913          946          908          898          930          181 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 
         911         1472          522         3295         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 
        2327         1958          519          406          701         1840 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6941 
         215         1665          641         1899         1952         1959 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7099 
        1948         1966         1957         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 
        1959         1979         1967         1960         1976         1974 
TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-A45O 
        1948         1947         1937         1973         1958          851 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 
        1970          750          717          321           77          491 
TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         568         1778         1081         1030          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         299          369          368          340          490          658 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 
          15          585            3          384           13          407 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
         133          414           37           55           44           24 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
          11           10           33         1057          122          441 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W 
         588          412          351          360          224           14 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1120          578         1917          357          245          218 
TCGA-QK-A6II 
         225 

  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                          2                           3 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                       3837                        3295 
  DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE 
                      569.5                       654.0 
[1] "2.0 - 3837.0 (569.5)" "3.0 - 3295.0 (654.0)"
[1] "hr=" "1.3"
D48V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 19(9P23) MUTATED        10       28        29        93         3
  DEL PEAK 19(9P23) WILD-TYPE      14       35        42        99         6
D48V3, multiclass
           clus
vv          DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  STAGE I                          10                          14
  STAGE II                         28                          35
  STAGE III                        29                          42
  STAGE IVA                        93                          99
  STAGE IVB                         3                           6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK 19(9P23) MUTATED   15 51 39 59
  DEL PEAK 19(9P23) WILD-TYPE 25 57 46 72
D48V4, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  T1                        15                          25
  T2                        51                          57
  T3                        39                          46
  T4                        59                          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                          N0 N1 N2 N3
  DEL PEAK 19(9P23) MUTATED   58 25 64  2
  DEL PEAK 19(9P23) WILD-TYPE 78 31 65  5
D48V5, multiclass
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  N0                        58                          78
  N1                        25                          31
  N2                        64                          65
  N3                         2                           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"
D48V6, binary
                             cls
clus                           0  1
  DEL PEAK 19(9P23) MUTATED   43 21
  DEL PEAK 19(9P23) WILD-TYPE 65 27
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED     43   21
  DEL PEAK 19(9P23) WILD-TYPE   65   27
    clus
vv   DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  M0                        43                          65
  MX                        21                          27
[1] 2 2
[1] FALSE
D48V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(9P23) MUTATED    47 139
  DEL PEAK 19(9P23) WILD-TYPE  74 157
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED     47  139
  DEL PEAK 19(9P23) WILD-TYPE   74  157
        clus
vv       DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  FEMALE                        47                          74
  MALE                         139                         157
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(9P23) MUTATED                                     185
  DEL PEAK 19(9P23) WILD-TYPE                                   225
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 19(9P23) MUTATED                                                             0
  DEL PEAK 19(9P23) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 19(9P23) MUTATED                                                     1
  DEL PEAK 19(9P23) WILD-TYPE                                                   5
D48V8, multiclass
                                                             clus
vv                                                            DEL PEAK 19(9P23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             185
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 1
                                                             clus
vv                                                            DEL PEAK 19(9P23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               225
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                             cls
clus                            0   1
  DEL PEAK 19(9P23) MUTATED    34 152
  DEL PEAK 19(9P23) WILD-TYPE  45 186
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED     34  152
  DEL PEAK 19(9P23) WILD-TYPE   45  186
     clus
vv    DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  NO                         34                          45
  YES                       152                         186
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(9P23) MUTATED                                  0     5
  DEL PEAK 19(9P23) WILD-TYPE                                1     5
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9P23) MUTATED                          20   155
  DEL PEAK 19(9P23) WILD-TYPE                        13   206
D48V12, multiclass
                                  clus
vv                                 DEL PEAK 19(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               20
  WHITE                                                  155
                                  clus
vv                                 DEL PEAK 19(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    206
[1] 4 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 19(9P23) MUTATED     8 168
  DEL PEAK 19(9P23) WILD-TYPE  10 213
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(9P23) MUTATED      8  168
  DEL PEAK 19(9P23) WILD-TYPE   10  213
                        clus
vv                       DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
  HISPANIC OR LATINO                             8                          10
  NOT HISPANIC OR LATINO                       168                         213
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 20(9P21.3) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(9P21.3) MUTATED   134  65
  DEL PEAK 20(9P21.3) WILD-TYPE 123  33
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                          199                           156 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                           65                            33 
$`DEL PEAK 20(9P21.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6868 
         462          415          276          248          520          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451           63          384          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7870 
         513          182          278          133          536         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4723 
         428          436         1955          624            4          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
         993          369          240         1330          811         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
         488          512         1081         1977         1980         1966 
TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 
         413          424          629          594           45           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970          202          224          318          611          394 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5324 
         429           46          526          348          367         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         654         1660          317          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
         985         1959         1959         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          901          877          613         1963          545 
TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6488 
         358         1050         1971          514         1969          379 
TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 
         350         1435         1191         1245          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 
          30          972          796         1954         1951          907 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5431 
         216          156          181         1077         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 
        1950         3295         1438          584          546         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 
         519          406         2641         1478         1315         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 
        1970         1948         1969         1952         1959         1969 
TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 
        1969         1959         1970         1936         1939         1945 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1987         1724         1444         1095          954          797 
TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1099         1955         1957         1937         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A461 
        1984         1958         1959         1981         1945         1954 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
         317          321          237          828          292          701 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 
         154          106          128          112          104         1081 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-7848 
         516          548         1965          575          324          564 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 
         490           15           92          384           14            6 
TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         407          133          403            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           55           24           25           11           49 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
         111           33          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X 
         360          440          360          224          210           34 
TCGA-MT-A67D TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
          56         1954          578         1968          400          553 
TCGA-QK-A6IH 
         228 

$`DEL PEAK 20(9P21.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
         283         1983          722         1288         1762          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DB 
         623         1636         1747          113          351          216 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
         187         2878          140          558          310          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4736 
         687          638            5          799          642          395 
TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5370 
        1960         1268          173         1980         1966         1975 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 
         290          630          433          629          432          424 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
         119          432          443          447          225          484 
TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         175         1466         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD 
         129          815         1461          968         1960          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         393          391          303          608         2562         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
        1152          799         1777         1521         1966         1125 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 
         362          311          345          354          234          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7377 
        1956         1440         1960          105         1979         1968 
TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
        1036          997         1430          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5440 
         908          898          930          911         1472         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 
        2886         2327         1958          701         1840          215 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1665          641         3835         1948         1966         1957 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7248 
        1959         3837         1970         1959         1979         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7428 
        1960         1976         1974         1948         1947         1973 
TCGA-CV-A45O TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-D6-6516 TCGA-D6-6824 
         851         1970          750          717          773           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         491          568         1778         1030          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50J 
         299          369          368          340          658          585 
TCGA-F7-A61S TCGA-F7-A620 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-HD-8314 TCGA-HD-A634 
           3           13           58          414           44           10 
TCGA-HL-7533 TCGA-IQ-A61H TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F 
        1057          412          351           14          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6T2 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
        1917          357          245          218          225           64 

  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                            2                             3 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                         3295                          3837 
  DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE 
                        553.0                         723.5 
[1] "2.0 - 3295.0 (553.0)" "3.0 - 3837.0 (723.5)"
[1] "hr=" "1.9"
D49V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 20(9P21.3) MUTATED        13       35        38       122         4
  DEL PEAK 20(9P21.3) WILD-TYPE      11       28        33        70         5
D49V3, multiclass
           clus
vv          DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  STAGE I                            13                            11
  STAGE II                           35                            28
  STAGE III                          38                            33
  STAGE IVA                         122                            70
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 20(9P21.3) MUTATED   19 62 52 80
  DEL PEAK 20(9P21.3) WILD-TYPE 21 46 33 51
D49V4, multiclass
    clus
vv   DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  T1                          19                            21
  T2                          62                            46
  T3                          52                            33
  T4                          80                            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 20(9P21.3) MUTATED   79 32 82  3
  DEL PEAK 20(9P21.3) WILD-TYPE 57 24 47  4
D49V5, multiclass
    clus
vv   DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  N0                          79                            57
  N1                          32                            24
  N2                          82                            47
  N3                           3                             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"
D49V6, binary
                               cls
clus                             0  1
  DEL PEAK 20(9P21.3) MUTATED   54 28
  DEL PEAK 20(9P21.3) WILD-TYPE 54 20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9P21.3) MUTATED     54   28
  DEL PEAK 20(9P21.3) WILD-TYPE   54   20
    clus
vv   DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  M0                          54                            54
  MX                          28                            20
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(9P21.3) MUTATED    72 164
  DEL PEAK 20(9P21.3) WILD-TYPE  49 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9P21.3) MUTATED     72  164
  DEL PEAK 20(9P21.3) WILD-TYPE   49  132
        clus
vv       DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  FEMALE                          72                            49
  MALE                           164                           132
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(9P21.3) MUTATED                                     234
  DEL PEAK 20(9P21.3) WILD-TYPE                                   176
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 20(9P21.3) MUTATED                                                             1
  DEL PEAK 20(9P21.3) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 20(9P21.3) MUTATED                                                     1
  DEL PEAK 20(9P21.3) WILD-TYPE                                                   5
D49V8, multiclass
                                                             clus
vv                                                            DEL PEAK 20(9P21.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               234
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 20(9P21.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 176
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                               cls
clus                              0   1
  DEL PEAK 20(9P21.3) MUTATED    43 193
  DEL PEAK 20(9P21.3) WILD-TYPE  36 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9P21.3) MUTATED     43  193
  DEL PEAK 20(9P21.3) WILD-TYPE   36  145
     clus
vv    DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
  NO                           43                            36
  YES                         193                           145
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(9P21.3) MUTATED                                  0     5
  DEL PEAK 20(9P21.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(9P21.3) MUTATED                          22   204
  DEL PEAK 20(9P21.3) WILD-TYPE                        11   157
D49V12, multiclass
                                  clus
vv                                 DEL PEAK 20(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    204
                                  clus
vv                                 DEL PEAK 20(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                               cls
clus                              0   1
  DEL PEAK 20(9P21.3) MUTATED    10 215
  DEL PEAK 20(9P21.3) WILD-TYPE   8 166
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(9P21.3) MUTATED     10  215
  DEL PEAK 20(9P21.3) WILD-TYPE    8  166
                        clus
vv                       DEL PEAK 20(9P21.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         215
                        clus
vv                       DEL PEAK 20(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           166
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 21(9Q21.11) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(9Q21.11) MUTATED    41  26
  DEL PEAK 21(9Q21.11) WILD-TYPE 216  72
  DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE 
                            67                            288 
  DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE 
                            26                             72 
$`DEL PEAK 21(9Q21.11) MUTATED`
TCGA-BA-4074 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BB-7870 
         462          451           63          384          236         1153 
TCGA-CN-4730 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5367 TCGA-CN-6018 TCGA-CN-6020 
         462          811          512         1966           45           98 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CQ-5332 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 
         318          611          317         1959          509          901 
TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6491 TCGA-CR-7364 
         545          358         1050         1971          350         1435 
TCGA-CR-7365 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CV-5430 
        1191         1960          759           30          972         1955 
TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7091 
        1438         2886         2641         1959         1969         1959 
TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7254 TCGA-CV-7432 
        1970         1945         1724          954         1976         1937 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8569 
        1959         1981          237          701          154          128 
TCGA-D6-A4Z9 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-F7-7848 TCGA-F7-A50I 
         112          516          548          575          564           92 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8224 
          14            6          414          403            5           55 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A67D TCGA-P3-A6SX TCGA-P3-A6T4 
          25          111          210           56         1954         1968 
TCGA-QK-A6IJ 
          64 

$`DEL PEAK 21(9Q21.11) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         283          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 
        1747          190          644          113          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         351          216          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687          638          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         452          613          392          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         488          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          413          290          630          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 
         629          433          594          629          432         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         202          424          224          394          119          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
         429           46          443          447          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 
         815         1461         1378         1007         1309          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE 
         968         1960          613         1963          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 
         799         1777         1521         1966         1125          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 
         379          479         1956         1440         1245          105 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
        1979          889         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         997         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
         181         1077          911         1472          522         1950 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
        3295          584          546         1978         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 
        2437          519          406          701         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         215         1315         1665          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1948         1969         1952         3835         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
        1957         1969         1959         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1959         1939         1987         1979         1444         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
         797         1967         1960         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1984         1958          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 
         750          717          317          321          828          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB 
         292           77          491          568          106          104 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 
        1778         1081         1030         1965          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
         299          369          368          324          340          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
         658           15          585            3          384           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         407           58          133            2           25           37 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          44           24           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W 
         412          440          351          360          224           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          34          392          111          112          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
        1652          721         1120          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 

  DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE 
                             5                              2 
  DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE 
                          2886                           3837 
  DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE 
                         548.0                          639.5 
[1] "5.0 - 2886.0 (548.0)" "2.0 - 3837.0 (639.5)"
[1] "hr=" "1.5"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 21(9Q21.11) MUTATED         4       13        16        34         0
  DEL PEAK 21(9Q21.11) WILD-TYPE      20       50        55       158         9
D50V3, multiclass
           clus
vv          DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE
  STAGE I                              4                             20
  STAGE II                            13                             50
  STAGE III                           16                             55
  STAGE IVA                           34                            158
  STAGE IVB                            0                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 21(9Q21.11) MUTATED     8  25  11  23
  DEL PEAK 21(9Q21.11) WILD-TYPE  32  83  74 108
D50V4, multiclass
    clus
vv   DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE
  T1                            8                             32
  T2                           25                             83
  T3                           11                             74
  T4                           23                            108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 21(9Q21.11) MUTATED    24  14  24   0
  DEL PEAK 21(9Q21.11) WILD-TYPE 112  42 105   7
D50V5, multiclass
    clus
vv   DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE
  N0                           24                            112
  N1                           14                             42
  N2                           24                            105
  N3                            0                              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"
D50V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(9Q21.11) MUTATED   21  9
  DEL PEAK 21(9Q21.11) WILD-TYPE 87 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(9Q21.11) MUTATED     21    9
  DEL PEAK 21(9Q21.11) WILD-TYPE   87   39
    clus
vv   DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE
  M0                           21                             87
  MX                            9                             39
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(9Q21.11) MUTATED    21  55
  DEL PEAK 21(9Q21.11) WILD-TYPE 100 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(9Q21.11) MUTATED     21   55
  DEL PEAK 21(9Q21.11) WILD-TYPE  100  241
        clus
vv       DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE
  FEMALE                           21                            100
  MALE                             55                            241
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(9Q21.11) MUTATED                                      76
  DEL PEAK 21(9Q21.11) WILD-TYPE                                   334
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 21(9Q21.11) MUTATED                                                             0
  DEL PEAK 21(9Q21.11) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 21(9Q21.11) MUTATED                                                     0
  DEL PEAK 21(9Q21.11) WILD-TYPE                                                   6
D50V8, multiclass
                                                             clus
vv                                                            DEL PEAK 21(9Q21.11) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 76
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 21(9Q21.11) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  334
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 21(9Q21.11) MUTATED    17  59
  DEL PEAK 21(9Q21.11) WILD-TYPE  62 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(9Q21.11) MUTATED     17   59
  DEL PEAK 21(9Q21.11) WILD-TYPE   62  279
     clus
vv    DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE
  NO                            17                             62
  YES                           59                            279
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(9Q21.11) MUTATED                                  0     1
  DEL PEAK 21(9Q21.11) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(9Q21.11) MUTATED                           7    66
  DEL PEAK 21(9Q21.11) WILD-TYPE                        26   295
D50V12, multiclass
                                  clus
vv                                 DEL PEAK 21(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK 21(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       295
[1] 4 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 21(9Q21.11) MUTATED     2  69
  DEL PEAK 21(9Q21.11) WILD-TYPE  16 312
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(9Q21.11) MUTATED      2   69
  DEL PEAK 21(9Q21.11) WILD-TYPE   16  312
                        clus
vv                       DEL PEAK 21(9Q21.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 21(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            312
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 22(9Q34.3) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9Q34.3) MUTATED    36  17
  DEL PEAK 22(9Q34.3) WILD-TYPE 221  81
  DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE 
                           53                           302 
  DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE 
                           17                            81 
$`DEL PEAK 22(9Q34.3) MUTATED`
TCGA-BA-6871 TCGA-BA-7269 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7864 TCGA-BB-7870 
          63          236          278          133          687         1153 
TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-A63U TCGA-CN-A63Y 
         369          811           45           98          526          175 
TCGA-CQ-5327 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4CA 
        1660         1959         1959          509          901         1963 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-7364 TCGA-CR-7372 
         391          358         1050         1971         1435          759 
TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 
          30          392          181         1955         3295         1438 
TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7090 
        2886         2641         1970         1959         1969         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7243 TCGA-CV-7435 TCGA-CV-7440 
        1959         1970         1970          954         1959         1981 
TCGA-CV-A45Q TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I TCGA-H7-A6C5 TCGA-HD-7753 
        1945          548          564           92          403            5 
TCGA-HD-8635 TCGA-IQ-7630 TCGA-KU-A66T TCGA-P3-A5QA TCGA-QK-A6IJ 
          25          485          210         1652           64 

$`DEL PEAK 22(9Q34.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
        1636         1747          190          644          451          384 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         113          895          513          351          216          182 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         187         2878          140          558          310          536 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         423          638          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
         488          512          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          424          629          433          594          629 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         432         1970          202          424          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 
         443          447          225          484          348          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207          654         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
         985          815         1461         1378         1007         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877          968         1960          613          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         393          303          608         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 
         799         1777         1521         1966         1125          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
         379          350          479         1956         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 
        1245         1960          105         1979          889          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1951          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         930          216          156         1077          911         1472 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
         522         1950          584          546         1978         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
        1958         2437          519          406          701         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1948         1969         1952         3835         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1957         1969         1959         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1724         1444         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A461 
        1972         1937         1984         1958          851         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          112          104 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
        1778         1081          516         1030         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
         340          490          658           15          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         133          414            2           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          44           24           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
          33         1057          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W 
         412          440          351          360          224           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          34          392           56          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910          721         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II 
         228          225 

  DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE 
                            5                             2 
  DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE 
                         3837                          3835 
  DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE 
                        811.0                         622.5 
[1] "5.0 - 3837.0 (811.0)" "2.0 - 3835.0 (622.5)"
[1] "hr=" "1.4"
D51V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 22(9Q34.3) MUTATED         5       12        10        27         1
  DEL PEAK 22(9Q34.3) WILD-TYPE      19       51        61       165         8
D51V3, multiclass
           clus
vv          DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE
  STAGE I                             5                            19
  STAGE II                           12                            51
  STAGE III                          10                            61
  STAGE IVA                          27                           165
  STAGE IVB                           1                             8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 22(9Q34.3) MUTATED     7  20  12  16
  DEL PEAK 22(9Q34.3) WILD-TYPE  33  88  73 115
D51V4, multiclass
    clus
vv   DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE
  T1                           7                            33
  T2                          20                            88
  T3                          12                            73
  T4                          16                           115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 22(9Q34.3) MUTATED    22   7  19   1
  DEL PEAK 22(9Q34.3) WILD-TYPE 114  49 110   6
D51V5, multiclass
    clus
vv   DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE
  N0                          22                           114
  N1                           7                            49
  N2                          19                           110
  N3                           1                             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"
D51V6, binary
                               cls
clus                             0  1
  DEL PEAK 22(9Q34.3) MUTATED   12  7
  DEL PEAK 22(9Q34.3) WILD-TYPE 96 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.3) MUTATED     12    7
  DEL PEAK 22(9Q34.3) WILD-TYPE   96   41
    clus
vv   DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE
  M0                          12                            96
  MX                           7                            41
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9Q34.3) MUTATED    20  42
  DEL PEAK 22(9Q34.3) WILD-TYPE 101 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.3) MUTATED     20   42
  DEL PEAK 22(9Q34.3) WILD-TYPE  101  254
        clus
vv       DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE
  FEMALE                          20                           101
  MALE                            42                           254
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(9Q34.3) MUTATED                                      62
  DEL PEAK 22(9Q34.3) WILD-TYPE                                   348
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 22(9Q34.3) MUTATED                                                             0
  DEL PEAK 22(9Q34.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 22(9Q34.3) MUTATED                                                     0
  DEL PEAK 22(9Q34.3) WILD-TYPE                                                   6
D51V8, multiclass
                                                             clus
vv                                                            DEL PEAK 22(9Q34.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                62
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   0
                                                             clus
vv                                                            DEL PEAK 22(9Q34.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 348
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(9Q34.3) MUTATED    12  50
  DEL PEAK 22(9Q34.3) WILD-TYPE  67 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.3) MUTATED     12   50
  DEL PEAK 22(9Q34.3) WILD-TYPE   67  288
     clus
vv    DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE
  NO                           12                            67
  YES                          50                           288
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(9Q34.3) MUTATED                                  0     1
  DEL PEAK 22(9Q34.3) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9Q34.3) MUTATED                           6    52
  DEL PEAK 22(9Q34.3) WILD-TYPE                        27   309
D51V12, multiclass
                                  clus
vv                                 DEL PEAK 22(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     52
                                  clus
vv                                 DEL PEAK 22(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      309
[1] 4 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 22(9Q34.3) MUTATED     4  53
  DEL PEAK 22(9Q34.3) WILD-TYPE  14 328
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.3) MUTATED      4   53
  DEL PEAK 22(9Q34.3) WILD-TYPE   14  328
                        clus
vv                       DEL PEAK 22(9Q34.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       DEL PEAK 22(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           328
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 23(10P15.3) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10P15.3) MUTATED    71  45
  DEL PEAK 23(10P15.3) WILD-TYPE 186  53
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           116                            239 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            45                             53 
$`DEL PEAK 23(10P15.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         283          415          276         1747          190          644 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BB-7870 
         451          384          113          236          895         1153 
TCGA-BB-7871 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         428          624            5          721          485          142 
TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 
         240          488         1980         1081         1977          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
         424          629           45          432           98          318 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 
         611          432           46          348          367         1466 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 
        1057          985         1959         1378          509          901 
TCGA-CQ-A4C7 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
        1960         1971          354         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 
        1960          105         1979          759          889         1968 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 TCGA-CR-7404 
         796         1954         1430          392          156         1472 
TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-5979 
        1438         1978         2437          519         1840         1315 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 
        1948         1952         3835         1966         1957         1959 
TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 
        3837         1970         1959         1939         1945         1724 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7418 TCGA-CV-7424 
        1095          954          797         1967         1955         1947 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A6JD TCGA-CX-7219 TCGA-D6-6517 
        1973         1937         1958         1970          828          292 
TCGA-D6-6826 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
         154          104          516          548         1965          775 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A620 TCGA-HD-8635 
         658           15           92          384           13           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T 
          11           49          360          412          440          210 
TCGA-MT-A51X TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
          34         1954         1917         1968          400          553 
TCGA-QK-A6IF TCGA-QK-A6IH 
         245          228 

$`DEL PEAK 23(10P15.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462         1983          248          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6871 TCGA-BA-A6D8 
         520          725          623         1636           63          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         351          216          182          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 
         687          638          436         1955            4          799 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         369          395         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1988          512          173         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        1975          413          630          433          594          629 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 
        1970          202          424          224          394          119 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         429          443          447          225          526          484 
TCGA-CN-A63Y TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
         175         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129          870         1000 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 
        1959          815         1461         1007         1309          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         968          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          608         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125          514         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 
          30          972         1036          997         1951          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         181         1077          911         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
        3295          584          546         2886         2327         1958 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 
         406          701         2641         1478          215         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6943 
         641         1899         1970         1969         1959         1948 
TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7180 
        1969         1969         1959         1970         1936         1987 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
        1979         1444         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 
        1948         1957         1937         1972         1984         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JN 
        1981          851         1945         1954          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 
         317          321          237          773          701           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 
         491          568          106          128          112         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1081         1030          575          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J 
         368          324          340          564          490          585 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
           3           14            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         414          403            2            5           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          55           44           24           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61L 
        1057          485          122          441          588          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         360          224           14          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6T0 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         578          357          218          225           64 

  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                             5                              2 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                          3837                           3295 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           767                            608 
[1] "5.0 - 3837.0 (767.0)" "2.0 - 3295.0 (608.0)"
[1] "hr=" "1.6"
D52V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 23(10P15.3) MUTATED         5       17        21        73         3
  DEL PEAK 23(10P15.3) WILD-TYPE      19       46        50       119         6
D52V3, multiclass
           clus
vv          DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  STAGE I                              5                             19
  STAGE II                            17                             46
  STAGE III                           21                             50
  STAGE IVA                           73                            119
  STAGE IVB                            3                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 23(10P15.3) MUTATED    8 32 27 52
  DEL PEAK 23(10P15.3) WILD-TYPE 32 76 58 79
D52V4, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  T1                            8                             32
  T2                           32                             76
  T3                           27                             58
  T4                           52                             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 23(10P15.3) MUTATED    35  22  51   1
  DEL PEAK 23(10P15.3) WILD-TYPE 101  34  78   6
D52V5, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  N0                           35                            101
  N1                           22                             34
  N2                           51                             78
  N3                            1                              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"
D52V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(10P15.3) MUTATED   32 17
  DEL PEAK 23(10P15.3) WILD-TYPE 76 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     32   17
  DEL PEAK 23(10P15.3) WILD-TYPE   76   31
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  M0                           32                             76
  MX                           17                             31
[1] 2 2
[1] FALSE
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    36  99
  DEL PEAK 23(10P15.3) WILD-TYPE  85 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     36   99
  DEL PEAK 23(10P15.3) WILD-TYPE   85  197
        clus
vv       DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  FEMALE                           36                             85
  MALE                             99                            197
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(10P15.3) MUTATED                                     135
  DEL PEAK 23(10P15.3) WILD-TYPE                                   275
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 23(10P15.3) MUTATED                                                             0
  DEL PEAK 23(10P15.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 23(10P15.3) MUTATED                                                     0
  DEL PEAK 23(10P15.3) WILD-TYPE                                                   6
D52V8, multiclass
                                                             clus
vv                                                            DEL PEAK 23(10P15.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                135
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 23(10P15.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  275
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    31 104
  DEL PEAK 23(10P15.3) WILD-TYPE  48 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     31  104
  DEL PEAK 23(10P15.3) WILD-TYPE   48  234
     clus
vv    DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  NO                            31                             48
  YES                          104                            234
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10P15.3) MUTATED                                  0     3
  DEL PEAK 23(10P15.3) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10P15.3) MUTATED                          16   114
  DEL PEAK 23(10P15.3) WILD-TYPE                        17   247
D52V12, multiclass
                                  clus
vv                                 DEL PEAK 23(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     114
                                  clus
vv                                 DEL PEAK 23(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       247
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED     6 125
  DEL PEAK 23(10P15.3) WILD-TYPE  12 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED      6  125
  DEL PEAK 23(10P15.3) WILD-TYPE   12  256
                        clus
vv                       DEL PEAK 23(10P15.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          125
                        clus
vv                       DEL PEAK 23(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            256
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 24(10P11.21) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10P11.21) MUTATED    68  39
  DEL PEAK 24(10P11.21) WILD-TYPE 189  59
  DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE 
                            107                             248 
  DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE 
                             39                              59 
$`DEL PEAK 24(10P11.21) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
         283          276         1747          190          451          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 
         113          236          513         1153          436          624 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5360 
           5          721          452          240          488         1081 
TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
        1977          290          424          629           45          432 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6998 TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5332 
          98          318           46          348         1466          317 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 
         870         1057          985         1959         1378          509 
TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7365 
         901         1960          608         1971          354         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960          105          759          889 
TCGA-CR-7374 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 
          30          796         1954         1430          392          156 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5977 
         522         1438         2437          519         2641         1840 
TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-6961 
        1315         1952         1959         3835         1957         1959 
TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7242 
        3837         1970         1959         1939         1945         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 
         954          797         1967         1955         1947         1973 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A6JD TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
        1937         1958         1970          828          292          701 
TCGA-D6-6826 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
         154          104          516          548         1965          775 
TCGA-DQ-7593 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-HD-A633 TCGA-IQ-A61G 
         369           15           92          384           49          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51X TCGA-P3-A5QA 
         412          440          360          210           34         1652 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH 
        1917         1968          400          553          228 

$`DEL PEAK 24(10P11.21) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
        1762          520          725          623         1636          644 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
          63          895          351          216          182          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        2878          278          140          133          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8596 
         536          423          687          638          428         1955 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
           4          799          485          142          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         462          993          642          369          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1988          512          173 
TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1980         1980         1966         1966         1975          413 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6022 
         630          433          594          629         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         424          224          611          394          119          432 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         429          443          447          225          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         175          367         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6227 
         896         1399          341          129         1000         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
         815         1461         1007         1309          877          968 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
        1777         1521         1966         1050         1125          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1969          362          311          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7371 TCGA-CR-7376 
         350          479         1956         1435         1979          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
        1968         1036          997         1951          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
         946          908          898          930          216          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        1077          911         1472         1955         1950         3295 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
         406          701         1478          215         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6943 TCGA-CV-6945 
        1899         1970         1948         1969         1948         1969 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7180 
        1966         1969         1959         1970         1936         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1979         1724         1444         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 
        1974         1948         1957         1937         1972         1984 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JE 
        1959         1981          851         1945         1954          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 
         717          317          321          237          773           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 
         491          568          106          128          112         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
        1081         1030          575          622          299          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J 
         324          340          564          490          658          585 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
           3           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          403            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          10          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A 
         441          588          351          224           14          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
          56          111          112          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1120         1954          578          357          245          218 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE 
                              5                               2 
  DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE 
                           3837                            3295 
  DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE 
                          721.0                           617.5 
[1] "5.0 - 3837.0 (721.0)" "2.0 - 3295.0 (617.5)"
[1] "hr=" "1.5"
D53V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 24(10P11.21) MUTATED         7       15        20        66
  DEL PEAK 24(10P11.21) WILD-TYPE      17       48        51       126
                                 vv
clus                              STAGE IVB
  DEL PEAK 24(10P11.21) MUTATED           4
  DEL PEAK 24(10P11.21) WILD-TYPE         5
D53V3, multiclass
           clus
vv          DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE
  STAGE I                               7                              17
  STAGE II                             15                              48
  STAGE III                            20                              51
  STAGE IVA                            66                             126
  STAGE IVB                             4                               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 24(10P11.21) MUTATED    9 31 23 49
  DEL PEAK 24(10P11.21) WILD-TYPE 31 77 62 82
D53V4, multiclass
    clus
vv   DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE
  T1                             9                              31
  T2                            31                              77
  T3                            23                              62
  T4                            49                              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                               N0  N1  N2  N3
  DEL PEAK 24(10P11.21) MUTATED    36  20  43   2
  DEL PEAK 24(10P11.21) WILD-TYPE 100  36  86   5
D53V5, multiclass
    clus
vv   DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE
  N0                            36                             100
  N1                            20                              36
  N2                            43                              86
  N3                             2                               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"
D53V6, binary
                                 cls
clus                               0  1
  DEL PEAK 24(10P11.21) MUTATED   30 13
  DEL PEAK 24(10P11.21) WILD-TYPE 78 35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10P11.21) MUTATED     30   13
  DEL PEAK 24(10P11.21) WILD-TYPE   78   35
    clus
vv   DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE
  M0                            30                              78
  MX                            13                              35
[1] 2 2
[1] FALSE
D53V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10P11.21) MUTATED    33  93
  DEL PEAK 24(10P11.21) WILD-TYPE  88 203
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10P11.21) MUTATED     33   93
  DEL PEAK 24(10P11.21) WILD-TYPE   88  203
        clus
vv       DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE
  FEMALE                            33                              88
  MALE                              93                             203
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(10P11.21) MUTATED                                     124
  DEL PEAK 24(10P11.21) WILD-TYPE                                   286
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 24(10P11.21) MUTATED                                                             1
  DEL PEAK 24(10P11.21) WILD-TYPE                                                           0
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 24(10P11.21) MUTATED                                                     1
  DEL PEAK 24(10P11.21) WILD-TYPE                                                   5
D53V8, multiclass
                                                             clus
vv                                                            DEL PEAK 24(10P11.21) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 124
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
                                                             clus
vv                                                            DEL PEAK 24(10P11.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   286
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10P11.21) MUTATED    31  95
  DEL PEAK 24(10P11.21) WILD-TYPE  48 243
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10P11.21) MUTATED     31   95
  DEL PEAK 24(10P11.21) WILD-TYPE   48  243
     clus
vv    DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE
  NO                             31                              48
  YES                            95                             243
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(10P11.21) MUTATED                                  0     4
  DEL PEAK 24(10P11.21) WILD-TYPE                                1     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10P11.21) MUTATED                          16   103
  DEL PEAK 24(10P11.21) WILD-TYPE                        17   258
D53V12, multiclass
                                  clus
vv                                 DEL PEAK 24(10P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      103
                                  clus
vv                                 DEL PEAK 24(10P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     17
  WHITE                                                        258
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10P11.21) MUTATED     8 111
  DEL PEAK 24(10P11.21) WILD-TYPE  10 270
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10P11.21) MUTATED      8  111
  DEL PEAK 24(10P11.21) WILD-TYPE   10  270
                        clus
vv                       DEL PEAK 24(10P11.21) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           111
                        clus
vv                       DEL PEAK 24(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             270
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 25(10Q23.31) MUTATION ANALYSIS
D54V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(10Q23.31) MUTATED    54  34
  DEL PEAK 25(10Q23.31) WILD-TYPE 203  64
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                             88                             267 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                             34                              64 
$`DEL PEAK 25(10Q23.31) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 
         462          283          276         1288          520         1747 
TCGA-BA-6869 TCGA-BA-A6D8 TCGA-BB-7861 TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z 
         644          513          310         1153          624            5 
TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 
         485          452          488         1980         1081          290 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 
         629           45          432           98         1970          224 
TCGA-CN-6998 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-7064 
          46          526          317         1000         1959         1378 
TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-7365 
        1521         1971          514          362          354         1191 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960          105          759          889           30 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1954         1430          156          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6935 
        1438          584         2641          215         1315         1969 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1959         1969         1969         1959         3837         1970 
TCGA-CV-7101 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 
        1939         1095          954          797         1967         1974 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7432 TCGA-D6-6823 TCGA-D6-A4ZB TCGA-DQ-5631 
        1955         1947         1937          701          104          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-HD-A6HZ 
        1965          575          775          369          340          111 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A6I9 
         360          412          440          210           34          254 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-QK-A6IH 
         721         1954          578          228 

$`DEL PEAK 25(10Q23.31) WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
         415         1983          248          722         1762          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
         623         1636          190          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         113          236          895          351          216          182 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
         536          423          687          638          428          436 
TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
        1955            4          799          721          142          613 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          462          993          642          369          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240         1960         1330          811         1268         1988 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         512          173         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        1975          413          630          424          433          594 
TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         629          202          424          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         119          432          429          443          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
         129          870         1057          985         1959          815 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1461         1007          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         968         1960          613         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         393          391          303          608         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6472 
        1663         1152          799         1777         1966         1050 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1125         1969          311          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7371 
         350          479         1956         1435         1440         1979 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 
         972         1968         1036          796          997         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         930          216          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
        1955          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 
        2437          519          406          701         1478         1840 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        1665          641         1899         1970         1948         1952 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 
        3835         1948         1966         1957         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1945         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 
        1444         1960         1976         1099         1948         1957 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1937         1973         1972         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         292           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         128          112         1778         1081          516         1030 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 
         622          299          368          324          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         414          403            2            5           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A 
         588          351          360          224           14          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW 
          56          111          112          910         1652         1120 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1917         1968          400          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         218          225           64 

  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                              5                               2 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                           3837                            3835 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                          672.5                           622.0 
[1] "5.0 - 3837.0 (672.5)" "2.0 - 3835.0 (622.0)"
[1] "hr=" "1.4"
D54V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 25(10Q23.31) MUTATED         3       14        20        46
  DEL PEAK 25(10Q23.31) WILD-TYPE      21       49        51       146
                                 vv
clus                              STAGE IVB
  DEL PEAK 25(10Q23.31) MUTATED           2
  DEL PEAK 25(10Q23.31) WILD-TYPE         7
D54V3, multiclass
           clus
vv          DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  STAGE I                               3                              21
  STAGE II                             14                              49
  STAGE III                            20                              51
  STAGE IVA                            46                             146
  STAGE IVB                             2                               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 25(10Q23.31) MUTATED     6  28  22  30
  DEL PEAK 25(10Q23.31) WILD-TYPE  34  80  63 101
D54V4, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  T1                             6                              34
  T2                            28                              80
  T3                            22                              63
  T4                            30                             101
[1] 4 2
[1] TRUE
[1] "dimension 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(10Q23.31) MUTATED    30  14  33   1
  DEL PEAK 25(10Q23.31) WILD-TYPE 106  42  96   6
D54V5, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  N0                            30                             106
  N1                            14                              42
  N2                            33                              96
  N3                             1                               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"
D54V6, binary
                                 cls
clus                               0  1
  DEL PEAK 25(10Q23.31) MUTATED   25 10
  DEL PEAK 25(10Q23.31) WILD-TYPE 83 38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     25   10
  DEL PEAK 25(10Q23.31) WILD-TYPE   83   38
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  M0                            25                              83
  MX                            10                              38
[1] 2 2
[1] FALSE
D54V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    24  76
  DEL PEAK 25(10Q23.31) WILD-TYPE  97 220
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     24   76
  DEL PEAK 25(10Q23.31) WILD-TYPE   97  220
        clus
vv       DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  FEMALE                            24                              97
  MALE                              76                             220
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(10Q23.31) MUTATED                                      99
  DEL PEAK 25(10Q23.31) WILD-TYPE                                   311
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 25(10Q23.31) MUTATED                                                             0
  DEL PEAK 25(10Q23.31) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 25(10Q23.31) MUTATED                                                     1
  DEL PEAK 25(10Q23.31) WILD-TYPE                                                   5
D54V8, multiclass
                                                             clus
vv                                                            DEL PEAK 25(10Q23.31) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  99
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
                                                             clus
vv                                                            DEL PEAK 25(10Q23.31) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   311
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    22  78
  DEL PEAK 25(10Q23.31) WILD-TYPE  57 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     22   78
  DEL PEAK 25(10Q23.31) WILD-TYPE   57  260
     clus
vv    DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  NO                             22                              57
  YES                            78                             260
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(10Q23.31) MUTATED                                  0     3
  DEL PEAK 25(10Q23.31) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q23.31) MUTATED                          12    84
  DEL PEAK 25(10Q23.31) WILD-TYPE                        21   277
D54V12, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       84
                                  clus
vv                                 DEL PEAK 25(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     21
  WHITE                                                        277
[1] 4 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 25(10Q23.31) MUTATED     6  90
  DEL PEAK 25(10Q23.31) WILD-TYPE  12 291
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED      6   90
  DEL PEAK 25(10Q23.31) WILD-TYPE   12  291
                        clus
vv                       DEL PEAK 25(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            90
                        clus
vv                       DEL PEAK 25(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             291
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 26(11P15.5) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11P15.5) MUTATED    75  33
  DEL PEAK 26(11P15.5) WILD-TYPE 182  65
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                           108                            247 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                            33                             65 
$`DEL PEAK 26(11P15.5) MUTATED`
TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
         276          520          190          451           63          384 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4227 TCGA-BB-7870 
         236          513          351          182          133         1153 
TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 
        1955          485          613          392          369          395 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
        1330          811          512         1980         1977         1980 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6020 
        1966          290          424          629          432           98 
TCGA-CN-6021 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 
        1970          318          611          394          429           46 
TCGA-CN-A63U TCGA-CN-A63Y TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-A4C9 
         526          175          317         1000         1959          613 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6478 
         608         2562          358         1663          514         1969 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7385 
         311          345          354           30         1954          997 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        1951          392          181         1472         1955         1950 
TCGA-CV-5439 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6945 
         546          215         1970         1952         3835         1969 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         1970         1970         1959         1939         1945 
TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7430 TCGA-CV-7435 TCGA-CX-7082 
        1724          797         1099         1972         1959          317 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7594 
         106          104         1778          516          575          368 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 
         340          564          490           15           92            6 
TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
         414            5           37           55           44           25 
TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A67G TCGA-MZ-A6I9 
         111          441          360          210          112          254 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IH 
        1120          578         1968          400          245          228 

$`DEL PEAK 26(11P15.5) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         462          283          415         1983          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          725          623         1636         1747 
TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 
         644          113          895          216          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         278          140          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z 
         687          638          428          436          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 
           4          799          721          142          452          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
         993          642          240         1960         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
         488          173         1081         1966         1975          413 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6022 
         630          433          594          629           45          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A49B 
         424          224          119          432          443          447 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         225          484          348          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 
         129          870         1057          985         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877          968         1960         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         393          391          303         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
        1521         1966         1050         1125         1971          362 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         759          889          972         1968         1036          796 
TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1430          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 
         930          216          156         1077          911          522 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        3295         1438          584         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1948         1969         1959         1948         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 
        1969         1959         3837         1936         1987         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444         1095          954         1967         1960         1976 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1973         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 
        1945         1954         1970          750          717          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5625 
         491          154          568          128          112         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548         1965          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         369          324          658          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 
          14           13          407           58          133          403 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
           2           25           24           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61H 
          33         1057          485          122          588          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X 
         440          351          360          224           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         392           56          111          910         1652          721 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II 
        1954         1917          553          357          218          225 
TCGA-QK-A6IJ 
          64 

  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                             5                              2 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                          3835                           3837 
  DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE 
                         487.5                          725.0 
[1] "5.0 - 3835.0 (487.5)" "2.0 - 3837.0 (725.0)"
[1] "hr=" "1.3"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 26(11P15.5) MUTATED         4       15        18        59         6
  DEL PEAK 26(11P15.5) WILD-TYPE      20       48        53       133         3
D55V3, multiclass
           clus
vv          DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  STAGE I                              4                             20
  STAGE II                            15                             48
  STAGE III                           18                             53
  STAGE IVA                           59                            133
  STAGE IVB                            6                              3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 26(11P15.5) MUTATED   10 30 24 41
  DEL PEAK 26(11P15.5) WILD-TYPE 30 78 61 90
D55V4, multiclass
    clus
vv   DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  T1                           10                             30
  T2                           30                             78
  T3                           24                             61
  T4                           41                             90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 26(11P15.5) MUTATED    31  15  39   5
  DEL PEAK 26(11P15.5) WILD-TYPE 105  41  90   2
D55V5, multiclass
    clus
vv   DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  N0                           31                            105
  N1                           15                             41
  N2                           39                             90
  N3                            5                              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"
D55V6, binary
                                cls
clus                              0  1
  DEL PEAK 26(11P15.5) MUTATED   26 16
  DEL PEAK 26(11P15.5) WILD-TYPE 82 32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     26   16
  DEL PEAK 26(11P15.5) WILD-TYPE   82   32
    clus
vv   DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  M0                           26                             82
  MX                           16                             32
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    35  94
  DEL PEAK 26(11P15.5) WILD-TYPE  86 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     35   94
  DEL PEAK 26(11P15.5) WILD-TYPE   86  202
        clus
vv       DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  FEMALE                           35                             86
  MALE                             94                            202
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(11P15.5) MUTATED                                     126
  DEL PEAK 26(11P15.5) WILD-TYPE                                   284
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 26(11P15.5) MUTATED                                                             0
  DEL PEAK 26(11P15.5) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 26(11P15.5) MUTATED                                                     3
  DEL PEAK 26(11P15.5) WILD-TYPE                                                   3
D55V8, multiclass
                                                             clus
vv                                                            DEL PEAK 26(11P15.5) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                126
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            DEL PEAK 26(11P15.5) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  284
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(11P15.5) MUTATED    25 104
  DEL PEAK 26(11P15.5) WILD-TYPE  54 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED     25  104
  DEL PEAK 26(11P15.5) WILD-TYPE   54  234
     clus
vv    DEL PEAK 26(11P15.5) MUTATED DEL PEAK 26(11P15.5) WILD-TYPE
  NO                            25                             54
  YES                          104                            234
[1] 2 2
[1] FALSE
D55V10, continuous
D55V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(11P15.5) MUTATED                                  0     1
  DEL PEAK 26(11P15.5) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(11P15.5) MUTATED                          14   110
  DEL PEAK 26(11P15.5) WILD-TYPE                        19   251
D55V12, multiclass
                                  clus
vv                                 DEL PEAK 26(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     110
                                  clus
vv                                 DEL PEAK 26(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       251
[1] 4 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 26(11P15.5) MUTATED     8 114
  DEL PEAK 26(11P15.5) WILD-TYPE  10 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11P15.5) MUTATED      8  114
  DEL PEAK 26(11P15.5) WILD-TYPE   10  267
                        clus
vv                       DEL PEAK 26(11P15.5) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       DEL PEAK 26(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            267
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 27(11Q23.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(11Q23.1) MUTATED   119  54
  DEL PEAK 27(11Q23.1) WILD-TYPE 138  44
  DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE 
                           173                            182 
  DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE 
                            54                             44 
$`DEL PEAK 27(11Q23.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5153 
         462          415         1983          276          248         1762 
TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
         520         1747          190          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 
         113          236          351          187         2878          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         558          310          638         1153          428         1955 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4741 
         452          613          392          369         1330         1268 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
        1975          290          424          629          433           98 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6998 
        1970          224          611          394          119           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         443          447          225          175          367         1466 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         317         1000          985         1959         1959          815 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CR-5243 
         509         1960         1963          545          548         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6493 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7377 TCGA-CR-7383 
        1956         1960          105         1979         1968         1954 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         997         1951          181         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5970 
        1950          546         1978         2886         1958          406 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        2641         1478         1840         1315         1665          641 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6961 
        1970         1969         1952         3835         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 
        3837         1959         1970         1970         1959         1939 
TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7428 
        1945         1724         1974         1955         1957         1973 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1937         1984         1959          750          717          317 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-DQ-7588 
         237          828          701          491          112         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
         575          775          622          369          368          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-8502 
         564          490           15           92            6          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8314 TCGA-HL-7533 TCGA-IQ-A61G 
         414          403            5           44         1057          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W 
         412          440          351          360          210           14 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX 
          34           56          112         1652         1120         1954 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
        1968          400          245          218          228 

$`DEL PEAK 27(11Q23.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         283          722         1288          725          623         1636 
TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4224 
         644          895          513          216          182          278 
TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-8601 
         140          536          423          687          436          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721          485          142 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         462          993          642          395          240         1960 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5373 
         811         1988          488          512          173          413 
TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 
         630          594          629           45          432          202 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63V 
         424          318          432          429          526          484 
TCGA-CN-A63W TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
         348         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-7063 
        1399          341          129          870         1057         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1378         1007         1309          901          877          968 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-6471 
         613          393          391          303          608         1966 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7372 
         479         1435         1191         1440         1245          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7386 
         889           30          972         1036          796         1430 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5434 
         930          216          156         1077          911         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 
        1438          584         2327         2437          519          701 
TCGA-CV-5978 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 
         215         1899         1948         1959         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1957         1969         1936         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7434 
        1099         1948         1947         1937         1972         1958 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7085 
        1981          851         1945         1954         1970          321 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         773          292           77          154          568          106 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         128          104         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S 
         548          299          324          658          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 
         384           14           13          407           58            2 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           37           55           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10          111           33          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-KU-A66S TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 
         441          588          224          392          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 
         910          721          578         1917          553          357 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE 
                             5                              2 
  DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE 
                          3837                           3295 
  DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE 
                         629.0                          626.5 
[1] "5.0 - 3837.0 (629.0)" "2.0 - 3295.0 (626.5)"
[1] "hr=" "1.3"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 27(11Q23.1) MUTATED        10       26        30        87         5
  DEL PEAK 27(11Q23.1) WILD-TYPE      14       37        41       105         4
D56V3, multiclass
           clus
vv          DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE
  STAGE I                             10                             14
  STAGE II                            26                             37
  STAGE III                           30                             41
  STAGE IVA                           87                            105
  STAGE IVB                            5                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 27(11Q23.1) MUTATED   18 50 38 55
  DEL PEAK 27(11Q23.1) WILD-TYPE 22 58 47 76
D56V4, multiclass
    clus
vv   DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE
  T1                           18                             22
  T2                           50                             58
  T3                           38                             47
  T4                           55                             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                             N0 N1 N2 N3
  DEL PEAK 27(11Q23.1) MUTATED   49 23 71  3
  DEL PEAK 27(11Q23.1) WILD-TYPE 87 33 58  4
D56V5, multiclass
    clus
vv   DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE
  N0                           49                             87
  N1                           23                             33
  N2                           71                             58
  N3                            3                              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 27(11Q23.1) MUTATED   43 23
  DEL PEAK 27(11Q23.1) WILD-TYPE 65 25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q23.1) MUTATED     43   23
  DEL PEAK 27(11Q23.1) WILD-TYPE   65   25
    clus
vv   DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE
  M0                           43                             65
  MX                           23                             25
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q23.1) MUTATED    39 156
  DEL PEAK 27(11Q23.1) WILD-TYPE  82 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q23.1) MUTATED     39  156
  DEL PEAK 27(11Q23.1) WILD-TYPE   82  140
        clus
vv       DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE
  FEMALE                           39                             82
  MALE                            156                            140
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(11Q23.1) MUTATED                                     192
  DEL PEAK 27(11Q23.1) WILD-TYPE                                   218
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 27(11Q23.1) MUTATED                                                             1
  DEL PEAK 27(11Q23.1) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 27(11Q23.1) MUTATED                                                     2
  DEL PEAK 27(11Q23.1) WILD-TYPE                                                   4
D56V8, multiclass
                                                             clus
vv                                                            DEL PEAK 27(11Q23.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                192
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    2
                                                             clus
vv                                                            DEL PEAK 27(11Q23.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  218
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q23.1) MUTATED    43 152
  DEL PEAK 27(11Q23.1) WILD-TYPE  36 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q23.1) MUTATED     43  152
  DEL PEAK 27(11Q23.1) WILD-TYPE   36  186
     clus
vv    DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE
  NO                            43                             36
  YES                          152                            186
[1] 2 2
[1] FALSE
D56V10, continuous
D56V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(11Q23.1) MUTATED                                  0     1
  DEL PEAK 27(11Q23.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(11Q23.1) MUTATED                          17   171
  DEL PEAK 27(11Q23.1) WILD-TYPE                        16   190
D56V12, multiclass
                                  clus
vv                                 DEL PEAK 27(11Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     171
                                  clus
vv                                 DEL PEAK 27(11Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       190
[1] 4 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 27(11Q23.1) MUTATED    11 175
  DEL PEAK 27(11Q23.1) WILD-TYPE   7 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q23.1) MUTATED     11  175
  DEL PEAK 27(11Q23.1) WILD-TYPE    7  206
                        clus
vv                       DEL PEAK 27(11Q23.1) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          175
                        clus
vv                       DEL PEAK 27(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            206
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 28(12Q24.33) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(12Q24.33) MUTATED    29  16
  DEL PEAK 28(12Q24.33) WILD-TYPE 228  82
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             45                             310 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             16                              82 
$`DEL PEAK 28(12Q24.33) MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         283          190          451          113          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BB-8596 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         513          182         1955          142          452          613 
TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6024 TCGA-CN-6988 
        1330          488         1980          290          224          318 
TCGA-CN-6994 TCGA-CN-A49B TCGA-CQ-5332 TCGA-CR-6493 TCGA-CR-7370 TCGA-CR-7383 
         119          447          317         1956          105         1954 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6935 
         907         1955          519         1478         1665         1969 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7254 TCGA-CV-7432 
        3837         1959         1939         1945         1976         1937 
TCGA-CV-7435 TCGA-CX-7219 TCGA-D6-A4Z9 TCGA-DQ-5629 TCGA-F7-7848 TCGA-H7-A6C5 
        1959          828          112          516          564          403 
TCGA-IQ-A61G TCGA-KU-A66T TCGA-P3-A5QA 
         360          210         1652 

$`DEL PEAK 28(12Q24.33) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-A6DA TCGA-BA-A6DB 
        1747          644           63          384          351          216 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         428          436          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         721          485          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         369          395          240         1960          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1988          512          173         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          413          630          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          433          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 
          98         1970          202          424          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U 
         432          429           46          443          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
         234          379          350          479         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
          30          972         1968         1036          796          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         911         1472          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 
        2437          406          701         2641         1840          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        1315          641         1899         1970         1948         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         1970         1970         1936         1959 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1987         1979         1724         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
         797         1967         1960         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1984         1958         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          321          237 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         568          106          128          104         1778         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
         299          369          368          324          340          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         414            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         111           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         588          412          440          351          360          224 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
          14           34          392           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         254          910          721         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1917         1968          400          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         218          228          225           64 

  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                            105                               2 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                           3837                            3835 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                            519                             634 
[1] "105.0 - 3837.0 (519.0)" "2.0 - 3835.0 (634.0)"  
[1] "hr=" "1.4"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 28(12Q24.33) MUTATED         3        7         6        28
  DEL PEAK 28(12Q24.33) WILD-TYPE      21       56        65       164
                                 vv
clus                              STAGE IVB
  DEL PEAK 28(12Q24.33) MUTATED           1
  DEL PEAK 28(12Q24.33) WILD-TYPE         8
D57V3, multiclass
           clus
vv          DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  STAGE I                               3                              21
  STAGE II                              7                              56
  STAGE III                             6                              65
  STAGE IVA                            28                             164
  STAGE IVB                             1                               8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 28(12Q24.33) MUTATED     3  11   9  22
  DEL PEAK 28(12Q24.33) WILD-TYPE  37  97  76 109
D57V4, multiclass
    clus
vv   DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  T1                             3                              37
  T2                            11                              97
  T3                             9                              76
  T4                            22                             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                               N0  N1  N2  N3
  DEL PEAK 28(12Q24.33) MUTATED    15   5  18   1
  DEL PEAK 28(12Q24.33) WILD-TYPE 121  51 111   6
D57V5, multiclass
    clus
vv   DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  N0                            15                             121
  N1                             5                              51
  N2                            18                             111
  N3                             1                               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"
D57V6, binary
                                 cls
clus                               0  1
  DEL PEAK 28(12Q24.33) MUTATED   11  9
  DEL PEAK 28(12Q24.33) WILD-TYPE 97 39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED     11    9
  DEL PEAK 28(12Q24.33) WILD-TYPE   97   39
    clus
vv   DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  M0                            11                              97
  MX                             9                              39
[1] 2 2
[1] FALSE
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q24.33) MUTATED    14  36
  DEL PEAK 28(12Q24.33) WILD-TYPE 107 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED     14   36
  DEL PEAK 28(12Q24.33) WILD-TYPE  107  260
        clus
vv       DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  FEMALE                            14                             107
  MALE                              36                             260
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(12Q24.33) MUTATED                                      50
  DEL PEAK 28(12Q24.33) WILD-TYPE                                   360
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 28(12Q24.33) MUTATED                                                             0
  DEL PEAK 28(12Q24.33) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 28(12Q24.33) MUTATED                                                     0
  DEL PEAK 28(12Q24.33) WILD-TYPE                                                   6
D57V8, multiclass
                                                             clus
vv                                                            DEL PEAK 28(12Q24.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  50
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     0
                                                             clus
vv                                                            DEL PEAK 28(12Q24.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   360
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q24.33) MUTATED    10  40
  DEL PEAK 28(12Q24.33) WILD-TYPE  69 298
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED     10   40
  DEL PEAK 28(12Q24.33) WILD-TYPE   69  298
     clus
vv    DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  NO                             10                              69
  YES                            40                             298
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(12Q24.33) MUTATED                                  0     0
  DEL PEAK 28(12Q24.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(12Q24.33) MUTATED                           8    40
  DEL PEAK 28(12Q24.33) WILD-TYPE                        25   321
D57V12, multiclass
                                  clus
vv                                 DEL PEAK 28(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       40
                                  clus
vv                                 DEL PEAK 28(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        321
[1] 4 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 28(12Q24.33) MUTATED     3  44
  DEL PEAK 28(12Q24.33) WILD-TYPE  15 337
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED      3   44
  DEL PEAK 28(12Q24.33) WILD-TYPE   15  337
                        clus
vv                       DEL PEAK 28(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            44
                        clus
vv                       DEL PEAK 28(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                  15
  NOT HISPANIC OR LATINO                             337
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 29(13Q12.11) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(13Q12.11) MUTATED   110  47
  DEL PEAK 29(13Q12.11) WILD-TYPE 147  51
  DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE 
                            157                             198 
  DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE 
                             47                              51 
$`DEL PEAK 29(13Q12.11) MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 
         462          276          248         1288          520         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         190          644           63          384          113          236 
TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 
         351          182          278          133          536          687 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 
        1153          428         1955          624            5          721 
TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
         485          392          462          240         1330          811 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
         512         1081         1977         1966          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 
         630          424          629           45           98         1970 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 
         202          224          318          119          429           46 
TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5330 TCGA-CQ-6221 
         443          225          526          348          896         1000 
TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1959         1378         1007          509         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
        1963          545          393          608         2562          358 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 
        1050         1969          311          234          379         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
        1435         1191         1440         1979          759           30 
TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 
        1036          997         1430          907          216          181 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 
         911         1955         1950         3295         1978         2886 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         519          406         1478         1840          215         1315 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 
        1970         1969         1959         3835         1969         1957 
TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         1970         1970         1936         1959 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 
        1945         1987         1724         1095          797         1967 
TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7435 TCGA-CV-A461 TCGA-CV-A6JE 
        1974         1955         1957         1959         1954          750 
TCGA-CV-A6JN TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 
         717          237          828          701          491          154 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
         106          112          516         1030         1965          575 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I 
         299          324          340          564           15           92 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 
          14            6          403            2            5           55 
TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61O 
          25           49          111          441          360          360 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IG 
         112          254         1652         1954         1968          218 
TCGA-QK-A6IH 
         228 

$`DEL PEAK 29(13Q12.11) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
         283          415         1983          722         1762          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
         623         1636          451          895          513          216 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
         187         2878          140          558          310          423 
TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 
         638          436            4          799          142          452 
TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         613          993          642          369          395         1960 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 
        1268         1988          488          173         1980         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
        1966         1975          433          594          629          432 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63V 
         424          611          394          432          447          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1399          317          341          129          870 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
        1057          985         1959          815         1461         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
         901          877          968          548          391          303 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
        1125         1971          514          362          345          354 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7373 
         350          479         1245         1960          105          889 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 
         972         1968          796         1954         1951          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 
         913          946          908          898          930          156 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1077         1472          522         1438          584          546 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6003 
        2327         1958         2437          701         2641         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6952 
         641         1899         1948         1952         1948         1966 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 
        1959         3837         1939         1979         1444          954 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 
        1960         1976         1099         1948         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1973         1972         1937         1984         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 
         851         1945         1970          317          321          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 
         292           77          568          128          104         1778 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
        1081          548          775          622          369          368 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
         490          658          585            3          384           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7754 TCGA-HD-7917 
         407           58          133          414           25           37 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
          44           24           11           10           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         485          122          588          412          440          351 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          210           14           34          392           56 
TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         111          910          721         1120          578         1917 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ 
         400          553          357          245          225           64 

  DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE 
                              2                               3 
  DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE 
                           3835                            3837 
  DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE 
                          608.0                           641.5 
[1] "2.0 - 3835.0 (608.0)" "3.0 - 3837.0 (641.5)"
[1] "hr=" "1.1"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 29(13Q12.11) MUTATED         8       19        30        92
  DEL PEAK 29(13Q12.11) WILD-TYPE      16       44        41       100
                                 vv
clus                              STAGE IVB
  DEL PEAK 29(13Q12.11) MUTATED           4
  DEL PEAK 29(13Q12.11) WILD-TYPE         5
D58V3, multiclass
           clus
vv          DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE
  STAGE I                               8                              16
  STAGE II                             19                              44
  STAGE III                            30                              41
  STAGE IVA                            92                             100
  STAGE IVB                             4                               5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 29(13Q12.11) MUTATED   13 43 36 63
  DEL PEAK 29(13Q12.11) WILD-TYPE 27 65 49 68
D58V4, multiclass
    clus
vv   DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE
  T1                            13                              27
  T2                            43                              65
  T3                            36                              49
  T4                            63                              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                              N0 N1 N2 N3
  DEL PEAK 29(13Q12.11) MUTATED   46 26 67  3
  DEL PEAK 29(13Q12.11) WILD-TYPE 90 30 62  4
D58V5, multiclass
    clus
vv   DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE
  N0                            46                              90
  N1                            26                              30
  N2                            67                              62
  N3                             3                               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 29(13Q12.11) MUTATED   44 18
  DEL PEAK 29(13Q12.11) WILD-TYPE 64 30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.11) MUTATED     44   18
  DEL PEAK 29(13Q12.11) WILD-TYPE   64   30
    clus
vv   DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE
  M0                            44                              64
  MX                            18                              30
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.11) MUTATED    44 136
  DEL PEAK 29(13Q12.11) WILD-TYPE  77 160
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.11) MUTATED     44  136
  DEL PEAK 29(13Q12.11) WILD-TYPE   77  160
        clus
vv       DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE
  FEMALE                            44                              77
  MALE                             136                             160
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(13Q12.11) MUTATED                                     178
  DEL PEAK 29(13Q12.11) WILD-TYPE                                   232
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 29(13Q12.11) MUTATED                                                             1
  DEL PEAK 29(13Q12.11) WILD-TYPE                                                           0
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 29(13Q12.11) MUTATED                                                     1
  DEL PEAK 29(13Q12.11) WILD-TYPE                                                   5
D58V8, multiclass
                                                             clus
vv                                                            DEL PEAK 29(13Q12.11) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 178
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
                                                             clus
vv                                                            DEL PEAK 29(13Q12.11) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   232
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.11) MUTATED    35 145
  DEL PEAK 29(13Q12.11) WILD-TYPE  44 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.11) MUTATED     35  145
  DEL PEAK 29(13Q12.11) WILD-TYPE   44  193
     clus
vv    DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE
  NO                             35                              44
  YES                           145                             193
[1] 2 2
[1] FALSE
D58V10, continuous
D58V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(13Q12.11) MUTATED                                  1     3
  DEL PEAK 29(13Q12.11) WILD-TYPE                                0     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(13Q12.11) MUTATED                          18   150
  DEL PEAK 29(13Q12.11) WILD-TYPE                        15   211
D58V12, multiclass
                                  clus
vv                                 DEL PEAK 29(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      150
                                  clus
vv                                 DEL PEAK 29(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     15
  WHITE                                                        211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.11) MUTATED    10 156
  DEL PEAK 29(13Q12.11) WILD-TYPE   8 225
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.11) MUTATED     10  156
  DEL PEAK 29(13Q12.11) WILD-TYPE    8  225
                        clus
vv                       DEL PEAK 29(13Q12.11) MUTATED
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           156
                        clus
vv                       DEL PEAK 29(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             225
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 30(13Q14.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(13Q14.2) MUTATED   111  38
  DEL PEAK 30(13Q14.2) WILD-TYPE 146  60
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           149                            206 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            38                             60 
$`DEL PEAK 30(13Q14.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         462          276          248         1288         1762          520 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 
        1747          644           63          113          236          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         351          216         2878          278          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         310          536          687         1153          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 
         624            5          721          485          462         1330 
TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
         811          512         1081         1977         1980         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 
         413          290          424          629           45           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 
        1970          202          224          318          119           46 
TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-6224 
         443          225          348         1466          896          985 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CD 
        1959         1378         1007          509         1963          548 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         393          608         2562          358         1663         1152 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 
        1777         1521         1050          514         1969          311 
TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 
         234         1435         1191          759           30         1036 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 
         997         1430          216          181          911         1472 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5977 TCGA-CV-5978 
        1955         1950         3295         2886         1840          215 
TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7091 
        1970         1959         3835         1957         1969         1959 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 
        1970         1936         1959         1987         1724         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7435 
         797         1967         1974         1955         1957         1959 
TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 
        1981         1954          750          717          317          237 
TCGA-CX-7219 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
         828          491          154          568          106          112 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7595 
        1030         1965          575          775          299          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 
         340          564           15           92           14            6 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A633 
           5           37           55           44           25           49 
TCGA-HD-A6HZ TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA 
         111          360          210          112          254         1652 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IH 
         721         1954         1968          218          228 

$`DEL PEAK 30(13Q14.2) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 
         283          415         1983          722          725          623 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6DE 
        1636          190          451          384          895          182 
TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A480 
         187          140          423          638          436            4 
TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
         799          142          452          613          392          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 
         642          369          395          240         1960         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5370 
        1988          488          173         1980         1966         1975 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 
         630          433          594          629          432          424 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63U 
         611          394          432          429          447          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         484          175          367         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1399          317          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
        1000         1057         1959          815         1461         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
         901          877          968         1960          613          545 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
         391          303          799         1966         1125         1971 
TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         362          345          354          379          350          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1956         1440         1245         1960          105         1979 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 
         889          972         1968          796         1954         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
         930          156         1077          522         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         1978         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 
         406          701         2641         1478         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6943 
         641         1899         1948         1969         1952         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 
        1969         1966         1959         3837         1970         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7254 
        1945         1979         1444          954         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1099         1948         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD 
        1937         1984         1958          851         1945         1970 
TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-8569 
         321          773          292          701           77          128 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7591 
         104         1778         1081          516          548          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S 
         369          368          490          658          585            3 
TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
         384           13          407           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 
         403            2           25           24           11           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W 
         360          412          440          351          224           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A6SW 
          34          392           56          111          910         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1917          400          553          357          245 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                             5                              2 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                          3835                           3837 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                         624.0                          629.5 
[1] "5.0 - 3835.0 (624.0)" "2.0 - 3837.0 (629.5)"
[1] "hr=" "1.2"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 30(13Q14.2) MUTATED        11       18        30        79         5
  DEL PEAK 30(13Q14.2) WILD-TYPE      13       45        41       113         4
D59V3, multiclass
           clus
vv          DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  STAGE I                             11                             13
  STAGE II                            18                             45
  STAGE III                           30                             41
  STAGE IVA                           79                            113
  STAGE IVB                            5                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 30(13Q14.2) MUTATED   19 44 29 53
  DEL PEAK 30(13Q14.2) WILD-TYPE 21 64 56 78
D59V4, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  T1                           19                             21
  T2                           44                             64
  T3                           29                             56
  T4                           53                             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                             N0 N1 N2 N3
  DEL PEAK 30(13Q14.2) MUTATED   46 23 58  4
  DEL PEAK 30(13Q14.2) WILD-TYPE 90 33 71  3
D59V5, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  N0                           46                             90
  N1                           23                             33
  N2                           58                             71
  N3                            4                              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"
D59V6, binary
                                cls
clus                              0  1
  DEL PEAK 30(13Q14.2) MUTATED   43 18
  DEL PEAK 30(13Q14.2) WILD-TYPE 65 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED     43   18
  DEL PEAK 30(13Q14.2) WILD-TYPE   65   30
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  M0                           43                             65
  MX                           18                             30
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED    43 127
  DEL PEAK 30(13Q14.2) WILD-TYPE  78 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED     43  127
  DEL PEAK 30(13Q14.2) WILD-TYPE   78  169
        clus
vv       DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  FEMALE                           43                             78
  MALE                            127                            169
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                     166
  DEL PEAK 30(13Q14.2) WILD-TYPE                                   244
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 30(13Q14.2) MUTATED                                                             1
  DEL PEAK 30(13Q14.2) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 30(13Q14.2) MUTATED                                                     3
  DEL PEAK 30(13Q14.2) WILD-TYPE                                                   3
D59V8, multiclass
                                                             clus
vv                                                            DEL PEAK 30(13Q14.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                166
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            DEL PEAK 30(13Q14.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  244
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED    34 136
  DEL PEAK 30(13Q14.2) WILD-TYPE  45 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED     34  136
  DEL PEAK 30(13Q14.2) WILD-TYPE   45  202
     clus
vv    DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  NO                            34                             45
  YES                          136                            202
[1] 2 2
[1] FALSE
D59V10, continuous
D59V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(13Q14.2) MUTATED                                  1     3
  DEL PEAK 30(13Q14.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(13Q14.2) MUTATED                          18   142
  DEL PEAK 30(13Q14.2) WILD-TYPE                        15   219
D59V12, multiclass
                                  clus
vv                                 DEL PEAK 30(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     142
                                  clus
vv                                 DEL PEAK 30(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED     8 150
  DEL PEAK 30(13Q14.2) WILD-TYPE  10 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED      8  150
  DEL PEAK 30(13Q14.2) WILD-TYPE   10  231
                        clus
vv                       DEL PEAK 30(13Q14.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          150
                        clus
vv                       DEL PEAK 30(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            231
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 31(14Q11.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(14Q11.2) MUTATED    28  16
  DEL PEAK 31(14Q11.2) WILD-TYPE 229  82
  DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE 
                            44                            311 
  DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE 
                            16                             82 
$`DEL PEAK 31(14Q11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A6D8 
         283          276         1288          644           63          513 
TCGA-BB-7862 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-6011 TCGA-CN-6019 
         536          485          392          369          424          432 
TCGA-CN-6020 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CR-5247 TCGA-CR-6472 
          98          526          317         1000          358         1050 
TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
         354          350         1956         1191         1440          105 
TCGA-CR-7388 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5435 TCGA-CV-5966 TCGA-CV-6935 
        1951          156          181         1438          519         1969 
TCGA-CV-6945 TCGA-CV-7180 TCGA-CV-7432 TCGA-CV-7435 TCGA-D6-6826 TCGA-D6-8569 
        1969         1987         1937         1959          154          128 
TCGA-D6-A4Z9 TCGA-DQ-5629 TCGA-F7-7848 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-8224 
         112          516          564          403            2           55 
TCGA-HD-A633 TCGA-P3-A6T0 
          49          578 

$`DEL PEAK 31(14Q11.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         462          415         1983          248          722         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
         520          725          623         1636         1747          190 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA 
         451          384          113          236          895          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          310          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          799          721          142          452          613 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         462          993          642          395          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         173         1980         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
        1966         1975          413          290          630          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 
         433          594          629           45         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         424          224          318          611          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         129          870         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         901          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         545          548          393          391          303          608 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1966         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7364 
         311          345          234          379          479         1435 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         898          930          216         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 
        1955          522         1950         3295          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
        1978         2886         2327         1958         2437          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        1665          641         1899         1970         1948         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1959         3835         1948         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1945         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1937         1973         1972         1984         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB 
         701           77          491          568          106          104 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1778         1081         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         340          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
           3          384           14           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
          58          133          414            5           25           37 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ 
          44           24           25           11           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         360          412          440          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         210           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1954         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         245          218          228          225           64 

  DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE 
                             2                              3 
  DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE 
                          1987                           3837 
  DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE 
                         458.5                          687.0 
[1] "2.0 - 1987.0 (458.5)" "3.0 - 3837.0 (687.0)"
[1] "hr=" "2.3"
D60V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 31(14Q11.2) MUTATED         0       10         8        26         0
  DEL PEAK 31(14Q11.2) WILD-TYPE      24       53        63       166         9
D60V3, multiclass
           clus
vv          DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE
  STAGE I                              0                             24
  STAGE II                            10                             53
  STAGE III                            8                             63
  STAGE IVA                           26                            166
  STAGE IVB                            0                              9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(14Q11.2) MUTATED     0  15  12  18
  DEL PEAK 31(14Q11.2) WILD-TYPE  40  93  73 113
D60V4, multiclass
    clus
vv   DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE
  T1                            0                             40
  T2                           15                             93
  T3                           12                             73
  T4                           18                            113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 31(14Q11.2) MUTATED    17   7  16   0
  DEL PEAK 31(14Q11.2) WILD-TYPE 119  49 113   7
D60V5, multiclass
    clus
vv   DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE
  N0                           17                            119
  N1                            7                             49
  N2                           16                            113
  N3                            0                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                                cls
clus                              0  1
  DEL PEAK 31(14Q11.2) MUTATED   11  4
  DEL PEAK 31(14Q11.2) WILD-TYPE 97 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q11.2) MUTATED     11    4
  DEL PEAK 31(14Q11.2) WILD-TYPE   97   44
    clus
vv   DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE
  M0                           11                             97
  MX                            4                             44
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q11.2) MUTATED    12  40
  DEL PEAK 31(14Q11.2) WILD-TYPE 109 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q11.2) MUTATED     12   40
  DEL PEAK 31(14Q11.2) WILD-TYPE  109  256
        clus
vv       DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE
  FEMALE                           12                            109
  MALE                             40                            256
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(14Q11.2) MUTATED                                      52
  DEL PEAK 31(14Q11.2) WILD-TYPE                                   358
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 31(14Q11.2) MUTATED                                                             0
  DEL PEAK 31(14Q11.2) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 31(14Q11.2) MUTATED                                                     0
  DEL PEAK 31(14Q11.2) WILD-TYPE                                                   6
D60V8, multiclass
                                                             clus
vv                                                            DEL PEAK 31(14Q11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 52
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 31(14Q11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  358
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q11.2) MUTATED    11  41
  DEL PEAK 31(14Q11.2) WILD-TYPE  68 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q11.2) MUTATED     11   41
  DEL PEAK 31(14Q11.2) WILD-TYPE   68  297
     clus
vv    DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE
  NO                            11                             68
  YES                           41                            297
[1] 2 2
[1] FALSE
D60V10, continuous
D60V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(14Q11.2) MUTATED                                  0     1
  DEL PEAK 31(14Q11.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(14Q11.2) MUTATED                           7    44
  DEL PEAK 31(14Q11.2) WILD-TYPE                        26   317
D60V12, multiclass
                                  clus
vv                                 DEL PEAK 31(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      44
                                  clus
vv                                 DEL PEAK 31(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       317
[1] 4 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 31(14Q11.2) MUTATED     0  48
  DEL PEAK 31(14Q11.2) WILD-TYPE  18 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q11.2) MUTATED      0   48
  DEL PEAK 31(14Q11.2) WILD-TYPE   18  333
                        clus
vv                       DEL PEAK 31(14Q11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       DEL PEAK 31(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            333
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 32(14Q32.32) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(14Q32.32) MUTATED    35  14
  DEL PEAK 32(14Q32.32) WILD-TYPE 222  84
  DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE 
                             49                             306 
  DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE 
                             14                              84 
$`DEL PEAK 32(14Q32.32) MUTATED`
TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
         276         1288         1762         1747          644          451 
TCGA-BA-6871 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7866 
          63         2878          140          558          536          638 
TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6992 TCGA-CN-A63U 
         613          369          432           98          394          526 
TCGA-CN-A63Y TCGA-CQ-6221 TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         175         1000          358          799         1777         1521 
TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5434 TCGA-CV-5442 
        1050          362          156          181         3295         2327 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-7248 
        1958          519          215          641         1969         1967 
TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7435 TCGA-D6-8569 TCGA-DQ-5631 TCGA-DQ-7590 
        1974         1957         1959          128          548          775 
TCGA-DQ-7593 TCGA-DQ-7596 TCGA-H7-A6C5 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-MZ-A6I9 
         369          340          403           55          111          254 
TCGA-P3-A6T0 
         578 

$`DEL PEAK 32(14Q32.32) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         462          283          415         1983          248          722 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6872 
         520          725          623         1636          190          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         113          236          895          513          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7863 
         182          187          278          133          310          423 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
         452          392          462          993          642          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
         488          512          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          424          629          433          594          629 
TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          45         1970          202          424          224          318 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         611          119          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 
         447          225          484          348          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
         317          341          129          870         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959          815         1461         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6471 
         303          608         2562         1663         1152         1966 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971          514         1969          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         930          216         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
         522         1950         1438          584          546         1978 
TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2886         2437          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1840         1315         1665         1899         1970         1948 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 
        1960         1976         1099         1948         1955         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         106          112          104         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
        1030         1965          575          622          299          368 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         324          564          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
         585            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 
         407           58          133          414            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           37           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         441          588          360          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          112          910         1652          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225           64 

  DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE 
                             55                               2 
  DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE 
                           3295                            3837 
  DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE 
                            548                             648 
[1] "55.0 - 3295.0 (548.0)" "2.0 - 3837.0 (648.0)" 
[1] "hr=" "1"  
D61V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 32(14Q32.32) MUTATED         0        9         7        21
  DEL PEAK 32(14Q32.32) WILD-TYPE      24       54        64       171
                                 vv
clus                              STAGE IVB
  DEL PEAK 32(14Q32.32) MUTATED           1
  DEL PEAK 32(14Q32.32) WILD-TYPE         8
D61V3, multiclass
           clus
vv          DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE
  STAGE I                               0                              24
  STAGE II                              9                              54
  STAGE III                             7                              64
  STAGE IVA                            21                             171
  STAGE IVB                             1                               8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 32(14Q32.32) MUTATED     0  15  13  12
  DEL PEAK 32(14Q32.32) WILD-TYPE  40  93  72 119
D61V4, multiclass
    clus
vv   DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE
  T1                             0                              40
  T2                            15                              93
  T3                            13                              72
  T4                            12                             119
[1] 4 2
[1] TRUE
[1] "dimension 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(14Q32.32) MUTATED    14   5  14   1
  DEL PEAK 32(14Q32.32) WILD-TYPE 122  51 115   6
D61V5, multiclass
    clus
vv   DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE
  N0                            14                             122
  N1                             5                              51
  N2                            14                             115
  N3                             1                               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"
D61V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.32) MUTATED     6   5
  DEL PEAK 32(14Q32.32) WILD-TYPE 102  43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.32) MUTATED      6    5
  DEL PEAK 32(14Q32.32) WILD-TYPE  102   43
    clus
vv   DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE
  M0                             6                             102
  MX                             5                              43
[1] 2 2
[1] FALSE
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.32) MUTATED    11  44
  DEL PEAK 32(14Q32.32) WILD-TYPE 110 252
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.32) MUTATED     11   44
  DEL PEAK 32(14Q32.32) WILD-TYPE  110  252
        clus
vv       DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE
  FEMALE                            11                             110
  MALE                              44                             252
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(14Q32.32) MUTATED                                      55
  DEL PEAK 32(14Q32.32) WILD-TYPE                                   355
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 32(14Q32.32) MUTATED                                                             0
  DEL PEAK 32(14Q32.32) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 32(14Q32.32) MUTATED                                                     0
  DEL PEAK 32(14Q32.32) WILD-TYPE                                                   6
D61V8, multiclass
                                                             clus
vv                                                            DEL PEAK 32(14Q32.32) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  55
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     0
                                                             clus
vv                                                            DEL PEAK 32(14Q32.32) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   355
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.32) MUTATED    15  40
  DEL PEAK 32(14Q32.32) WILD-TYPE  64 298
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.32) MUTATED     15   40
  DEL PEAK 32(14Q32.32) WILD-TYPE   64  298
     clus
vv    DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE
  NO                             15                              64
  YES                            40                             298
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(14Q32.32) MUTATED                                  0     0
  DEL PEAK 32(14Q32.32) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(14Q32.32) MUTATED                           8    47
  DEL PEAK 32(14Q32.32) WILD-TYPE                        25   314
D61V12, multiclass
                                  clus
vv                                 DEL PEAK 32(14Q32.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       47
                                  clus
vv                                 DEL PEAK 32(14Q32.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        314
[1] 4 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 32(14Q32.32) MUTATED     1  50
  DEL PEAK 32(14Q32.32) WILD-TYPE  17 331
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.32) MUTATED      1   50
  DEL PEAK 32(14Q32.32) WILD-TYPE   17  331
                        clus
vv                       DEL PEAK 32(14Q32.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            50
                        clus
vv                       DEL PEAK 32(14Q32.32) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                             331
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 33(15Q15.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q15.1) MUTATED    52  28
  DEL PEAK 33(15Q15.1) WILD-TYPE 205  70
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                            80                            275 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                            28                             70 
$`DEL PEAK 33(15Q15.1) MUTATED`
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
        1288         1762          520         1747          190          644 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7866 
         236          895          182         2878          140          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-5359 
        1153          428          485          613          462         1980 
TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6021 TCGA-CN-6024 
        1977         1975          629          594         1970          224 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5330 
         432          429           46          348          367          896 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-A4C6 
         317          985         1959          815          509          968 
TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 
        1960          393         2562         1971         1969          362 
TCGA-CR-7373 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5970 
         889          911         1438         2886          519          406 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6954 TCGA-CV-6960 
        1478         1840         1315         1970         1957         1969 
TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7254 
        1959         1970         1724         1095          954         1976 
TCGA-CV-7261 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CX-7219 TCGA-D6-6517 
        1099         1947         1937         1959          828          292 
TCGA-D6-6823 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5631 TCGA-F7-A50I TCGA-F7-A61S 
         701          154         1778          548           92            3 
TCGA-F7-A623 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-P3-A5QA 
           6          588          412          360          210         1652 
TCGA-P3-A6T4 TCGA-QK-A6IG 
        1968          218 

$`DEL PEAK 33(15Q15.1) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6871 
         722          725          623         1636          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 
         384          113          513          351          216          187 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         278          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         687          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 
         799          721          142          452          392          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642          369          395          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988          488          512          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1081         1980         1966         1966          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         630          424          433          629           45          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
          98          202          424          318          611          394 
TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         119          443          447          225          526          484 
TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         175         1466         1207          654         1660         1422 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129          870         1000         1057 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1959         1461         1378         1007         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
         877          613         1963          545          548          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          608          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
        1777         1521         1966         1050         1125          514 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
        1960          105         1979          759           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
        1472         1955          522         1950         3295          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5971 
         546         1978         2327         1958         2437          701 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
        2641          215         1665          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1966         3837         1959         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7245 
        1939         1945         1987         1979         1444          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1967         1960         1974         1948         1955         1957 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1937         1973         1972         1984         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 
         317          321          237          773           77          491 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 
         568          106          128          112          104         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
         490          658           15          585          384           14 
TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          13          407           58          133          414          403 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           2            5           25           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
          33         1057          485          122          441          360 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         440          351          224           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
          56          111          112          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          228          225           64 

  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                             3                              2 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                          2886                           3837 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                           892                            585 
[1] "3.0 - 2886.0 (892.0)" "2.0 - 3837.0 (585.0)"
[1] "hr=" "1"  
D62V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 33(15Q15.1) MUTATED         3       17        14        45         2
  DEL PEAK 33(15Q15.1) WILD-TYPE      21       46        57       147         7
D62V3, multiclass
           clus
vv          DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  STAGE I                              3                             21
  STAGE II                            17                             46
  STAGE III                           14                             57
  STAGE IVA                           45                            147
  STAGE IVB                            2                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 33(15Q15.1) MUTATED     4  28  22  28
  DEL PEAK 33(15Q15.1) WILD-TYPE  36  80  63 103
D62V4, multiclass
    clus
vv   DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  T1                            4                             36
  T2                           28                             80
  T3                           22                             63
  T4                           28                            103
[1] 4 2
[1] TRUE
[1] "dimension 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(15Q15.1) MUTATED    27  11  32   2
  DEL PEAK 33(15Q15.1) WILD-TYPE 109  45  97   5
D62V5, multiclass
    clus
vv   DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  N0                           27                            109
  N1                           11                             45
  N2                           32                             97
  N3                            2                              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 33(15Q15.1) MUTATED   16 11
  DEL PEAK 33(15Q15.1) WILD-TYPE 92 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.1) MUTATED     16   11
  DEL PEAK 33(15Q15.1) WILD-TYPE   92   37
    clus
vv   DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  M0                           16                             92
  MX                           11                             37
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.1) MUTATED    24  71
  DEL PEAK 33(15Q15.1) WILD-TYPE  97 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.1) MUTATED     24   71
  DEL PEAK 33(15Q15.1) WILD-TYPE   97  225
        clus
vv       DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  FEMALE                           24                             97
  MALE                             71                            225
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(15Q15.1) MUTATED                                      94
  DEL PEAK 33(15Q15.1) WILD-TYPE                                   316
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 33(15Q15.1) MUTATED                                                             1
  DEL PEAK 33(15Q15.1) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 33(15Q15.1) MUTATED                                                     0
  DEL PEAK 33(15Q15.1) WILD-TYPE                                                   6
D62V8, multiclass
                                                             clus
vv                                                            DEL PEAK 33(15Q15.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 94
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 33(15Q15.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  316
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.1) MUTATED    22  73
  DEL PEAK 33(15Q15.1) WILD-TYPE  57 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.1) MUTATED     22   73
  DEL PEAK 33(15Q15.1) WILD-TYPE   57  265
     clus
vv    DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  NO                            22                             57
  YES                           73                            265
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(15Q15.1) MUTATED                                  0     2
  DEL PEAK 33(15Q15.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(15Q15.1) MUTATED                           6    84
  DEL PEAK 33(15Q15.1) WILD-TYPE                        27   277
D62V12, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      84
                                  clus
vv                                 DEL PEAK 33(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       277
[1] 4 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 33(15Q15.1) MUTATED     6  84
  DEL PEAK 33(15Q15.1) WILD-TYPE  12 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.1) MUTATED      6   84
  DEL PEAK 33(15Q15.1) WILD-TYPE   12  297
                        clus
vv                       DEL PEAK 33(15Q15.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 33(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            297
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 34(16Q23.3) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16Q23.3) MUTATED    53  18
  DEL PEAK 34(16Q23.3) WILD-TYPE 204  80
  DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE 
                            71                            284 
  DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE 
                            18                             80 
$`DEL PEAK 34(16Q23.3) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-A6DA 
         415          276          722         1762         1747          351 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 
         140          310          536          638         1153         1955 
TCGA-BB-8601 TCGA-CN-4729 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 
         624          392          512         1081         1977          290 
TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6996 TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5324 
         629         1970          432          225          526         1207 
TCGA-CQ-5327 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CR-5243 TCGA-CR-6467 
        1660          870          985         1960         2562         1777 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 
        1050         1125          311          354         1245          105 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5441 TCGA-CV-5443 
         156          911         1955         1950         2886         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-7095 TCGA-CV-7097 
        2437          519          215         1959         1970         1970 
TCGA-CV-7235 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 
        1724         1099         1955         1947         1973         1937 
TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-DQ-7588 TCGA-DQ-7589 
         317          237          568          112         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50I TCGA-HD-8224 TCGA-IQ-A61E 
         775          622          299           92           55          588 
TCGA-IQ-A61H TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T8 TCGA-QK-A6IF 
         412          721         1120          400          245 

$`DEL PEAK 34(16Q23.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5555 
         462          283         1983          248         1288          520 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         725          623         1636          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
          63          384          113          236          895          513 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
         216          182          187         2878          278          133 
TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z 
         558          423          687          428          436            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721          485          142          452 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         613          462          993          642          369          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         488          173         1980         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        1975          413          630          424          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
         629           45          432           98          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
         224          318          611          394          119          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
          46          443          447          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
         367         1466          654         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
         317          341          129         1000         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          901          877          968          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         545          548          393          391          303          608 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
         358         1663         1152          799         1521         1966 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 
        1971          514         1969          362          345          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1440         1960         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
         908          898          930          216          181         1077 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1472          522         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1978         2327          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840         1315         1665          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1948         1969         1952         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1936         1959         1939         1945         1987         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 
        1976         1974         1948         1957         1937         1972 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1984         1958         1959         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7219 
        1954         1970          750          717          321          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         106          128          104         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
        1030          548          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
         564          490          658           15          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          403            2            5           25 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          10          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         441          360          440          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         210           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 
         112          254          910         1652         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH 
        1917         1968          553          357          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE 
                            55                              2 
  DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE 
                          2886                           3837 
  DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE 
                           722                            612 
[1] "55.0 - 2886.0 (722.0)" "2.0 - 3837.0 (612.0)" 
[1] "hr=" "1.2"
D63V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 34(16Q23.3) MUTATED         2        7        16        34         3
  DEL PEAK 34(16Q23.3) WILD-TYPE      22       56        55       158         6
D63V3, multiclass
           clus
vv          DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE
  STAGE I                              2                             22
  STAGE II                             7                             56
  STAGE III                           16                             55
  STAGE IVA                           34                            158
  STAGE IVB                            3                              6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(16Q23.3) MUTATED     4  16  21  22
  DEL PEAK 34(16Q23.3) WILD-TYPE  36  92  64 109
D63V4, multiclass
    clus
vv   DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE
  T1                            4                             36
  T2                           16                             92
  T3                           21                             64
  T4                           22                            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                              N0  N1  N2  N3
  DEL PEAK 34(16Q23.3) MUTATED    17  11  24   3
  DEL PEAK 34(16Q23.3) WILD-TYPE 119  45 105   4
D63V5, multiclass
    clus
vv   DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE
  N0                           17                            119
  N1                           11                             45
  N2                           24                            105
  N3                            3                              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"
D63V6, binary
                                cls
clus                              0  1
  DEL PEAK 34(16Q23.3) MUTATED   14  9
  DEL PEAK 34(16Q23.3) WILD-TYPE 94 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.3) MUTATED     14    9
  DEL PEAK 34(16Q23.3) WILD-TYPE   94   39
    clus
vv   DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE
  M0                           14                             94
  MX                            9                             39
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.3) MUTATED    20  61
  DEL PEAK 34(16Q23.3) WILD-TYPE 101 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.3) MUTATED     20   61
  DEL PEAK 34(16Q23.3) WILD-TYPE  101  235
        clus
vv       DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE
  FEMALE                           20                            101
  MALE                             61                            235
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(16Q23.3) MUTATED                                      79
  DEL PEAK 34(16Q23.3) WILD-TYPE                                   331
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 34(16Q23.3) MUTATED                                                             0
  DEL PEAK 34(16Q23.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 34(16Q23.3) MUTATED                                                     2
  DEL PEAK 34(16Q23.3) WILD-TYPE                                                   4
D63V8, multiclass
                                                             clus
vv                                                            DEL PEAK 34(16Q23.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 79
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    2
                                                             clus
vv                                                            DEL PEAK 34(16Q23.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  331
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.3) MUTATED    16  65
  DEL PEAK 34(16Q23.3) WILD-TYPE  63 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.3) MUTATED     16   65
  DEL PEAK 34(16Q23.3) WILD-TYPE   63  273
     clus
vv    DEL PEAK 34(16Q23.3) MUTATED DEL PEAK 34(16Q23.3) WILD-TYPE
  NO                            16                             63
  YES                           65                            273
[1] 2 2
[1] FALSE
D63V10, continuous
D63V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(16Q23.3) MUTATED                                  1     3
  DEL PEAK 34(16Q23.3) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(16Q23.3) MUTATED                           8    68
  DEL PEAK 34(16Q23.3) WILD-TYPE                        25   293
D63V12, multiclass
                                  clus
vv                                 DEL PEAK 34(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      68
                                  clus
vv                                 DEL PEAK 34(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       293
[1] 4 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 34(16Q23.3) MUTATED     4  76
  DEL PEAK 34(16Q23.3) WILD-TYPE  14 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.3) MUTATED      4   76
  DEL PEAK 34(16Q23.3) WILD-TYPE   14  305
                        clus
vv                       DEL PEAK 34(16Q23.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           76
                        clus
vv                       DEL PEAK 34(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            305
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 35(17Q25.3) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(17Q25.3) MUTATED    37  16
  DEL PEAK 35(17Q25.3) WILD-TYPE 220  82
  DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE 
                            53                            302 
  DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE 
                            16                             82 
$`DEL PEAK 35(17Q25.3) MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BB-4223 TCGA-BB-4227 
         283          190          451           63         2878          133 
TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6992 TCGA-CN-A63Y 
         721         1330          290          424          394          175 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CR-5248 
         317         1000          985          509          613         1663 
TCGA-CR-5249 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7374 
        1152         1966         1971          311          354           30 
TCGA-CR-7385 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5966 TCGA-CV-7091 TCGA-CV-7095 
         997         1472         1955          519         1959         1970 
TCGA-CV-7101 TCGA-CV-7248 TCGA-D6-6826 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7594 
        1939         1967          154          548         1965          368 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-A6HZ 
          15           92            6           25           55          111 
TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67G 
         485          360          412          360          210          112 
TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-QK-A6IJ 
         254         1652          721         1954           64 

$`DEL PEAK 35(17Q25.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
        1747          644          384          113          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 
         513          351          216          182          187          278 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         140          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         638         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           5            4          799          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
         488          512          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1980         1966         1966         1975          413          630 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          433          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202          424          224          318 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         611          119          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 
         447          225          526          484          348          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 
        1399          341          129          870         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         901          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         2562 
TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 
         358          799         1777         1521         1050         1125 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
         514         1969          362          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479         1956         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245         1960          105         1979          759          889 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
         972         1968         1036          796         1954         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
         911          522         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1966         1957         1969         1959         3837         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1945         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 
        1444         1095          954          797         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         773          292          701           77          491          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         516         1030          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         369          324          340          564          490          658 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          10           33         1057          122          441          588 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         440          351          224           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
          56          111          910         1120          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II 
         228          225 

  DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE 
                             6                              2 
  DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE 
                          2878                           3837 
  DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE 
                           424                            649 
[1] "6.0 - 2878.0 (424.0)" "2.0 - 3837.0 (649.0)"
[1] "hr=" "1.6"
D64V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 35(17Q25.3) MUTATED         3        6         8        26         2
  DEL PEAK 35(17Q25.3) WILD-TYPE      21       57        63       166         7
D64V3, multiclass
           clus
vv          DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE
  STAGE I                              3                             21
  STAGE II                             6                             57
  STAGE III                            8                             63
  STAGE IVA                           26                            166
  STAGE IVB                            2                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 35(17Q25.3) MUTATED     6  19   5  17
  DEL PEAK 35(17Q25.3) WILD-TYPE  34  89  80 114
D64V4, multiclass
    clus
vv   DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE
  T1                            6                             34
  T2                           19                             89
  T3                            5                             80
  T4                           17                            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                              N0  N1  N2  N3
  DEL PEAK 35(17Q25.3) MUTATED    13   8  18   2
  DEL PEAK 35(17Q25.3) WILD-TYPE 123  48 111   5
D64V5, multiclass
    clus
vv   DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE
  N0                           13                            123
  N1                            8                             48
  N2                           18                            111
  N3                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                cls
clus                              0  1
  DEL PEAK 35(17Q25.3) MUTATED   15 11
  DEL PEAK 35(17Q25.3) WILD-TYPE 93 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(17Q25.3) MUTATED     15   11
  DEL PEAK 35(17Q25.3) WILD-TYPE   93   37
    clus
vv   DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE
  M0                           15                             93
  MX                           11                             37
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(17Q25.3) MUTATED    14  44
  DEL PEAK 35(17Q25.3) WILD-TYPE 107 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(17Q25.3) MUTATED     14   44
  DEL PEAK 35(17Q25.3) WILD-TYPE  107  252
        clus
vv       DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE
  FEMALE                           14                            107
  MALE                             44                            252
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(17Q25.3) MUTATED                                      56
  DEL PEAK 35(17Q25.3) WILD-TYPE                                   354
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 35(17Q25.3) MUTATED                                                             1
  DEL PEAK 35(17Q25.3) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 35(17Q25.3) MUTATED                                                     1
  DEL PEAK 35(17Q25.3) WILD-TYPE                                                   5
D64V8, multiclass
                                                             clus
vv                                                            DEL PEAK 35(17Q25.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 56
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
                                                             clus
vv                                                            DEL PEAK 35(17Q25.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  354
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(17Q25.3) MUTATED    14  44
  DEL PEAK 35(17Q25.3) WILD-TYPE  65 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(17Q25.3) MUTATED     14   44
  DEL PEAK 35(17Q25.3) WILD-TYPE   65  294
     clus
vv    DEL PEAK 35(17Q25.3) MUTATED DEL PEAK 35(17Q25.3) WILD-TYPE
  NO                            14                             65
  YES                           44                            294
[1] 2 2
[1] FALSE
D64V10, continuous
D64V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(17Q25.3) MUTATED                                  0     1
  DEL PEAK 35(17Q25.3) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(17Q25.3) MUTATED                           5    49
  DEL PEAK 35(17Q25.3) WILD-TYPE                        28   312
D64V12, multiclass
                                  clus
vv                                 DEL PEAK 35(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      49
                                  clus
vv                                 DEL PEAK 35(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    28
  WHITE                                                       312
[1] 4 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 35(17Q25.3) MUTATED     7  47
  DEL PEAK 35(17Q25.3) WILD-TYPE  11 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(17Q25.3) MUTATED      7   47
  DEL PEAK 35(17Q25.3) WILD-TYPE   11  334
                        clus
vv                       DEL PEAK 35(17Q25.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 35(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            334
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 36(18Q21.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(18Q21.2) MUTATED   129  58
  DEL PEAK 36(18Q21.2) WILD-TYPE 128  40
  DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE 
                           187                            168 
  DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE 
                            58                             40 
$`DEL PEAK 36(18Q21.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5557 TCGA-BA-5558 
         462          283          415         1288          623         1636 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         190          451           63          384          113          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 
         895          513          216          182          187          278 
TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z 
         536         1153          428          436          624            5 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          721          485          142          452          613 
TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 
         462          369          240         1330          811          488 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1977         1966         1966         1975          413          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 
         424          629           45          432           98          202 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
         224          318          394          119          432           46 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5332 
         225          526          348          367          654          317 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         870         1057          985         1959         1959          815 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
        1378         1007          509          968         1960          545 
TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6484 
         391          608          358         1971          362          354 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7370 
         379          350          479         1956         1191          105 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 
         759          889           30         1968         1036         1954 
TCGA-CR-7386 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5435 
        1430          181         1077          911         1950         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 
         584          546         1978         2886         2437          519 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
         406         2641         1478         1840         1315         1665 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 
        1970         1969         3835         1969         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
        1959         3837         1959         1970         1970         1939 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1987         1724         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1960         1955         1947         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JN TCGA-CX-7086 
        1958         1959         1981         1954          717          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 
         828          773          701          491          106          128 
TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
         112         1778          516         1030         1965          575 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         299          324          564          658           15           92 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13            6           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 
         403            2            5           37           55           25 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L 
         111          485          588          360          412          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
         360          224          210           14           34           56 
TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1652          578         1968          400          553          357 
TCGA-QK-A6IH 
         228 

$`DEL PEAK 36(18Q21.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
        1983          276          248          722         1762          520 
TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-A6DA TCGA-BB-4223 TCGA-BB-4225 
         725         1747          644          351         2878          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          310          423          687          638 
TCGA-BB-8596 TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        1955          799          392          993          642          395 
TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1960         1268         1988          512          173         1980 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        1081         1980          290          433          594          629 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B 
        1970          424          611          429          443          447 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 
         484          175         1466         1207         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 
         896         1399          341          129         1000         1461 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD 
        1309          901          877          613         1963          548 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         393          303         2562         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
        1777         1521         1966         1050         1125          514 
TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7367 
        1969          311          345          234         1435         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 
        1245         1960         1979          972          796          997 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5430 
         898          930          216          156         1472         1955 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5978 
         522         3295         2327         1958          701          215 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 
         641         1899         1948         1952         1959         1948 
TCGA-CV-6952 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 
        1966         1936         1959         1945         1979         1444 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 
        1976         1099         1974         1948         1957         1937 
TCGA-CV-7428 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7082 
        1973          851         1945         1970          750          317 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB 
         321          292           77          154          568          104 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
        1081          548          775          622          369          368 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-7774 
         340          490          585            3          384          407 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          25           44           24           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61J TCGA-MT-A67A 
          33         1057          122          441          440          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
        1954         1917          245          218          225           64 

  DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE 
                             2                              3 
  DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE 
                          3837                           3295 
  DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE 
                         546.0                          762.5 
[1] "2.0 - 3837.0 (546.0)" "3.0 - 3295.0 (762.5)"
[1] "hr=" "1.3"
D65V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 36(18Q21.2) MUTATED        15       32        37       108         4
  DEL PEAK 36(18Q21.2) WILD-TYPE       9       31        34        84         5
D65V3, multiclass
           clus
vv          DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE
  STAGE I                             15                              9
  STAGE II                            32                             31
  STAGE III                           37                             34
  STAGE IVA                          108                             84
  STAGE IVB                            4                              5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 36(18Q21.2) MUTATED   23 53 45 75
  DEL PEAK 36(18Q21.2) WILD-TYPE 17 55 40 56
D65V4, multiclass
    clus
vv   DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE
  T1                           23                             17
  T2                           53                             55
  T3                           45                             40
  T4                           75                             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 36(18Q21.2) MUTATED   69 33 76  3
  DEL PEAK 36(18Q21.2) WILD-TYPE 67 23 53  4
D65V5, multiclass
    clus
vv   DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE
  N0                           69                             67
  N1                           33                             23
  N2                           76                             53
  N3                            3                              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"
D65V6, binary
                                cls
clus                              0  1
  DEL PEAK 36(18Q21.2) MUTATED   53 27
  DEL PEAK 36(18Q21.2) WILD-TYPE 55 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(18Q21.2) MUTATED     53   27
  DEL PEAK 36(18Q21.2) WILD-TYPE   55   21
    clus
vv   DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE
  M0                           53                             55
  MX                           27                             21
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(18Q21.2) MUTATED    54 164
  DEL PEAK 36(18Q21.2) WILD-TYPE  67 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(18Q21.2) MUTATED     54  164
  DEL PEAK 36(18Q21.2) WILD-TYPE   67  132
        clus
vv       DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE
  FEMALE                           54                             67
  MALE                            164                            132
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(18Q21.2) MUTATED                                     215
  DEL PEAK 36(18Q21.2) WILD-TYPE                                   195
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 36(18Q21.2) MUTATED                                                             1
  DEL PEAK 36(18Q21.2) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 36(18Q21.2) MUTATED                                                     2
  DEL PEAK 36(18Q21.2) WILD-TYPE                                                   4
D65V8, multiclass
                                                             clus
vv                                                            DEL PEAK 36(18Q21.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                215
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    2
                                                             clus
vv                                                            DEL PEAK 36(18Q21.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  195
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(18Q21.2) MUTATED    43 175
  DEL PEAK 36(18Q21.2) WILD-TYPE  36 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(18Q21.2) MUTATED     43  175
  DEL PEAK 36(18Q21.2) WILD-TYPE   36  163
     clus
vv    DEL PEAK 36(18Q21.2) MUTATED DEL PEAK 36(18Q21.2) WILD-TYPE
  NO                            43                             36
  YES                          175                            163
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(18Q21.2) MUTATED                                  1     8
  DEL PEAK 36(18Q21.2) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(18Q21.2) MUTATED                          24   177
  DEL PEAK 36(18Q21.2) WILD-TYPE                         9   184
D65V12, multiclass
                                  clus
vv                                 DEL PEAK 36(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     177
                                  clus
vv                                 DEL PEAK 36(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                                cls
clus                               0   1
  DEL PEAK 36(18Q21.2) MUTATED    15 194
  DEL PEAK 36(18Q21.2) WILD-TYPE   3 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(18Q21.2) MUTATED     15  194
  DEL PEAK 36(18Q21.2) WILD-TYPE    3  187
                        clus
vv                       DEL PEAK 36(18Q21.2) MUTATED
  HISPANIC OR LATINO                               15
  NOT HISPANIC OR LATINO                          194
                        clus
vv                       DEL PEAK 36(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            187
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 37(18Q23) MUTATION ANALYSIS
D66V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 37(18Q23) MUTATED   135  63
  DEL PEAK 37(18Q23) WILD-TYPE 122  35
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                         198                          157 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                          63                           35 
$`DEL PEAK 37(18Q23) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5557 
         462          283          415          248         1288          623 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1636          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         113          895          513          351          216          182 
TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         278          536         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         624            5            4          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 
         452          613          392          462          369          240 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 
        1330          811         1988          488         1980         1977 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          413          630          424 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 
         629           45          432           98          202          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49B 
         318          394          119          432           46          447 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5332 
         225          526          348          367          654          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         815         1378         1007          509          968         1960 
TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6480 
         545          391          608          358         1971          362 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 
         354          379          350          479         1956         1191 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 
         105          759          889           30         1968         1036 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        1954         1430          181         1077          911         1472 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295         1438          546         1978         2886 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2437          519          406         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6942 
         215         1315         1665         1970         1969         3835 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1969         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 
        1970         1970         1939         1945         1987         1724 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1099         1957         1947         1972         1937         1984 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        1959         1981         1954          317          237          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         292          701          491          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
         104         1778          516         1030         1965          575 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         299          324          564          658           15           92 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13            6           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 
         403            2            5           37           55           25 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L 
         111          485          588          360          412          351 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA 
         360          210           14           34           56         1652 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
         578         1968          400          553          357          228 

$`DEL PEAK 37(18Q23) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        1983          276          722         1762          520          725 
TCGA-BA-5559 TCGA-BA-7269 TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        1747          236          187         2878          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-CN-4722 
         558          310          423          687          638          799 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-5356 
         993          642          395         1960         1268          512 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 
         173         1081         1980          290          433          594 
TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A498 
         629         1970          424          611          429          443 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 
         484          175         1466         1207         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 
         896         1399          341          129         1461         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE 
         901          877          613         1963          548          393 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         303         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 
        1521         1966         1050         1125          514         1969 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
         311          345          234         1435         1440         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 
        1960         1979          972          796          997         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 
         930          216          156         1955          522          584 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
        2327         1958          701          641         1899         1948 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-7099 TCGA-CV-7100 
        1952         1959         1948         1966         1936         1959 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 
        1979         1444         1974         1948         1955         1937 
TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE 
        1973         1958          851         1945         1970          750 
TCGA-CV-A6JN TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
         717          321          773           77          154          568 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
        1081          548          775          622          369          368 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-7774 
         340          490          585            3          384          407 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          25           44           24           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61J TCGA-KU-A66S 
          33         1057          122          441          440          224 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
        1120         1954         1917          245          218          225 
TCGA-QK-A6IJ 
          64 

  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                           2                            3 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                        3837                         2878 
  DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE 
                       549.5                        725.0 
[1] "2.0 - 3837.0 (549.5)" "3.0 - 2878.0 (725.0)"
[1] "hr=" "1.1"
D66V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 37(18Q23) MUTATED        14       34        40       116         5
  DEL PEAK 37(18Q23) WILD-TYPE      10       29        31        76         4
D66V3, multiclass
           clus
vv          DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  STAGE I                           14                           10
  STAGE II                          34                           29
  STAGE III                         40                           31
  STAGE IVA                        116                           76
  STAGE IVB                          5                            4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T1 T2 T3 T4
  DEL PEAK 37(18Q23) MUTATED   21 56 50 83
  DEL PEAK 37(18Q23) WILD-TYPE 19 52 35 48
D66V4, multiclass
    clus
vv   DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  T1                         21                           19
  T2                         56                           52
  T3                         50                           35
  T4                         83                           48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 37(18Q23) MUTATED   73 33 80  4
  DEL PEAK 37(18Q23) WILD-TYPE 63 23 49  3
D66V5, multiclass
    clus
vv   DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  N0                         73                           63
  N1                         33                           23
  N2                         80                           49
  N3                          4                            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"
D66V6, binary
                              cls
clus                            0  1
  DEL PEAK 37(18Q23) MUTATED   58 29
  DEL PEAK 37(18Q23) WILD-TYPE 50 19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(18Q23) MUTATED     58   29
  DEL PEAK 37(18Q23) WILD-TYPE   50   19
    clus
vv   DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  M0                         58                           50
  MX                         29                           19
[1] 2 2
[1] FALSE
D66V7, binary
                              cls
clus                             0   1
  DEL PEAK 37(18Q23) MUTATED    61 171
  DEL PEAK 37(18Q23) WILD-TYPE  60 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(18Q23) MUTATED     61  171
  DEL PEAK 37(18Q23) WILD-TYPE   60  125
        clus
vv       DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  FEMALE                         61                           60
  MALE                          171                          125
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(18Q23) MUTATED                                     230
  DEL PEAK 37(18Q23) WILD-TYPE                                   180
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 37(18Q23) MUTATED                                                             1
  DEL PEAK 37(18Q23) WILD-TYPE                                                           0
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 37(18Q23) MUTATED                                                     1
  DEL PEAK 37(18Q23) WILD-TYPE                                                   5
D66V8, multiclass
                                                             clus
vv                                                            DEL PEAK 37(18Q23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                              230
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  1
                                                             clus
vv                                                            DEL PEAK 37(18Q23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                180
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                              cls
clus                             0   1
  DEL PEAK 37(18Q23) MUTATED    46 186
  DEL PEAK 37(18Q23) WILD-TYPE  33 152
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(18Q23) MUTATED     46  186
  DEL PEAK 37(18Q23) WILD-TYPE   33  152
     clus
vv    DEL PEAK 37(18Q23) MUTATED DEL PEAK 37(18Q23) WILD-TYPE
  NO                          46                           33
  YES                        186                          152
[1] 2 2
[1] FALSE
D66V10, continuous
D66V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(18Q23) MUTATED                                  1     8
  DEL PEAK 37(18Q23) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(18Q23) MUTATED                          24   192
  DEL PEAK 37(18Q23) WILD-TYPE                         9   169
D66V12, multiclass
                                  clus
vv                                 DEL PEAK 37(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     8
  BLACK OR AFRICAN AMERICAN                                24
  WHITE                                                   192
                                  clus
vv                                 DEL PEAK 37(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                     169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                              cls
clus                             0   1
  DEL PEAK 37(18Q23) MUTATED    14 208
  DEL PEAK 37(18Q23) WILD-TYPE   4 173
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(18Q23) MUTATED     14  208
  DEL PEAK 37(18Q23) WILD-TYPE    4  173
                        clus
vv                       DEL PEAK 37(18Q23) MUTATED
  HISPANIC OR LATINO                             14
  NOT HISPANIC OR LATINO                        208
                        clus
vv                       DEL PEAK 37(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          173
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 38(19P13.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(19P13.3) MUTATED    78  42
  DEL PEAK 38(19P13.3) WILD-TYPE 179  56
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           120                            235 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                            42                             56 
$`DEL PEAK 38(19P13.3) MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-6871 
         283          248         1288         1762          190           63 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BB-4227 TCGA-BB-7871 
         113          236          895          351          133          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4731 
         436         1955            5          485          392          993 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-5356 
         369          395          240         1960         1268          512 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 
        1980         1977         1980         1975          290          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6022 
         629          433          594           45           98          202 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A63T TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5330 
         119          432          225          367         1466          896 
TCGA-CQ-6223 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1057         1378          901         1960          613         1963 
TCGA-CQ-A4CD TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7371 
         548          514          354         1435         1191         1979 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7386 TCGA-CR-7398 TCGA-CR-7399 
         889           30         1968         1430          156          181 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5970 
        1950         3295         1438          546         1978          406 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6952 
        1315         1665         1970         1952         1969         1966 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 
        1959         1959         1970         1970         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7428 
        1945         1987          797         1976         1099         1973 
TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JN TCGA-D6-6516 
        1972         1959         1981         1954          717          773 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7589 
         491          154          128         1778         1965          575 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I 
         622          299          324          564           15           92 
TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-8635 TCGA-HD-A6HZ 
         585           14            6            5           25          111 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X TCGA-P3-A5QA 
         588          360          351          210           34         1652 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ 
        1954         1968          400          357          225           64 

$`DEL PEAK 38(19P13.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5555 
         462          415         1983          276          722          520 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
         725          623         1636         1747          644          451 
TCGA-BA-6872 TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         384          513          216          182          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         278          140          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
         687          638         1153          624            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 
         721          142          452          613          462          642 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
        1330          811         1988          488          173         1081 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 
        1966         1966          413          630          629          432 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970          424          224          318          611          394 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V 
         429           46          443          447          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         348          175         1207          654         1660         1422 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129          870         1000 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959          815         1461         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CE 
         509         1309          877          968          545          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          608         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 
         234          379          350          479         1956         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7379 
        1245         1960          105          759          972         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         796         1954          997         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 
        1077          911         1472         1955          522          584 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 
        2886         2327         1958         2437          519          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
        2641         1478         1840          215          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6954 
        1948         1969         1959         3835         1948         1957 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1969         3837         1936         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 
        1095          954         1967         1960         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7433 
        1955         1957         1947         1937         1937         1984 
TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7082 
        1958          851         1945         1970          750          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         321          237          828          292          701           77 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 
         568          106          112          104         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
        1030          548          775          369          368          340 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 
         490          658            3          384           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 
          58          133          414          403            2           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
          37           55           44           24           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10           33         1057          485          122          441 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A 
         412          440          360          224           14          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
          56          111          112          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG 
        1120          578         1917          553          245          218 
TCGA-QK-A6IH 
         228 

  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                             5                              2 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                          3295                           3837 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                         603.5                          638.0 
[1] "5.0 - 3295.0 (603.5)" "2.0 - 3837.0 (638.0)"
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 38(19P13.3) MUTATED         7       17        30        68         2
  DEL PEAK 38(19P13.3) WILD-TYPE      17       46        41       124         7
D67V3, multiclass
           clus
vv          DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  STAGE I                              7                             17
  STAGE II                            17                             46
  STAGE III                           30                             41
  STAGE IVA                           68                            124
  STAGE IVB                            2                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 38(19P13.3) MUTATED   13 35 30 48
  DEL PEAK 38(19P13.3) WILD-TYPE 27 73 55 83
D67V4, multiclass
    clus
vv   DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  T1                           13                             27
  T2                           35                             73
  T3                           30                             55
  T4                           48                             83
[1] 4 2
[1] TRUE
[1] "dimension 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 38(19P13.3) MUTATED   40 25 47  2
  DEL PEAK 38(19P13.3) WILD-TYPE 96 31 82  5
D67V5, multiclass
    clus
vv   DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  N0                           40                             96
  N1                           25                             31
  N2                           47                             82
  N3                            2                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                                cls
clus                              0  1
  DEL PEAK 38(19P13.3) MUTATED   37 15
  DEL PEAK 38(19P13.3) WILD-TYPE 71 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED     37   15
  DEL PEAK 38(19P13.3) WILD-TYPE   71   33
    clus
vv   DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  M0                           37                             71
  MX                           15                             33
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED    36 103
  DEL PEAK 38(19P13.3) WILD-TYPE  85 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED     36  103
  DEL PEAK 38(19P13.3) WILD-TYPE   85  193
        clus
vv       DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  FEMALE                           36                             85
  MALE                            103                            193
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                     139
  DEL PEAK 38(19P13.3) WILD-TYPE                                   271
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 38(19P13.3) MUTATED                                                             0
  DEL PEAK 38(19P13.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 38(19P13.3) MUTATED                                                     0
  DEL PEAK 38(19P13.3) WILD-TYPE                                                   6
D67V8, multiclass
                                                             clus
vv                                                            DEL PEAK 38(19P13.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                139
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 38(19P13.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  271
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED    30 109
  DEL PEAK 38(19P13.3) WILD-TYPE  49 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED     30  109
  DEL PEAK 38(19P13.3) WILD-TYPE   49  229
     clus
vv    DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  NO                            30                             49
  YES                          109                            229
[1] 2 2
[1] FALSE
D67V10, continuous
D67V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(19P13.3) MUTATED                                  1     4
  DEL PEAK 38(19P13.3) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(19P13.3) MUTATED                           8   120
  DEL PEAK 38(19P13.3) WILD-TYPE                        25   241
D67V12, multiclass
                                  clus
vv                                 DEL PEAK 38(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                     120
                                  clus
vv                                 DEL PEAK 38(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED     8 125
  DEL PEAK 38(19P13.3) WILD-TYPE  10 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED      8  125
  DEL PEAK 38(19P13.3) WILD-TYPE   10  256
                        clus
vv                       DEL PEAK 38(19P13.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          125
                        clus
vv                       DEL PEAK 38(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            256
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 39(19Q13.43) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 39(19Q13.43) MUTATED    47  23
  DEL PEAK 39(19Q13.43) WILD-TYPE 210  75
  DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE 
                             70                             285 
  DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE 
                             23                              75 
$`DEL PEAK 39(19Q13.43) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 
         283          415          248          520          451          384 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7871 
         113          895          216          133          536          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4737 
        1955          624            5          485          142          240 
TCGA-CN-5356 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6989 
         512          290          629           45         1970          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A641 
         394          119          432          429          526          367 
TCGA-CQ-5332 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
         317         1378          901         1960          613          608 
TCGA-CR-5248 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7390 
        1663          379         1191          889           30          907 
TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5979 
         156          522         3295         1438          546         1315 
TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6960 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7235 
        1665         1959         1969         1970         1987         1724 
TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7430 TCGA-CV-A6JN TCGA-D6-6517 
         797         1976         1099         1972          717          292 
TCGA-D6-6826 TCGA-D6-8569 TCGA-DQ-7588 TCGA-F7-A61W TCGA-HD-7753 TCGA-IQ-A61L 
         154          128         1965           14            5          351 
TCGA-MT-A51X TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ 
          34          357          228           64 

$`DEL PEAK 39(19Q13.43) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462         1983          276          722         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         725          623         1636         1747          190          644 
TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 
          63          236          513          351          182          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        2878          278          140          558          310          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 
         687          638         1153          436            4          799 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         721          452          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642          369          395         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1268         1988          488          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          413 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         630          424          433          594          629          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6998 
          98          202          424          224          318           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         443          447          225          484          348          175 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959          815         1461         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         509         1309          877          968         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 
         548          393          391          303         2562          358 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          354          234          350          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1435         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         759          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
         908          898          930          216          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5440 
         911         1472         1955         1950          584         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 
         701         2641         1478         1840          215          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
        1899         1970         1948         1969         1952         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 
        1948         1969         1966         1957         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         1970         1936         1959         1939         1945 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        1979         1444         1095          954         1967         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1973         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7082 
         851         1945         1954         1970          750          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 
         321          237          828          773          701           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 
         491          568          106          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 
        1081          516         1030          548          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         564          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
           3          384           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         133          414          403            2           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          10          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
         441          588          360          412          440          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         224          210           14          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
         245          218          225 

  DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE 
                              5                               2 
  DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE 
                           3295                            3837 
  DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE 
                            516                             701 
[1] "5.0 - 3295.0 (516.0)" "2.0 - 3837.0 (701.0)"
[1] "hr=" "1.5"
D68V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 39(19Q13.43) MUTATED         2       11        19        38
  DEL PEAK 39(19Q13.43) WILD-TYPE      22       52        52       154
                                 vv
clus                              STAGE IVB
  DEL PEAK 39(19Q13.43) MUTATED           2
  DEL PEAK 39(19Q13.43) WILD-TYPE         7
D68V3, multiclass
           clus
vv          DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE
  STAGE I                               2                              22
  STAGE II                             11                              52
  STAGE III                            19                              52
  STAGE IVA                            38                             154
  STAGE IVB                             2                               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 39(19Q13.43) MUTATED     5  21  24  22
  DEL PEAK 39(19Q13.43) WILD-TYPE  35  87  61 109
D68V4, multiclass
    clus
vv   DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE
  T1                             5                              35
  T2                            21                              87
  T3                            24                              61
  T4                            22                             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                               N0  N1  N2  N3
  DEL PEAK 39(19Q13.43) MUTATED    22  13  29   1
  DEL PEAK 39(19Q13.43) WILD-TYPE 114  43 100   6
D68V5, multiclass
    clus
vv   DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE
  N0                            22                             114
  N1                            13                              43
  N2                            29                             100
  N3                             1                               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"
D68V6, binary
                                 cls
clus                               0  1
  DEL PEAK 39(19Q13.43) MUTATED   19  6
  DEL PEAK 39(19Q13.43) WILD-TYPE 89 42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(19Q13.43) MUTATED     19    6
  DEL PEAK 39(19Q13.43) WILD-TYPE   89   42
    clus
vv   DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE
  M0                            19                              89
  MX                             6                              42
[1] 2 2
[1] FALSE
D68V7, binary
                                 cls
clus                                0   1
  DEL PEAK 39(19Q13.43) MUTATED    22  59
  DEL PEAK 39(19Q13.43) WILD-TYPE  99 237
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(19Q13.43) MUTATED     22   59
  DEL PEAK 39(19Q13.43) WILD-TYPE   99  237
        clus
vv       DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE
  FEMALE                            22                              99
  MALE                              59                             237
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(19Q13.43) MUTATED                                      80
  DEL PEAK 39(19Q13.43) WILD-TYPE                                   330
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 39(19Q13.43) MUTATED                                                             0
  DEL PEAK 39(19Q13.43) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 39(19Q13.43) MUTATED                                                     1
  DEL PEAK 39(19Q13.43) WILD-TYPE                                                   5
D68V8, multiclass
                                                             clus
vv                                                            DEL PEAK 39(19Q13.43) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  80
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
                                                             clus
vv                                                            DEL PEAK 39(19Q13.43) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   330
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                                 cls
clus                                0   1
  DEL PEAK 39(19Q13.43) MUTATED    17  64
  DEL PEAK 39(19Q13.43) WILD-TYPE  62 274
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(19Q13.43) MUTATED     17   64
  DEL PEAK 39(19Q13.43) WILD-TYPE   62  274
     clus
vv    DEL PEAK 39(19Q13.43) MUTATED DEL PEAK 39(19Q13.43) WILD-TYPE
  NO                             17                              62
  YES                            64                             274
[1] 2 2
[1] FALSE
D68V10, continuous
D68V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(19Q13.43) MUTATED                                  0     2
  DEL PEAK 39(19Q13.43) WILD-TYPE                                1     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(19Q13.43) MUTATED                           8    68
  DEL PEAK 39(19Q13.43) WILD-TYPE                        25   293
D68V12, multiclass
                                  clus
vv                                 DEL PEAK 39(19Q13.43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       68
                                  clus
vv                                 DEL PEAK 39(19Q13.43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        293
[1] 4 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 39(19Q13.43) MUTATED     6  73
  DEL PEAK 39(19Q13.43) WILD-TYPE  12 308
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(19Q13.43) MUTATED      6   73
  DEL PEAK 39(19Q13.43) WILD-TYPE   12  308
                        clus
vv                       DEL PEAK 39(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            73
                        clus
vv                       DEL PEAK 39(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             308
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 40(21Q22.3) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(21Q22.3) MUTATED   104  43
  DEL PEAK 40(21Q22.3) WILD-TYPE 153  55
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                           147                            208 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                            43                             55 
$`DEL PEAK 40(21Q22.3) MUTATED`
TCGA-BA-4075 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         283         1636         1747          190          451           63 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-8596 
         513          351          536          687          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
         624            5          485          142          613          392 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 
         488         1081         1977         1980         1975          290 
TCGA-CN-6010 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6988 TCGA-CN-6992 
         630           45          432         1970          318          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63T 
         119          432          429           46          447          225 
TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-6224 
         348         1466          896          317         1057          985 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 
         815         1378         1007          509          901          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-6477 
        1960          613          393          303          608          514 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
         354          379          350         1191         1440         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7388 TCGA-CR-7389 
         105         1979          889           30         1951          392 
TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 
         181          522          546         2437          519         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        1478         1840          215         1315         1665         1970 
TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1948         1959         1957         1959         3837         1959 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1939         1987         1724         1095          954          797 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7428 
        1967         1976         1099         1957         1947         1973 
TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1937         1959         1981          750          717          317 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-DQ-5624 
         237          828          701          491          154         1778 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         516         1965          299           15           92          585 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 
         384           14           13           58          133          403 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E 
           2            5           24           49          111          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X 
         360          412          440          351          210           34 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1652         1954          578         1917         1968          400 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
         218          228           64 

$`DEL PEAK 40(21Q22.3) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6869 
        1288         1762          520          725          623          644 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DE 
         384          113          236          895          216          182 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-C9-A480 
         310          423          638         1153          436            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         799          721          452          462          993          642 
TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 
         369          811          512          173         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1966          413          424          629          433          594 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 
         629           98          202          424          224          611 
TCGA-CN-A498 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 
         443          526          484          175          367         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1422         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 
         870         1000         1959         1959         1461         1309 
TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 
         877         1963          545          548          391         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 
        1966         1050         1125         1971         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         311          345          234          479         1956         1435 
TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1245          759          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1954          997         1430          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         911         1472         1955         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 
         584         1978         2886         2327         1958          406 
TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
         701          641         1899         1969         1952         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7097 
        1948         1969         1966         1969         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 
        1936         1959         1945         1979         1444         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 
        1974         1948         1955         1937         1972         1984 
TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7085 
        1958          851         1945         1954         1970          321 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         773          292           77          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
         112          104         1081         1030          548          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         775          622          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-7774 
         564          490          658            3            6          407 
TCGA-H7-A6C4 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
         414           25           37           55           44           25 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          11           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         441          360          224           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910          721         1120 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II 
         553          357          245          225 

  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                             2                              3 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                          3837                           3835 
  DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE 
                           585                            649 
[1] "2.0 - 3837.0 (585.0)" "3.0 - 3835.0 (649.0)"
[1] "hr=" "1.1"
D69V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 40(21Q22.3) MUTATED         7       26        31        80         5
  DEL PEAK 40(21Q22.3) WILD-TYPE      17       37        40       112         4
D69V3, multiclass
           clus
vv          DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  STAGE I                              7                             17
  STAGE II                            26                             37
  STAGE III                           31                             40
  STAGE IVA                           80                            112
  STAGE IVB                            5                              4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 40(21Q22.3) MUTATED    9 48 38 55
  DEL PEAK 40(21Q22.3) WILD-TYPE 31 60 47 76
D69V4, multiclass
    clus
vv   DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  T1                            9                             31
  T2                           48                             60
  T3                           38                             47
  T4                           55                             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                             N0 N1 N2 N3
  DEL PEAK 40(21Q22.3) MUTATED   51 28 54  4
  DEL PEAK 40(21Q22.3) WILD-TYPE 85 28 75  3
D69V5, multiclass
    clus
vv   DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  N0                           51                             85
  N1                           28                             28
  N2                           54                             75
  N3                            4                              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"
D69V6, binary
                                cls
clus                              0  1
  DEL PEAK 40(21Q22.3) MUTATED   39 24
  DEL PEAK 40(21Q22.3) WILD-TYPE 69 24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(21Q22.3) MUTATED     39   24
  DEL PEAK 40(21Q22.3) WILD-TYPE   69   24
    clus
vv   DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  M0                           39                             69
  MX                           24                             24
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(21Q22.3) MUTATED    47 120
  DEL PEAK 40(21Q22.3) WILD-TYPE  74 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(21Q22.3) MUTATED     47  120
  DEL PEAK 40(21Q22.3) WILD-TYPE   74  176
        clus
vv       DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  FEMALE                           47                             74
  MALE                            120                            176
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(21Q22.3) MUTATED                                     166
  DEL PEAK 40(21Q22.3) WILD-TYPE                                   244
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 40(21Q22.3) MUTATED                                                             0
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 40(21Q22.3) MUTATED                                                     1
  DEL PEAK 40(21Q22.3) WILD-TYPE                                                   5
D69V8, multiclass
                                                             clus
vv                                                            DEL PEAK 40(21Q22.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                166
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
                                                             clus
vv                                                            DEL PEAK 40(21Q22.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  244
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(21Q22.3) MUTATED    28 139
  DEL PEAK 40(21Q22.3) WILD-TYPE  51 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(21Q22.3) MUTATED     28  139
  DEL PEAK 40(21Q22.3) WILD-TYPE   51  199
     clus
vv    DEL PEAK 40(21Q22.3) MUTATED DEL PEAK 40(21Q22.3) WILD-TYPE
  NO                            28                             51
  YES                          139                            199
[1] 2 2
[1] FALSE
D69V10, continuous
D69V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(21Q22.3) MUTATED                                  1     7
  DEL PEAK 40(21Q22.3) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(21Q22.3) MUTATED                          18   137
  DEL PEAK 40(21Q22.3) WILD-TYPE                        15   224
D69V12, multiclass
                                  clus
vv                                 DEL PEAK 40(21Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     137
                                  clus
vv                                 DEL PEAK 40(21Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    15
  WHITE                                                       224
[1] 4 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 40(21Q22.3) MUTATED     8 151
  DEL PEAK 40(21Q22.3) WILD-TYPE  10 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(21Q22.3) MUTATED      8  151
  DEL PEAK 40(21Q22.3) WILD-TYPE   10  230
                        clus
vv                       DEL PEAK 40(21Q22.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          151
                        clus
vv                       DEL PEAK 40(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            230
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 41(22Q13.31) MUTATION ANALYSIS
D70V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 41(22Q13.31) MUTATED    46  20
  DEL PEAK 41(22Q13.31) WILD-TYPE 211  78
  DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE 
                             66                             289 
  DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE 
                             20                              78 
$`DEL PEAK 41(22Q13.31) MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6DE 
         283          248         1636          451           63          182 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7872 TCGA-C9-A47Z 
        2878          278          140          310          436            5 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5370 
           4          485          462         1330          488         1975 
TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6996 TCGA-CN-6998 TCGA-CQ-5323 TCGA-CQ-5327 
          45         1970          432           46         1466         1660 
TCGA-CQ-5332 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CR-5248 
         317         1378         1007         1960          393         1663 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7379 
        1050         1969          379         1956          889         1036 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6945 
         156          181          519         2641         1840         1969 
TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7432 TCGA-CX-7086 
        1957         1959         1939         1987         1937          237 
TCGA-D6-6516 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 
         773          128          112          548          775          299 
TCGA-DQ-7593 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-A633 TCGA-IQ-7630 
         369           15          585            6           49          485 
TCGA-IQ-A61E TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-QK-A6IH TCGA-QK-A6IJ 
         588          112         1652          578          228           64 

$`DEL PEAK 41(22Q13.31) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          276          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
        1762          520          725          623         1747          190 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         644          384          113          236          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
         351          216          187          133          558          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         423          687          638         1153          428         1955 
TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         624          799          721          142          452          613 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         392          993          642          369          395          240 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1960          811         1268         1988          512          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         413          290          630          424          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
         594          629          432           98          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
         224          318          611          394          119          429 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         443          447          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
         175          367         1207          654         1422          896 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7067 
         985         1959         1959          815         1461          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          901          877          968          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         545          548          391          303          608         2562 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
         358         1152          799         1777         1521         1966 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971          514          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
         354          234          350          479         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
          30          972         1968          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
         908          898          930          216         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
        2437          406          701         1478          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1952         1959         3835         1948         1966         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         1970         1970         1936         1959 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1945         1979         1724         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1945         1954         1970          750          717          317 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         321          828          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         154          568          106          104         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7594 
         516         1030         1965          575          622          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
         324          340          564          490          658           92 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 
           3          384           14           13          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          403            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
          10          111           33         1057          122          441 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         360          412          440          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         210           14           34          392           56          111 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
         254          910          721         1120         1954         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6II 
         225 

  DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE 
                              4                               2 
  DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE 
                           2878                            3837 
  DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE 
                          486.5                           644.0 
[1] "4.0 - 2878.0 (486.5)" "2.0 - 3837.0 (644.0)"
[1] "hr=" "1.3"
D70V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 41(22Q13.31) MUTATED         5       12        15        28
  DEL PEAK 41(22Q13.31) WILD-TYPE      19       51        56       164
                                 vv
clus                              STAGE IVB
  DEL PEAK 41(22Q13.31) MUTATED           2
  DEL PEAK 41(22Q13.31) WILD-TYPE         7
D70V3, multiclass
           clus
vv          DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE
  STAGE I                               5                              19
  STAGE II                             12                              51
  STAGE III                            15                              56
  STAGE IVA                            28                             164
  STAGE IVB                             2                               7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 41(22Q13.31) MUTATED     8  18  18  18
  DEL PEAK 41(22Q13.31) WILD-TYPE  32  90  67 113
D70V4, multiclass
    clus
vv   DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE
  T1                             8                              32
  T2                            18                              90
  T3                            18                              67
  T4                            18                             113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 41(22Q13.31) MUTATED    26  12  17   1
  DEL PEAK 41(22Q13.31) WILD-TYPE 110  44 112   6
D70V5, multiclass
    clus
vv   DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE
  N0                            26                             110
  N1                            12                              44
  N2                            17                             112
  N3                             1                               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"
D70V6, binary
                                 cls
clus                               0  1
  DEL PEAK 41(22Q13.31) MUTATED   20  5
  DEL PEAK 41(22Q13.31) WILD-TYPE 88 43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(22Q13.31) MUTATED     20    5
  DEL PEAK 41(22Q13.31) WILD-TYPE   88   43
    clus
vv   DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE
  M0                            20                              88
  MX                             5                              43
[1] 2 2
[1] FALSE
D70V7, binary
                                 cls
clus                                0   1
  DEL PEAK 41(22Q13.31) MUTATED    26  48
  DEL PEAK 41(22Q13.31) WILD-TYPE  95 248
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(22Q13.31) MUTATED     26   48
  DEL PEAK 41(22Q13.31) WILD-TYPE   95  248
        clus
vv       DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE
  FEMALE                            26                              95
  MALE                              48                             248
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(22Q13.31) MUTATED                                      74
  DEL PEAK 41(22Q13.31) WILD-TYPE                                   336
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 41(22Q13.31) MUTATED                                                             0
  DEL PEAK 41(22Q13.31) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 41(22Q13.31) MUTATED                                                     0
  DEL PEAK 41(22Q13.31) WILD-TYPE                                                   6
D70V8, multiclass
                                                             clus
vv                                                            DEL PEAK 41(22Q13.31) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  74
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     0
                                                             clus
vv                                                            DEL PEAK 41(22Q13.31) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   336
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                                 cls
clus                                0   1
  DEL PEAK 41(22Q13.31) MUTATED    10  64
  DEL PEAK 41(22Q13.31) WILD-TYPE  69 274
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(22Q13.31) MUTATED     10   64
  DEL PEAK 41(22Q13.31) WILD-TYPE   69  274
     clus
vv    DEL PEAK 41(22Q13.31) MUTATED DEL PEAK 41(22Q13.31) WILD-TYPE
  NO                             10                              69
  YES                            64                             274
[1] 2 2
[1] FALSE
D70V10, continuous
D70V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(22Q13.31) MUTATED                                  1     5
  DEL PEAK 41(22Q13.31) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(22Q13.31) MUTATED                           6    60
  DEL PEAK 41(22Q13.31) WILD-TYPE                        27   301
D70V12, multiclass
                                  clus
vv                                 DEL PEAK 41(22Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                       60
                                  clus
vv                                 DEL PEAK 41(22Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        301
[1] 4 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 41(22Q13.31) MUTATED     2  67
  DEL PEAK 41(22Q13.31) WILD-TYPE  16 314
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(22Q13.31) MUTATED      2   67
  DEL PEAK 41(22Q13.31) WILD-TYPE   16  314
                        clus
vv                       DEL PEAK 41(22Q13.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            67
                        clus
vv                       DEL PEAK 41(22Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             314
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 42(XP22.2) MUTATION ANALYSIS
D71V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 42(XP22.2) MUTATED    62  36
  DEL PEAK 42(XP22.2) WILD-TYPE 195  62
  DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE 
                           98                           257 
  DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE 
                           36                            62 
$`DEL PEAK 42(XP22.2) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-A6D8 
         415          276          248          190          384          513 
TCGA-BA-A6DE TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 
         182          536          428         1955          485          613 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5360 
         392          369          395          240         1980         1081 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 
         290          630          629           45          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B 
         318          611          394          432          429          447 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 
         896          317          870         1000         1959          815 
TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6477 
        1960          608          358         1663         1050          514 
TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 
         234         1956           30         1954          907          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
         156          181         1955         3295         1438          546 
TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 
         406         1478         1840         1970         1969         1952 
TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 
        1969         1970         1939         1945         1724          954 
TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7418 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-A45Q 
         797         1976         1955         1972         1937         1945 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 
         717          317          237          773          154          568 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
         106          104         1081          516          548         1965 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W 
         622          299          564          658           15           14 
TCGA-F7-A620 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8635 TCGA-IQ-A61G TCGA-P3-A5QE 
          13          403           37           25          360          721 
TCGA-P3-A6T4 TCGA-QK-A6IH 
        1968          228 

$`DEL PEAK 42(XP22.2) WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462          283         1983          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
         520          725          623         1636         1747          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA 
         451           63          113          236          895          351 
TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         216          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         558          310          423          687          638         1153 
TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436          624            5            4          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 
         142          452          462          993          642         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
         173         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         413          424          433          594          629          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 
          98         1970          202          119           46          443 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         225          526          484          348          175          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
        1466         1207          654         1660         1422         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 
         341          129         1057          985         1959         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1378         1007          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         968          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         391          303         2562         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 
        1521         1966         1125         1971         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          345          354          379          350          479 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1979          759          889          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
         796          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 
         946          908          898          930         1077          911 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
        1472          522         1950          584         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958         2437          519          701         2641 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
         215         1315         1665          641         1899         1948 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         1959         1970         1936         1959 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 
        1987         1979         1444         1095         1967         1960 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1099         1974         1948         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1973         1984         1958         1959         1981          851 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 
        1954         1970          750          321          828          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 
         701           77          491          128          112         1778 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
        1030          575          775          369          368          324 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         340          490           92          585            3          384 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 
           6          407           58          133          414            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
           5           25           55           44           24           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         122          441          588          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          56          111          112          254          910         1652 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          225           64 

  DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE 
                           13                             2 
  DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE 
                         3295                          3837 
  DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE 
                          556                           687 
[1] "13.0 - 3295.0 (556.0)" "2.0 - 3837.0 (687.0)" 
[1] "hr=" "2"  
D71V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 42(XP22.2) MUTATED         5       14        20        56         4
  DEL PEAK 42(XP22.2) WILD-TYPE      19       49        51       136         5
D71V3, multiclass
           clus
vv          DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE
  STAGE I                             5                            19
  STAGE II                           14                            49
  STAGE III                          20                            51
  STAGE IVA                          56                           136
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 42(XP22.2) MUTATED    7 24 36 34
  DEL PEAK 42(XP22.2) WILD-TYPE 33 84 49 97
D71V4, multiclass
    clus
vv   DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE
  T1                           7                            33
  T2                          24                            84
  T3                          36                            49
  T4                          34                            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                             N0  N1  N2  N3
  DEL PEAK 42(XP22.2) MUTATED    28  14  47   2
  DEL PEAK 42(XP22.2) WILD-TYPE 108  42  82   5
D71V5, multiclass
    clus
vv   DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE
  N0                          28                           108
  N1                          14                            42
  N2                          47                            82
  N3                           2                             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 42(XP22.2) MUTATED   22 10
  DEL PEAK 42(XP22.2) WILD-TYPE 86 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XP22.2) MUTATED     22   10
  DEL PEAK 42(XP22.2) WILD-TYPE   86   38
    clus
vv   DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE
  M0                          22                            86
  MX                          10                            38
[1] 2 2
[1] FALSE
D71V7, binary
                               cls
clus                              0   1
  DEL PEAK 42(XP22.2) MUTATED    30  88
  DEL PEAK 42(XP22.2) WILD-TYPE  91 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XP22.2) MUTATED     30   88
  DEL PEAK 42(XP22.2) WILD-TYPE   91  208
        clus
vv       DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE
  FEMALE                          30                            91
  MALE                            88                           208
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(XP22.2) MUTATED                                     116
  DEL PEAK 42(XP22.2) WILD-TYPE                                   294
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 42(XP22.2) MUTATED                                                             0
  DEL PEAK 42(XP22.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 42(XP22.2) MUTATED                                                     2
  DEL PEAK 42(XP22.2) WILD-TYPE                                                   4
D71V8, multiclass
                                                             clus
vv                                                            DEL PEAK 42(XP22.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               116
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            DEL PEAK 42(XP22.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 294
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                               cls
clus                              0   1
  DEL PEAK 42(XP22.2) MUTATED    29  89
  DEL PEAK 42(XP22.2) WILD-TYPE  50 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XP22.2) MUTATED     29   89
  DEL PEAK 42(XP22.2) WILD-TYPE   50  249
     clus
vv    DEL PEAK 42(XP22.2) MUTATED DEL PEAK 42(XP22.2) WILD-TYPE
  NO                           29                            50
  YES                          89                           249
[1] 2 2
[1] FALSE
D71V10, continuous
D71V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(XP22.2) MUTATED                                  1     1
  DEL PEAK 42(XP22.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(XP22.2) MUTATED                           9   106
  DEL PEAK 42(XP22.2) WILD-TYPE                        24   255
D71V12, multiclass
                                  clus
vv                                 DEL PEAK 42(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                    106
                                  clus
vv                                 DEL PEAK 42(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      255
[1] 4 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 42(XP22.2) MUTATED     6 110
  DEL PEAK 42(XP22.2) WILD-TYPE  12 271
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 42(XP22.2) MUTATED      6  110
  DEL PEAK 42(XP22.2) WILD-TYPE   12  271
                        clus
vv                       DEL PEAK 42(XP22.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         110
                        clus
vv                       DEL PEAK 42(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           271
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 43(XP21.3) MUTATION ANALYSIS
D72V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 43(XP21.3) MUTATED    69  36
  DEL PEAK 43(XP21.3) WILD-TYPE 188  62
  DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE 
                          105                           250 
  DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE 
                           36                            62 
$`DEL PEAK 43(XP21.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-A6D8 
         462          415          276          248          384          513 
TCGA-BA-A6DE TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-4725 
         182          133          536          428         1955          485 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4742 
         613          392          369          395          240         1988 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1980         1081          290          630          424          629 
TCGA-CN-6018 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
          45          224          318          611          394          432 
TCGA-CN-6997 TCGA-CN-A49B TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         429          447         1660          896         1399          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
         870         1000         1959          815         1378         1007 
TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 
        1960          608          358         1663         1050          234 
TCGA-CR-6493 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
        1956           30         1954          907          216          156 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 
         181         1955         1438          546         2437          406 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6960 
        1478         1840         1970         1969         1952         1969 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 
        1970         1939         1945         1724          954          797 
TCGA-CV-7254 TCGA-CV-7418 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-A45Q TCGA-CX-7082 
        1976         1955         1972         1937         1945          317 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 
         237          773          701          154          106          112 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 
        1081          516          548         1965          622          299 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-A6C5 
         564          658           15           14           13          403 
TCGA-HD-7917 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A51X 
          37           25           11          360          210           34 
TCGA-P3-A5QE TCGA-P3-A6T4 TCGA-QK-A6IH 
         721         1968          228 

$`DEL PEAK 43(XP21.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         283         1983          722         1288         1762          520 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         725          623         1636         1747          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA 
         451           63          113          236          895          351 
TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         216          187         2878          278          140          558 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
         310          423          687          638         1153          436 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
         624            5            4          799          721          142 
TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-4739 
         452          462          993          642         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 
         811         1268          488          512          173         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 
        1980         1966         1966         1975          413          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         594          629          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U 
         424          119           46          443          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 
         654         1422          341          129         1057          985 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1959         1461          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         968          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         391          303         2562         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1521         1966         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
         362          311          345          354          379          350 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1435         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
         105         1979          759          889          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036          796          997         1430         1951          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 
         913          946          908          898          930         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
         911         1472          522         1950         3295          584 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 
        1978         2886         2327         1958          519          701 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        2641          215         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1948         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        1957         1959         3837         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 
        1959         1987         1979         1444         1095         1967 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 
        1960         1099         1974         1948         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1937         1973         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 
         851         1954         1970          750          717          321 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 
         828          292           77          491          568          128 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 
         104         1778         1030          575          775          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J 
         368          324          340          490           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
           3          384            6          407           58          133 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 
         414            2            5           25           55           44 
TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          24           49           10          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
         485          122          441          588          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         351          360          224           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW 
         111          112          254          910         1652         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1954          578         1917          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         245          218          225           64 

  DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE 
                           11                             2 
  DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE 
                         2437                          3837 
  DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE 
                          564                           649 
[1] "11.0 - 2437.0 (564.0)" "2.0 - 3837.0 (649.0)" 
[1] "hr=" "1.8"
D72V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 43(XP21.3) MUTATED         4       17        20        59         4
  DEL PEAK 43(XP21.3) WILD-TYPE      20       46        51       133         5
D72V3, multiclass
           clus
vv          DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE
  STAGE I                             4                            20
  STAGE II                           17                            46
  STAGE III                          20                            51
  STAGE IVA                          59                           133
  STAGE IVB                           4                             5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 43(XP21.3) MUTATED    7 30 35 35
  DEL PEAK 43(XP21.3) WILD-TYPE 33 78 50 96
D72V4, multiclass
    clus
vv   DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE
  T1                           7                            33
  T2                          30                            78
  T3                          35                            50
  T4                          35                            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                             N0  N1  N2  N3
  DEL PEAK 43(XP21.3) MUTATED    29  15  49   2
  DEL PEAK 43(XP21.3) WILD-TYPE 107  41  80   5
D72V5, multiclass
    clus
vv   DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE
  N0                          29                           107
  N1                          15                            41
  N2                          49                            80
  N3                           2                             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"
D72V6, binary
                               cls
clus                             0  1
  DEL PEAK 43(XP21.3) MUTATED   25 11
  DEL PEAK 43(XP21.3) WILD-TYPE 83 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 43(XP21.3) MUTATED     25   11
  DEL PEAK 43(XP21.3) WILD-TYPE   83   37
    clus
vv   DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE
  M0                          25                            83
  MX                          11                            37
[1] 2 2
[1] FALSE
D72V7, binary
                               cls
clus                              0   1
  DEL PEAK 43(XP21.3) MUTATED    33  88
  DEL PEAK 43(XP21.3) WILD-TYPE  88 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 43(XP21.3) MUTATED     33   88
  DEL PEAK 43(XP21.3) WILD-TYPE   88  208
        clus
vv       DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE
  FEMALE                          33                            88
  MALE                            88                           208
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(XP21.3) MUTATED                                     119
  DEL PEAK 43(XP21.3) WILD-TYPE                                   291
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 43(XP21.3) MUTATED                                                             0
  DEL PEAK 43(XP21.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 43(XP21.3) MUTATED                                                     2
  DEL PEAK 43(XP21.3) WILD-TYPE                                                   4
D72V8, multiclass
                                                             clus
vv                                                            DEL PEAK 43(XP21.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               119
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            DEL PEAK 43(XP21.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 291
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                               cls
clus                              0   1
  DEL PEAK 43(XP21.3) MUTATED    30  91
  DEL PEAK 43(XP21.3) WILD-TYPE  49 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 43(XP21.3) MUTATED     30   91
  DEL PEAK 43(XP21.3) WILD-TYPE   49  247
     clus
vv    DEL PEAK 43(XP21.3) MUTATED DEL PEAK 43(XP21.3) WILD-TYPE
  NO                           30                            49
  YES                          91                           247
[1] 2 2
[1] FALSE
D72V10, continuous
D72V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(XP21.3) MUTATED                                  1     3
  DEL PEAK 43(XP21.3) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(XP21.3) MUTATED                           9   106
  DEL PEAK 43(XP21.3) WILD-TYPE                        24   255
D72V12, multiclass
                                  clus
vv                                 DEL PEAK 43(XP21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                    106
                                  clus
vv                                 DEL PEAK 43(XP21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      255
[1] 4 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 43(XP21.3) MUTATED     6 112
  DEL PEAK 43(XP21.3) WILD-TYPE  12 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 43(XP21.3) MUTATED      6  112
  DEL PEAK 43(XP21.3) WILD-TYPE   12  269
                        clus
vv                       DEL PEAK 43(XP21.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         112
                        clus
vv                       DEL PEAK 43(XP21.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           269
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 44(XQ21.33) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(XQ21.33) MUTATED    40  15
  DEL PEAK 44(XQ21.33) WILD-TYPE 217  83
  DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE 
                            55                            300 
  DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE 
                            15                             83 
$`DEL PEAK 44(XQ21.33) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-6872 TCGA-BA-7269 
         462          415         1983          276          384          236 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 
         513          182          140          133          536          687 
TCGA-BB-7871 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5360 TCGA-CN-6011 TCGA-CN-6992 
         428          392          369         1081          424          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7065 
         119          429         1000         1959         1378         1007 
TCGA-CQ-7067 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 
         509          608          358         1663         1050          234 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7388 TCGA-CV-5973 TCGA-CV-6441 
         105         1979           30         1951         2641         1970 
TCGA-CV-6935 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7418 TCGA-CV-7430 
        1969         1969         3837         1970         1955         1972 
TCGA-CV-7435 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6827 TCGA-F7-7848 TCGA-F7-A50G 
        1959          317          828          568          564           15 
TCGA-F7-A61W TCGA-IQ-A61G TCGA-IQ-A61J TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T4 
          14          360          440         1652          721         1968 
TCGA-QK-A6IH 
         228 

$`DEL PEAK 44(XQ21.33) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         283          248          722         1288         1762          520 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         725          623         1636         1747          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB 
         451           63          113          895          351          216 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
         187         2878          278          558          310          423 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         638         1153          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721          485          142          452 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
         613          462          993          642          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         512          173         1980         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
        1966         1975          413          290          630          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202          424          224          318          611 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
         432           46          443          447          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
         341          129          870         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
         815         1461         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         391          303         2562         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1521         1966         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
         362          311          345          354          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1960          759          889          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 
         796         1954          997         1430          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         406          701         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 
        1665          641         1899         1948         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 
        3835         1948         1969         1966         1957         1959 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         1970         1936         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1987         1979         1724         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
        1948         1957         1947         1937         1973         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1984         1958         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
        1970          750          717          321          237          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 
         292          701           77          491          154          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         128          112          104         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
         299          369          368          324          340          490 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
         658           92          585            3          384           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           2            5           25           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         412          351          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          34          392           56          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
         910         1120         1954          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          218          225           64 

  DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE 
                            14                              2 
  DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE 
                          3837                           3835 
  DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE 
                         536.0                          639.5 
[1] "14.0 - 3837.0 (536.0)" "2.0 - 3835.0 (639.5)" 
[1] "hr=" "1.3"
D73V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 44(XQ21.33) MUTATED         4        4        11        29         2
  DEL PEAK 44(XQ21.33) WILD-TYPE      20       59        60       163         7
D73V3, multiclass
           clus
vv          DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE
  STAGE I                              4                             20
  STAGE II                             4                             59
  STAGE III                           11                             60
  STAGE IVA                           29                            163
  STAGE IVB                            2                              7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 44(XQ21.33) MUTATED     4  14  15  18
  DEL PEAK 44(XQ21.33) WILD-TYPE  36  94  70 113
D73V4, multiclass
    clus
vv   DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE
  T1                            4                             36
  T2                           14                             94
  T3                           15                             70
  T4                           18                            113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 44(XQ21.33) MUTATED    13  11  21   1
  DEL PEAK 44(XQ21.33) WILD-TYPE 123  45 108   6
D73V5, multiclass
    clus
vv   DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE
  N0                           13                            123
  N1                           11                             45
  N2                           21                            108
  N3                            1                              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"
D73V6, binary
                                cls
clus                              0  1
  DEL PEAK 44(XQ21.33) MUTATED   14  5
  DEL PEAK 44(XQ21.33) WILD-TYPE 94 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(XQ21.33) MUTATED     14    5
  DEL PEAK 44(XQ21.33) WILD-TYPE   94   43
    clus
vv   DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE
  M0                           14                             94
  MX                            5                             43
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(XQ21.33) MUTATED    17  44
  DEL PEAK 44(XQ21.33) WILD-TYPE 104 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(XQ21.33) MUTATED     17   44
  DEL PEAK 44(XQ21.33) WILD-TYPE  104  252
        clus
vv       DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE
  FEMALE                           17                            104
  MALE                             44                            252
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(XQ21.33) MUTATED                                      59
  DEL PEAK 44(XQ21.33) WILD-TYPE                                   351
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 44(XQ21.33) MUTATED                                                             0
  DEL PEAK 44(XQ21.33) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 44(XQ21.33) MUTATED                                                     2
  DEL PEAK 44(XQ21.33) WILD-TYPE                                                   4
D73V8, multiclass
                                                             clus
vv                                                            DEL PEAK 44(XQ21.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 59
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    2
                                                             clus
vv                                                            DEL PEAK 44(XQ21.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  351
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                                cls
clus                               0   1
  DEL PEAK 44(XQ21.33) MUTATED    10  51
  DEL PEAK 44(XQ21.33) WILD-TYPE  69 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(XQ21.33) MUTATED     10   51
  DEL PEAK 44(XQ21.33) WILD-TYPE   69  287
     clus
vv    DEL PEAK 44(XQ21.33) MUTATED DEL PEAK 44(XQ21.33) WILD-TYPE
  NO                            10                             69
  YES                           51                            287
[1] 2 2
[1] FALSE
D73V10, continuous
D73V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(XQ21.33) MUTATED                                  0     2
  DEL PEAK 44(XQ21.33) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(XQ21.33) MUTATED                           5    51
  DEL PEAK 44(XQ21.33) WILD-TYPE                        28   310
D73V12, multiclass
                                  clus
vv                                 DEL PEAK 44(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 44(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    28
  WHITE                                                       310
[1] 4 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 44(XQ21.33) MUTATED     4  54
  DEL PEAK 44(XQ21.33) WILD-TYPE  14 327
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(XQ21.33) MUTATED      4   54
  DEL PEAK 44(XQ21.33) WILD-TYPE   14  327
                        clus
vv                       DEL PEAK 44(XQ21.33) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK 44(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            327
[1] 2 2
[1] FALSE
