[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/11541491/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/11544937/transformed.cor.cli.txt"

nPatients in clinical file=494, in cluster file=522, common to both=488
[1]  77 488
[1] "AMP PEAK  1(2Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          102                           386 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          102                           386 
[1] "AMP PEAK  2(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          106                           382 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          106                           382 
[1] "AMP PEAK  3(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           355                            133 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           355                            133 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           225                            263 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           225                            263 
[1] "AMP PEAK  5(6P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                          100                           388 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                          100                           388 
[1] "AMP PEAK  6(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         88                         400 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         88                         400 
[1] "AMP PEAK  7(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                          208                           280 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                          208                           280 
[1] "AMP PEAK  8(7Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                          162                           326 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                          162                           326 
[1] "AMP PEAK  9(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                           152                            336 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                           152                            336 
[1] "AMP PEAK 10(8Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                           291                            197 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                           291                            197 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           361                            127 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           361                            127 
[1] "AMP PEAK 12(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                          116                           372 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                          116                           372 
[1] "AMP PEAK 13(9P23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                        114                         374 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                        114                         374 
[1] "AMP PEAK 14(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          129                           359 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          129                           359 
[1] "AMP PEAK 15(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                          164                           324 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                          164                           324 
[1] "AMP PEAK 16(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          95                          393 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          95                          393 
[1] "AMP PEAK 17(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                           221                            267 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                           221                            267 
[1] "AMP PEAK 18(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                            157                             331 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                            157                             331 
[1] "AMP PEAK 19(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                          94                          394 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                          94                          394 
[1] "AMP PEAK 20(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                           100                            388 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                           100                            388 
[1] "AMP PEAK 21(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                          97                          391 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                          97                          391 
[1] "AMP PEAK 22(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            98                            390 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            98                            390 
[1] "AMP PEAK 23(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          85                          403 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          85                          403 
[1] "AMP PEAK 24(18P11.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                            144                             344 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                            144                             344 
[1] "AMP PEAK 25(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                           100                            388 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                           100                            388 
[1] "AMP PEAK 26(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            53                            435 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            53                            435 
[1] "AMP PEAK 27(20P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           181                            307 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           181                            307 
[1] "AMP PEAK 28(20Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            213                             275 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            213                             275 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        133                         355 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        133                         355 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            89                            399 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            89                            399 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          123                           365 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          123                           365 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         45                         443 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         45                         443 
[1] "DEL PEAK  4(2Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           73                           415 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           73                           415 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          114                           374 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          114                           374 
[1] "DEL PEAK  6(2Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          148                           340 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          148                           340 
[1] "DEL PEAK  7(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          332                           156 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          332                           156 
[1] "DEL PEAK  8(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          351                           137 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          351                           137 
[1] "DEL PEAK  9(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          354                           134 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          354                           134 
[1] "DEL PEAK 10(3P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          326                           162 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          326                           162 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          198                           290 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          198                           290 
[1] "DEL PEAK 12(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                          143                           345 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                          143                           345 
[1] "DEL PEAK 13(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                          155                           333 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                          155                           333 
[1] "DEL PEAK 14(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          201                           287 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          201                           287 
[1] "DEL PEAK 15(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          204                           284 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          204                           284 
[1] "DEL PEAK 16(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                        215                         273 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                        215                         273 
[1] "DEL PEAK 17(5Q35.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                          191                           297 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                          191                           297 
[1] "DEL PEAK 18(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           91                           397 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           91                           397 
[1] "DEL PEAK 19(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           73                           415 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           73                           415 
[1] "DEL PEAK 20(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                          124                           364 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                          124                           364 
[1] "DEL PEAK 21(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          283                           205 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          283                           205 
[1] "DEL PEAK 22(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        224                         264 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        224                         264 
[1] "DEL PEAK 23(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          284                           204 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          284                           204 
[1] "DEL PEAK 24(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                            98                            390 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                            98                            390 
[1] "DEL PEAK 25(9Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           74                           414 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           74                           414 
[1] "DEL PEAK 26(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           157                            331 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           157                            331 
[1] "DEL PEAK 27(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                            153                             335 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                            153                             335 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            127                             361 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            127                             361 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           157                            331 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           157                            331 
[1] "DEL PEAK 30(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                           230                            258 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                           230                            258 
[1] "DEL PEAK 31(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             58                             430 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             58                             430 
[1] "DEL PEAK 32(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            219                             269 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            219                             269 
[1] "DEL PEAK 33(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                           202                            286 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                           202                            286 
[1] "DEL PEAK 34(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            70                            418 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            70                            418 
[1] "DEL PEAK 35(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             68                             420 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             68                             420 
[1] "DEL PEAK 36(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                           115                            373 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                           115                            373 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            89                            399 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            89                            399 
[1] "DEL PEAK 38(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                            96                            392 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                            96                            392 
[1] "DEL PEAK 39(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            93                            395 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            93                            395 
[1] "DEL PEAK 40(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            66                            422 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            66                            422 
[1] "DEL PEAK 41(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           253                            235 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           253                            235 
[1] "DEL PEAK 42(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         272                          216 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         272                          216 
[1] "DEL PEAK 43(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           163                            325 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           163                            325 
[1] "DEL PEAK 44(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             93                             395 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             93                             395 
[1] "DEL PEAK 45(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           198                            290 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           198                            290 
[1] "DEL PEAK 46(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          141                           347 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          141                           347 
[1] "DEL PEAK 47(XP21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          145                           343 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          145                           343 
[1] "DEL PEAK 48(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            75                            413 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            75                            413 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 488 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415           NA          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
          63          384          113          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
         622          918          850          351          216           NA 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
         182           NA           NA           NA          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          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-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         2161          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625           NA         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
          NA         1007         1045          173           NA         1081 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
          NA           NA           NA           NA           NA           NA 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
          NA          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          NA          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         394          735           NA          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         443          535          391          904          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
         526          484          348          175           NA          367 
TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
          NA          223          298         1466         1207          654 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
          NA         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
         341          129         1253           NA         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
         985           NA           NA           NA         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1560         1007          509         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353           NA          707           NA          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         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-6477 TCGA-CR-6478 
          NA         1050         1125           NA          514           NA 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479           NA         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245           NA          105           NA          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
          30          972           NA         1036           NA          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
          NA          997         1430           NA          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         4241 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         3930         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        3270         2886         2327         2784         2437          519 
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-6933 
        1315         1665          641         1899           NA           NA 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
          NA           NA         3835           NA           NA           NA 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         3381           NA           NA           NA           NA 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
          NA         3497         2347           NA         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
         954          797           NA           NA           NA           NA 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
          NA           NA           NA         1099           NA           NA 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
          NA           NA           NA         4335           NA           NA 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
          NA          851           NA         5480           NA           NA 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
          NA           NA         1722           NA           NA           NA 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1075           NA          906           NA          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         646          714          606          685           NA          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
         321          237          828           NA          773          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-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548           NA          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 
        1131          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
           3          384           14           13           NA            6 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          NA          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
         206            2            5           25           NA           NA 
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-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-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
         122          441          588          360          412           NA 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         440           NA          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         111          112           NA          254          240          910 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
          NA         1726         1559           NA         1120           NA 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
         578         1917           NA           NA           NA           NA 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
          NA          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 
         228          225          387          567          198           NA 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1663           NA         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS TCGA-UF-A7JV 
         413           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=168,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=316,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=4,	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=48,	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=85,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=60,	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=23,	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 488 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  46 127  94 162 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   47   127    94   162 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  46 127  94 162 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   47   127    94   162 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
170  63 152   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
170  63 152   8 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
170  63 152   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
170  63 152   8 
PATHOLOGY.M.STAGE, nv=3, 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=85, 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    54  25
  AMP PEAK  1(2Q11.2) WILD-TYPE 247  88
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           79                           335 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           25                            88 
$`AMP PEAK  1(2Q11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5555 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6DL 
         283          415          520          384          895          623 
TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4728 
         142          687         1153         1955         1230         1151 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 
         625          811         1988         1045         1980          630 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 
         629           45         1110          224          318          735 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 
         225          348          317         1950          358          514 
TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 
        1969          354         1191         1440          105          759 
TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1954          907         1955          522         1950         3295 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5973 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6960 
         584         1978         2641         1952         1959         1969 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 
        1095          797         1960         1976         1099         1957 
TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CX-7086 TCGA-CX-7219 
        1947         1959         1940         1075          237          828 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
         128          376          424          516         1965          575 
TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-7229 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-KU-A66T 
         299            6            2          111           33          552 
TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A7J9 TCGA-UF-A7JF 
         387          198          135         1663         1043         1497 
TCGA-UF-A7JJ 
         214 

$`AMP PEAK  1(2Q11.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         102          462         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-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 
         190          644          451           63          113          236 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         182         1976          314          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         1157          142          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
         993          642         1250          395         1960         1330 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1268         1007          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          683          290          933 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         628          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-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
         443          535          391          904          645          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309         1274          877         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         707         1963          893          998          785          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          950         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-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-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-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          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-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5441 
        1077          911         1472         1438          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-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        1478         1840          215         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6943 
        1899         1970         1948         1969         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1969         1966         1957         1959         3837         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-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 
        1987         1979         1952         1444          954         1967 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1974         1948         1955         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-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        5480         1960         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1970          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          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-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         568          106          539          483          232          435 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         368          389          338         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         1131          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-H7-A76A TCGA-HD-7753 
          58          133          414          403          206            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-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          11           49           10         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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         360          224          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         392           56          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1726         1559         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-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
         218          228          225          567          149          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         157          168         1326         1319         1252         1278 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS 
        1894          484          735          665          413 

  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                          5480 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          759                           685 
[1] "2.0 - 3295.0 (759.0)" "3.0 - 5480.0 (685.0)"
[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       11        17        57         2
  AMP PEAK  1(2Q11.2) WILD-TYPE      24       64        57       178        10
                               vv
clus                            STAGE IVC
  AMP PEAK  1(2Q11.2) MUTATED           0
  AMP PEAK  1(2Q11.2) WILD-TYPE         1
D1V3, multiclass
           clus
vv          AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  STAGE I                             2                            24
  STAGE II                           11                            64
  STAGE III                          17                            57
  STAGE IVA                          57                           178
  STAGE IVB                           2                            10
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  1(2Q11.2) MUTATED       5  18  25  42
  AMP PEAK  1(2Q11.2) WILD-TYPE    42 109  69 120
D1V4, multiclass
       clus
vv      AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  T0+T1                           5                            42
  T2                             18                           109
  T3                             25                            69
  T4                             42                           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
  AMP PEAK  1(2Q11.2) MUTATED    35   9  38   2
  AMP PEAK  1(2Q11.2) WILD-TYPE 135  54 114   6
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  N0                          35                           135
  N1                           9                            54
  N2                          38                           114
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK  1(2Q11.2) MUTATED    32   0  10
  AMP PEAK  1(2Q11.2) WILD-TYPE 135   1  48
D1V6, multiclass
    clus
vv   AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  M0                          32                           135
  M1                           0                             1
  MX                          10                            48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED    21  81
  AMP PEAK  1(2Q11.2) WILD-TYPE 111 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     21   81
  AMP PEAK  1(2Q11.2) WILD-TYPE  111  275
        clus
vv       AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  FEMALE                          21                           111
  MALE                            81                           275
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(2Q11.2) MUTATED                                     101
  AMP PEAK  1(2Q11.2) WILD-TYPE                                   376
                               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                                                     1
  AMP PEAK  1(2Q11.2) WILD-TYPE                                                   9
D1V8, multiclass
                                                             clus
vv                                                            AMP PEAK  1(2Q11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               101
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            AMP PEAK  1(2Q11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 376
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
[1] 3 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  84
  AMP PEAK  1(2Q11.2) WILD-TYPE  61 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     18   84
  AMP PEAK  1(2Q11.2) WILD-TYPE   61  325
     clus
vv    AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  NO                           18                            61
  YES                          84                           325
[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                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(2Q11.2) MUTATED                          12    83
  AMP PEAK  1(2Q11.2) WILD-TYPE                        32   332
D1V12, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     83
                                  clus
vv                                 AMP PEAK  1(2Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      332
[1] 4 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     6  87
  AMP PEAK  1(2Q11.2) WILD-TYPE  18 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED      6   87
  AMP PEAK  1(2Q11.2) WILD-TYPE   18  344
                        clus
vv                       AMP PEAK  1(2Q11.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       AMP PEAK  1(2Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           344
[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    56  29
  AMP PEAK  2(2Q31.2) WILD-TYPE 245  84
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           85                           329 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           29                            84 
$`AMP PEAK  2(2Q31.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4IG 
         283          415         1983          384          895          855 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-8596 
         918          850          623          142          687         1955 
TCGA-CN-4728 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6024 
        1151         1988         1980          629         1970          224 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5331 TCGA-CQ-5332 
         611          735          225          348         1399          317 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5247 
         985         1959         1950          707          950          358 
TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7390 
         514         1191          105           30         1954          907 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 
        1955          522         1950         3295          584         1978 
TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7095 
         215         1969         1959         1969         1959         1970 
TCGA-CV-7097 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 
        1970         1952         1095          797         1960         1976 
TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A45Z 
        1099         1955         1957         1947         1959         1940 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5629 
         237          828          701          128          376          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-MZ-A7D7 TCGA-P3-A6T8 
         360          412          552           56          240          400 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JF 
         149          135         1663         1319         1043         1497 
TCGA-UF-A7JJ 
         214 

$`AMP PEAK  2(2Q31.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          462          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-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 
         190          644          451           63          113          236 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         622          351          216          182         1976          314 
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-7866 TCGA-BB-7870 TCGA-BB-7871 
         310          536          423          638         1153          428 
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-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        1157          142         1230          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
         811         1268         1007         1045          173         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          630          933          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
          45          432           98          202         1110          318 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         394          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         391          904          645          526          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1660         1422         1393          341          129         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        1000         1057         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1007          509         1309         1274          877         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1960         1963          893          998          785          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-6474 TCGA-CR-6478 
        1521         1966         1050         1125         1971         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
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-7376 TCGA-CR-7377 
        1960         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-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 
         156          181         1077          911         1472         1438 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
         406          701         2641         1478         1840         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-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        3835         1948         1966         1957         1969         1959 
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-7238 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7410 
        1979         1444          954         1967         1974         1948 
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-A45R TCGA-CV-A45Y TCGA-CV-A460 
        1981          851         1945         5480         1960         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 
         685         1950          317          321          773          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
          77          491          154          568          106          539 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
         338         1778         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-A50G TCGA-F7-A50I TCGA-F7-A50J 
        1131          490          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-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            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-KU-A6H7 
         588          440          351          360          224          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
         168           14           34          392          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          910         1726         1559         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1917         1968          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         218          228          225          387          567          198 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A71E 
         135          157          168         1326         1252         1278 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS 
        1894          484          735          665          413 

  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                          5480 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          850                           658 
[1] "6.0 - 3295.0 (850.0)" "2.0 - 5480.0 (658.0)"
[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       17        13        56         3
  AMP PEAK  2(2Q31.2) WILD-TYPE      24       58        61       179         9
                               vv
clus                            STAGE IVC
  AMP PEAK  2(2Q31.2) MUTATED           0
  AMP PEAK  2(2Q31.2) WILD-TYPE         1
D2V3, multiclass
           clus
vv          AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  STAGE I                             2                            24
  STAGE II                           17                            58
  STAGE III                          13                            61
  STAGE IVA                          56                           179
  STAGE IVB                           3                             9
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  2(2Q31.2) MUTATED       7  26  21  40
  AMP PEAK  2(2Q31.2) WILD-TYPE    40 101  73 122
D2V4, multiclass
       clus
vv      AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  T0+T1                           7                            40
  T2                             26                           101
  T3                             21                            73
  T4                             40                           122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  2(2Q31.2) MUTATED    33   8  39   2
  AMP PEAK  2(2Q31.2) WILD-TYPE 137  55 113   6
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  N0                          33                           137
  N1                           8                            55
  N2                          39                           113
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK  2(2Q31.2) MUTATED    28   0  17
  AMP PEAK  2(2Q31.2) WILD-TYPE 139   1  41
D2V6, multiclass
    clus
vv   AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  M0                          28                           139
  M1                           0                             1
  MX                          17                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED    22  84
  AMP PEAK  2(2Q31.2) WILD-TYPE 110 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     22   84
  AMP PEAK  2(2Q31.2) WILD-TYPE  110  272
        clus
vv       AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  FEMALE                          22                           110
  MALE                            84                           272
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2Q31.2) MUTATED                                     105
  AMP PEAK  2(2Q31.2) WILD-TYPE                                   372
                               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                                                   9
D2V8, multiclass
                                                             clus
vv                                                            AMP PEAK  2(2Q31.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               105
  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                                                 372
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
[1] 3 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  89
  AMP PEAK  2(2Q31.2) WILD-TYPE  62 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     17   89
  AMP PEAK  2(2Q31.2) WILD-TYPE   62  320
     clus
vv    AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  NO                           17                            62
  YES                          89                           320
[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                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2Q31.2) MUTATED                          12    86
  AMP PEAK  2(2Q31.2) WILD-TYPE                        32   329
D2V12, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     86
                                  clus
vv                                 AMP PEAK  2(2Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      329
[1] 4 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  88
  AMP PEAK  2(2Q31.2) WILD-TYPE  16 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED      8   88
  AMP PEAK  2(2Q31.2) WILD-TYPE   16  343
                        clus
vv                       AMP PEAK  2(2Q31.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       AMP PEAK  2(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           343
[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   215  85
  AMP PEAK  3(3Q26.33) WILD-TYPE  86  28
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           300                            114 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                            85                             28 
$`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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         895          855          622          918          850          351 
TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
        1976          623          142         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 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988         1007         1045          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 
         683          290          630          629          628          594 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
         224          318          611          394          735          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         225          526          348          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        1466         1422          317         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1959         1179         1560         1007          509 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1274         1950         1353         1960          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         893          785          391          950         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-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1958         1959         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CX-7082 TCGA-CX-7086 
        1954         1075          110          714          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-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         539          376          232          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         389          338         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-KU-A6H7 
         360          412          440          351          552          378 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
          14           34          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1726         1120         1954         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         357          228          387          567          198          149 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         135          157         1326         1663         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1278         1043         1894          735         1497          665 

$`AMP PEAK  3(3Q26.33) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-A6DB TCGA-BA-A6DE 
         102          462         1288          725          216          182 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7866 TCGA-CN-4722 
         314          187          558          536          638          799 
TCGA-CN-4733 TCGA-CN-5370 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6996 TCGA-CN-A63V 
         642         1975          933          629          432          484 
TCGA-CN-A63Y TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 
         175         1207          654         1660         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 
         341          129         1253         1750         1309          877 
TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6482 TCGA-CR-6493 
         998          303          799         1966          345         1956 
TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7391 TCGA-CR-7392 
        1440          889          972          796          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CV-5441 TCGA-CV-5443 
         908          898          930          156         2886         1958 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6942 
         701         1478         1315         1899         1970         3835 
TCGA-CV-6943 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7183 TCGA-CV-7235 
        1948         1969         1970         1936         1979         1952 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1973         1937         1981          851         1945 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1722         1977         1970          906         1959          670 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6516 
         646          606          685         1950          321          773 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-7588 
          77          154          568          483         1081         1965 
TCGA-DQ-7590 TCGA-DQ-7593 TCGA-F7-7848 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
         775          369         1131          407           58          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
         403          206           11           33          485          122 
TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D 
         441          360          224          168          392           56 
TCGA-MT-A67F TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG 
         111         1559          578         1917          245          218 
TCGA-QK-A6II TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JS 
         225          135          168          484          214          413 

  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 
                          5480                           3835 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           685                            749 
[1] "2.0 - 5480.0 (685.0)"  "11.0 - 3835.0 (749.0)"
[1] "hr=" "1"  
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  3(3Q26.33) MUTATED        16       48        57       171        11
  AMP PEAK  3(3Q26.33) WILD-TYPE      10       27        17        64         1
                                vv
clus                             STAGE IVC
  AMP PEAK  3(3Q26.33) MUTATED           1
  AMP PEAK  3(3Q26.33) WILD-TYPE         0
D3V3, multiclass
           clus
vv          AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  STAGE I                             16                             10
  STAGE II                            48                             27
  STAGE III                           57                             17
  STAGE IVA                          171                             64
  STAGE IVB                           11                              1
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK  3(3Q26.33) MUTATED      33  87  71 119
  AMP PEAK  3(3Q26.33) WILD-TYPE    14  40  23  43
D3V4, multiclass
       clus
vv      AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  T0+T1                           33                             14
  T2                              87                             40
  T3                              71                             23
  T4                             119                             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  3(3Q26.33) MUTATED   116  48 116   7
  AMP PEAK  3(3Q26.33) WILD-TYPE  54  15  36   1
D3V5, multiclass
    clus
vv   AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  N0                          116                             54
  N1                           48                             15
  N2                          116                             36
  N3                            7                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK  3(3Q26.33) MUTATED   117   1  41
  AMP PEAK  3(3Q26.33) WILD-TYPE  50   0  17
D3V6, multiclass
    clus
vv   AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  M0                          117                             50
  M1                            1                              0
  MX                           41                             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED    84 271
  AMP PEAK  3(3Q26.33) WILD-TYPE  48  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     84  271
  AMP PEAK  3(3Q26.33) WILD-TYPE   48   85
        clus
vv       AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  FEMALE                           84                             48
  MALE                            271                             85
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(3Q26.33) MUTATED                                     347
  AMP PEAK  3(3Q26.33) WILD-TYPE                                   130
                                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                                                     8
  AMP PEAK  3(3Q26.33) WILD-TYPE                                                   2
D3V8, multiclass
                                                             clus
vv                                                            AMP PEAK  3(3Q26.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                347
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
                                                             clus
vv                                                            AMP PEAK  3(3Q26.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  130
  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    62 293
  AMP PEAK  3(3Q26.33) WILD-TYPE  17 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     62  293
  AMP PEAK  3(3Q26.33) WILD-TYPE   17  116
     clus
vv    AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  NO                            62                             17
  YES                          293                            116
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(3Q26.33) MUTATED                                  2     8
  AMP PEAK  3(3Q26.33) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q26.33) MUTATED                          35   298
  AMP PEAK  3(3Q26.33) WILD-TYPE                         9   117
D3V12, multiclass
                                  clus
vv                                 AMP PEAK  3(3Q26.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  35
  WHITE                                                     298
                                  clus
vv                                 AMP PEAK  3(3Q26.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       117
[1] 4 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    17 312
  AMP PEAK  3(3Q26.33) WILD-TYPE   7 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     17  312
  AMP PEAK  3(3Q26.33) WILD-TYPE    7  119
                        clus
vv                       AMP PEAK  3(3Q26.33) MUTATED
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          312
                        clus
vv                       AMP PEAK  3(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            119
[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   142  51
  AMP PEAK  4(5P15.33) WILD-TYPE 159  62
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           193                            221 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            51                             62 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         520          725         1636         1747          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         451           63          384          113          236          895 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DL 
         855          918          850          216          182          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         142          187         2878          278          133          558 
TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         310          687          638         1955          624            5 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         721         1157         1230          392          817          993 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5363 
         395          625         1960         1330         1980         1977 
TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6023 
        1966          630          933          432           98         1110 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A 
         318          394          735          429          443          391 
TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V3 TCGA-CQ-5330 TCGA-CQ-6221 
         904          526          348          298         1393         1000 
TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CA TCGA-CQ-A4CD 
         985         1560          509         1950         1963          998 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 
         950         2562         1663         1777         1966         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
        1971          514         1969          379          479         1956 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7383 
        1191         1440         1245         1960         1036         1954 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         392          907          946          216          156          181 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
        1472          522         3295         1438          546         1978 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-6441 
        2327         2437          519          406         2641         1970 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 
        1952         1959         1969         1957         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1959         1970         1970         1939         1945         1987 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7424 TCGA-CV-7435 
        1952         1095          797         1976         1947         1959 
TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A468 TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-6517 
        5480         1940         1977         1075          237          292 
TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO TCGA-DQ-5624 TCGA-DQ-5629 
         701          106          128          435         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-H7-A76A TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 
           6          133          206            5           37           55 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61J 
          25          111         1057          485          588          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X 
         360          224          552          378           14           34 
TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
          56          240         1726         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 TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J 
         387          567          198          149          135          157 
TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH 
         168         1319         1252         1894         1497          665 
TCGA-UF-A7JS 
         413 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5557 TCGA-BA-A4IH 
         248          722         1288         1762          623          622 
TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7863 
         351         1976          314          140          536          423 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 
        1153          428          436            4          799          142 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
        1151          642         1250          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 
        1007         1045          173         1081         1980         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1975          683          290          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 
         629           45         1970          202          224          611 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
         432           46          535          645          225          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         175          367          223         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 
        1253         1057         1959         1959         1179         1750 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309         1274          877         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5247 
         707          893          785          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-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
         851         1945         1960         1946         1954         1722 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1970          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         828          773           77          491          154          568 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ 
         539          376          483          232          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 
         389          338         1081          622          369          324 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
        1131          490          658           15           92          384 
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-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          44           24           11           49           10           33 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-KU-A6H8 
         122          441          360          412          351          168 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910         1559 
TCGA-P3-A6T0 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A719 
         578          245          225          135         1326         1663 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ 
        1278         1043          484          735          214 

  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 
                          5480                           3835 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           638                            735 
[1] "3.0 - 5480.0 (638.0)" "2.0 - 3835.0 (735.0)"
[1] "hr=" "1.3"
D4V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  4(5P15.33) MUTATED         8       30        38       104         7
  AMP PEAK  4(5P15.33) WILD-TYPE      18       45        36       131         5
                                vv
clus                             STAGE IVC
  AMP PEAK  4(5P15.33) MUTATED           1
  AMP PEAK  4(5P15.33) WILD-TYPE         0
D4V3, multiclass
           clus
vv          AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  STAGE I                              8                             18
  STAGE II                            30                             45
  STAGE III                           38                             36
  STAGE IVA                          104                            131
  STAGE IVB                            7                              5
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK  4(5P15.33) MUTATED      18 60 44 70
  AMP PEAK  4(5P15.33) WILD-TYPE    29 67 50 92
D4V4, multiclass
       clus
vv      AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  T0+T1                           18                             29
  T2                              60                             67
  T3                              44                             50
  T4                              70                             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  4(5P15.33) MUTATED    61  34  73   4
  AMP PEAK  4(5P15.33) WILD-TYPE 109  29  79   4
D4V5, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  N0                           61                            109
  N1                           34                             29
  N2                           73                             79
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  AMP PEAK  4(5P15.33) MUTATED   73  1 33
  AMP PEAK  4(5P15.33) WILD-TYPE 94  0 25
D4V6, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  M0                           73                             94
  M1                            1                              0
  MX                           33                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    51 174
  AMP PEAK  4(5P15.33) WILD-TYPE  81 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     51  174
  AMP PEAK  4(5P15.33) WILD-TYPE   81  182
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                           51                             81
  MALE                            174                            182
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                     219
  AMP PEAK  4(5P15.33) WILD-TYPE                                   258
                                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                                                     5
  AMP PEAK  4(5P15.33) WILD-TYPE                                                   5
D4V8, multiclass
                                                             clus
vv                                                            AMP PEAK  4(5P15.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                219
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
                                                             clus
vv                                                            AMP PEAK  4(5P15.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  258
  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"
D4V9, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    42 183
  AMP PEAK  4(5P15.33) WILD-TYPE  37 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     42  183
  AMP PEAK  4(5P15.33) WILD-TYPE   37  226
     clus
vv    AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  NO                            42                             37
  YES                          183                            226
[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                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5P15.33) MUTATED                          27   187
  AMP PEAK  4(5P15.33) WILD-TYPE                        17   228
D4V12, multiclass
                                  clus
vv                                 AMP PEAK  4(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     187
                                  clus
vv                                 AMP PEAK  4(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       228
[1] 4 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    14 198
  AMP PEAK  4(5P15.33) WILD-TYPE  10 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     14  198
  AMP PEAK  4(5P15.33) WILD-TYPE   10  233
                        clus
vv                       AMP PEAK  4(5P15.33) MUTATED
  HISPANIC OR LATINO                               14
  NOT HISPANIC OR LATINO                          198
                        clus
vv                       AMP PEAK  4(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            233
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(6P12.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(6P12.1) MUTATED    64  20
  AMP PEAK  5(6P12.1) WILD-TYPE 237  93
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                           84                           330 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                           20                            93 
$`AMP PEAK  5(6P12.1) MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4II 
         283          520          190          384          113          918 
TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4736 TCGA-CN-5356 
        1153            5          721         1157          395         1045 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 
        1980         1966           98          202         1110          611 
TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
         391          526          348         1422         1399          317 
TCGA-CQ-5334 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5247 
         129          509         1960         1963          785          358 
TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7399 TCGA-CR-7402 
         234         1245          392          946          181          911 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5977 
        1955         1950         1438         2886         2327         1840 
TCGA-CV-6003 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7243 
        1665         1969         1957         1939         1952          954 
TCGA-CV-7248 TCGA-CV-7418 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A6JE 
        1967         1955         1959         1981         5480         1075 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-D6-6823 TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5624 
         670          110          701          424          338         1778 
TCGA-DQ-5625 TCGA-DQ-7589 TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 
        1081          575            6          133            5           37 
TCGA-HD-8224 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W 
          55           33          588          351          552           14 
TCGA-MT-A67D TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-QK-A8Z9 
          56         1120         1917          218          198          149 
TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
         135         1663         1043          735         1497          665 

$`AMP PEAK  5(6P12.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF 
        1747          644          451           63          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          850          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          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-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         624            4          799          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
         392          817          993          642         1250          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         683          290          630          933          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 
         594          629           45          432         1970          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         318          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
         443          535          904          645          225          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 
         654         1660         1393          341         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1560         1007         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1353          707          893          998          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         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-A45Y TCGA-CV-A45Z 
        1984         1958          851         1945         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
        1946         1954         1722         1977         1970          906 
TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        1959          646          714          606          685         1950 
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-D6-6824 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-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ 
         539          376          483          232          435          368 
TCGA-D6-A6ES TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
         389          516         1030          548         1965          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 
        1131          490          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-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 
         414          403          206            2           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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
         440          360          224          378          168           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392          111          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1726         1559         1954          578         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B 
         567          135          157          168         1326         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JS 
        1252         1278         1894          484          214          413 

  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                            5                             2 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                         5480                          3837 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                          711                           694 
[1] "5.0 - 5480.0 (711.0)" "2.0 - 3837.0 (694.0)"
[1] "hr=" "1.1"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  5(6P12.1) MUTATED         4       16        17        46         4
  AMP PEAK  5(6P12.1) WILD-TYPE      22       59        57       189         8
                               vv
clus                            STAGE IVC
  AMP PEAK  5(6P12.1) MUTATED           0
  AMP PEAK  5(6P12.1) WILD-TYPE         1
D5V3, multiclass
           clus
vv          AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  STAGE I                             4                            22
  STAGE II                           16                            59
  STAGE III                          17                            57
  STAGE IVA                          46                           189
  STAGE IVB                           4                             8
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  5(6P12.1) MUTATED       6  27  24  32
  AMP PEAK  5(6P12.1) WILD-TYPE    41 100  70 130
D5V4, multiclass
       clus
vv      AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  T0+T1                           6                            41
  T2                             27                           100
  T3                             24                            70
  T4                             32                           130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  5(6P12.1) MUTATED    36  11  34   2
  AMP PEAK  5(6P12.1) WILD-TYPE 134  52 118   6
D5V5, multiclass
    clus
vv   AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  N0                          36                           134
  N1                          11                            52
  N2                          34                           118
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK  5(6P12.1) MUTATED    33   0  12
  AMP PEAK  5(6P12.1) WILD-TYPE 134   1  46
D5V6, multiclass
    clus
vv   AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  M0                          33                           134
  M1                           0                             1
  MX                          12                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P12.1) MUTATED    25  75
  AMP PEAK  5(6P12.1) WILD-TYPE 107 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P12.1) MUTATED     25   75
  AMP PEAK  5(6P12.1) WILD-TYPE  107  281
        clus
vv       AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  FEMALE                          25                           107
  MALE                            75                           281
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(6P12.1) MUTATED                                      98
  AMP PEAK  5(6P12.1) WILD-TYPE                                   379
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  5(6P12.1) MUTATED                                                             0
  AMP PEAK  5(6P12.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  5(6P12.1) MUTATED                                                     2
  AMP PEAK  5(6P12.1) WILD-TYPE                                                   8
D5V8, multiclass
                                                             clus
vv                                                            AMP PEAK  5(6P12.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                98
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            AMP PEAK  5(6P12.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 379
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
[1] 3 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(6P12.1) MUTATED    11  89
  AMP PEAK  5(6P12.1) WILD-TYPE  68 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P12.1) MUTATED     11   89
  AMP PEAK  5(6P12.1) WILD-TYPE   68  320
     clus
vv    AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  NO                           11                            68
  YES                          89                           320
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(6P12.1) MUTATED                                  0     1
  AMP PEAK  5(6P12.1) WILD-TYPE                                2    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(6P12.1) MUTATED                          16    78
  AMP PEAK  5(6P12.1) WILD-TYPE                        28   337
D5V12, multiclass
                                  clus
vv                                 AMP PEAK  5(6P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     78
                                  clus
vv                                 AMP PEAK  5(6P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      337
[1] 4 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(6P12.1) MUTATED     5  87
  AMP PEAK  5(6P12.1) WILD-TYPE  19 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P12.1) MUTATED      5   87
  AMP PEAK  5(6P12.1) WILD-TYPE   19  344
                        clus
vv                       AMP PEAK  5(6P12.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       AMP PEAK  5(6P12.1) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           344
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(6Q12) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  6(6Q12) MUTATED    54  17
  AMP PEAK  6(6Q12) WILD-TYPE 247  96
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         71                         343 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         17                          96 
$`AMP PEAK  6(6Q12) MUTATED`
TCGA-BA-4075 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4II TCGA-BA-A6DL TCGA-BA-A8YP 
         283          384          113          918          623          142 
TCGA-BB-7862 TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-4740 
         536         1153            5          721          395          811 
TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6022 TCGA-CN-6023 
        1045         1980         1966          630          202         1110 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
         526          348         1422         1399          317          129 
TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6478 TCGA-CR-6487 
         509         1963          785          358         1969          234 
TCGA-CR-6491 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7397 TCGA-CV-5430 TCGA-CV-5432 
         350          105          392          216         1955         1950 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6954 
        1978         2327         2641         1840         1665         1957 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1952          954         1967         1958         1959         1981 
TCGA-CV-A45R TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6823 
        5480         1954         1075          317          828          701 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5625 TCGA-HD-7229 TCGA-HD-7917 
         424          368         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          552           14 
TCGA-MT-A67D TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A7JD 
          56          218          149          135          735 

$`AMP PEAK  6(6Q12) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          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-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
         236          895          855          622          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
         216          182         1976          314          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
         278          140          133          558          310          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-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          799         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
         392          817          993          642         1250          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
        1960         1330         1268         1988         1007          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 
        1980         1081         1977         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 
          45          432           98         1970          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         443          535          391          904          645          225 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 
        1207          654         1660         1393          341         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1750         1560         1007         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1950         1353         1960          707          893          998 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         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-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971          514          362          311          345          354 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         379          479         1956         1435         1191         1440 
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-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         898          930          156          181         1077          911 
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-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2886         1958         2437          519          406          701 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1478          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-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1969         1966         1969         1959         3837         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-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
        1987         1979         1444         1095          797         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         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-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 
         851         1945         1960         1940         1946         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1977         1970          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
         646          714          606          685         1950          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-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 
         232          435          389          338          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          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         1131          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-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 
         414          403          206            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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
         440          360          224          378          168           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392          111          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1726         1559         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
        1968          400          553          357          245          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J 
         225          387          567          198          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         168         1326         1663         1319         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1043         1894          484         1497          665          214 
TCGA-UF-A7JS 
         413 

  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                          2                           3 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                       5480                        3837 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                        630                         707 
[1] "2.0 - 5480.0 (630.0)" "3.0 - 3837.0 (707.0)"
[1] "hr=" "1.3"
D6V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  6(6Q12) MUTATED         3       13        16        39         2
  AMP PEAK  6(6Q12) WILD-TYPE      23       62        58       196        10
                             vv
clus                          STAGE IVC
  AMP PEAK  6(6Q12) MUTATED           0
  AMP PEAK  6(6Q12) WILD-TYPE         1
D6V3, multiclass
           clus
vv          AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  STAGE I                           3                          23
  STAGE II                         13                          62
  STAGE III                        16                          58
  STAGE IVA                        39                         196
  STAGE IVB                         2                          10
  STAGE IVC                         0                           1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK  6(6Q12) MUTATED       5  24  20  27
  AMP PEAK  6(6Q12) WILD-TYPE    42 103  74 135
D6V4, multiclass
       clus
vv      AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  T0+T1                         5                          42
  T2                           24                         103
  T3                           20                          74
  T4                           27                         135
[1] 4 2
[1] TRUE
[1] "dimension 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(6Q12) MUTATED    29  11  27   2
  AMP PEAK  6(6Q12) WILD-TYPE 141  52 125   6
D6V5, multiclass
    clus
vv   AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  N0                        29                         141
  N1                        11                          52
  N2                        27                         125
  N3                         2                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1  MX
  AMP PEAK  6(6Q12) MUTATED    26   0   8
  AMP PEAK  6(6Q12) WILD-TYPE 141   1  50
D6V6, multiclass
    clus
vv   AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  M0                        26                         141
  M1                         0                           1
  MX                         8                          50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                             cls
clus                            0   1
  AMP PEAK  6(6Q12) MUTATED    26  62
  AMP PEAK  6(6Q12) WILD-TYPE 106 294
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(6Q12) MUTATED     26   62
  AMP PEAK  6(6Q12) WILD-TYPE  106  294
        clus
vv       AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  FEMALE                        26                         106
  MALE                          62                         294
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(6Q12) MUTATED                                      88
  AMP PEAK  6(6Q12) WILD-TYPE                                   389
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  6(6Q12) MUTATED                                                             0
  AMP PEAK  6(6Q12) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  6(6Q12) MUTATED                                                     0
  AMP PEAK  6(6Q12) WILD-TYPE                                                  10
D6V8, multiclass
                                                             clus
vv                                                            AMP PEAK  6(6Q12) 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                                                            AMP PEAK  6(6Q12) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               389
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  10
[1] 3 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(6Q12) MUTATED     9  79
  AMP PEAK  6(6Q12) WILD-TYPE  70 330
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(6Q12) MUTATED      9   79
  AMP PEAK  6(6Q12) WILD-TYPE   70  330
     clus
vv    AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  NO                          9                          70
  YES                        79                         330
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(6Q12) MUTATED                                  0     1
  AMP PEAK  6(6Q12) WILD-TYPE                                2    10
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(6Q12) MUTATED                          12    70
  AMP PEAK  6(6Q12) WILD-TYPE                        32   345
D6V12, multiclass
                                  clus
vv                                 AMP PEAK  6(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                               12
  WHITE                                                   70
                                  clus
vv                                 AMP PEAK  6(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                 32
  WHITE                                                    345
[1] 4 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(6Q12) MUTATED     7  75
  AMP PEAK  6(6Q12) WILD-TYPE  17 356
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(6Q12) MUTATED      7   75
  AMP PEAK  6(6Q12) WILD-TYPE   17  356
                        clus
vv                       AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             7                          17
  NOT HISPANIC OR LATINO                        75                         356
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(7P11.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(7P11.2) MUTATED   118  51
  AMP PEAK  7(7P11.2) WILD-TYPE 183  62
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                          169                           245 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                           51                            62 
$`AMP PEAK  7(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-A4II TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DL 
         384          236          918          182         1976          623 
TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         278          423         1153         1955          624            5 
TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 
         799          142          392          817          993          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
        1960         1330         1045          173         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1980         1966         1966          933          629          628 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
          98          202         1110          224          318          394 
TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
         429          391          904          225          484          348 
TCGA-CN-A641 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6229 TCGA-CQ-7067 
         367         1422         1393          129         1179          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309         1274         1950         1960          707         1963 
TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7364 
         303         1971          514         1969          354         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 
        1191         1440          105          889         1968         1036 
TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 
         796          392          907          216          156         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
         522         1950          546         1978         2327         2437 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1478          215         1948         1969         1952         1959 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1969         1957         1969         3837         1959         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 
        1939         1945         1987         1952         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 
         797         1967         1955         1957         1947         1959 
TCGA-CV-7440 TCGA-CV-A45Z TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CV-A6K0 
        1981         1940         1959          670          714          606 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 
         237          828          773          292          701          154 
TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ 
         568          128          483          232          424          368 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1778         1081          516          548         1965          575 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         299         1131          490           92          585            3 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A633 
         414            2            5           37           24           49 
TCGA-HD-A6HZ TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T 
         111          122          441          412          360          552 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 
          14           34          392           56          112          240 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A8Z7 
        1954         1968          400          228          225          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD 
         149          135          168         1278         1043          735 
TCGA-UF-A7JH 
         665 

$`AMP PEAK  7(7P11.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         102         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-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
          63          113          895          855          622          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
         351          216          314          142          187         2878 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
         140          133          558          310          536          687 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
         638          428          436            4          721         1157 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 
        1230         1151          642         1250          395          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5370 TCGA-CN-5373 
        1268         1988         1007         1081         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         290          630          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
        1970          611          735          432           46          443 
TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 
         535          645          526          175          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 
        1466         1207          654         1660         1399          317 
TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         341         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1959         1750         1560         1007          877         1353 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 
         893          998          785          391          950         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-6480 TCGA-CR-6481 TCGA-CR-6482 
        1966         1050         1125          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7368 
         234          379          350          479         1956         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7383 
        1960         1979          759           30          972         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1430         1951          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         898          930          181         1077          911         1472 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 
        3295         1438          584         2886         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
         406          701         2641         1840         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
         641         1899         1970         3835         1948         1966 
TCGA-CV-6961 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 
        1959         1970         1936         1959         1979         1444 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7427 
        1960         1976         1099         1974         1948         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1973         1972         1937         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        1945         5480         1960         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY 
        1977         1970         1075          906          110          646 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 
         685         1950          317          321           77          491 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q 
         106          539          376          435          389          338 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
        1030          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         340          658           15          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A 
           6          407           58          133          403          206 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
          25           55           44           25           11           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J 
          33         1057          485          588          360          440 
TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A6I9 
         351          224          378          168          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1726         1559         1120          578         1917 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6V9 
         553          357          245          218          387          567 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         135          157         1326         1663         1319         1252 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          484         1497          214          413 

  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                            2                             4 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                         3837                          5480 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                          628                           735 
[1] "2.0 - 3837.0 (628.0)" "4.0 - 5480.0 (735.0)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  7(7P11.2) MUTATED        10       34        32       106         7
  AMP PEAK  7(7P11.2) WILD-TYPE      16       41        42       129         5
                               vv
clus                            STAGE IVC
  AMP PEAK  7(7P11.2) MUTATED           1
  AMP PEAK  7(7P11.2) WILD-TYPE         0
D7V3, multiclass
           clus
vv          AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  STAGE I                            10                            16
  STAGE II                           34                            41
  STAGE III                          32                            42
  STAGE IVA                         106                           129
  STAGE IVB                           7                             5
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  7(7P11.2) MUTATED      14 55 49 73
  AMP PEAK  7(7P11.2) WILD-TYPE    33 72 45 89
D7V4, multiclass
       clus
vv      AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  T0+T1                          14                            33
  T2                             55                            72
  T3                             49                            45
  T4                             73                            89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  AMP PEAK  7(7P11.2) MUTATED   73 26 71  4
  AMP PEAK  7(7P11.2) WILD-TYPE 97 37 81  4
D7V5, multiclass
    clus
vv   AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  N0                          73                            97
  N1                          26                            37
  N2                          71                            81
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  AMP PEAK  7(7P11.2) MUTATED   68  1 27
  AMP PEAK  7(7P11.2) WILD-TYPE 99  0 31
D7V6, multiclass
    clus
vv   AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  M0                          68                            99
  M1                           1                             0
  MX                          27                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(7P11.2) MUTATED    58 150
  AMP PEAK  7(7P11.2) WILD-TYPE  74 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P11.2) MUTATED     58  150
  AMP PEAK  7(7P11.2) WILD-TYPE   74  206
        clus
vv       AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  FEMALE                          58                            74
  MALE                           150                           206
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(7P11.2) MUTATED                                     205
  AMP PEAK  7(7P11.2) WILD-TYPE                                   272
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  7(7P11.2) MUTATED                                                             1
  AMP PEAK  7(7P11.2) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  7(7P11.2) MUTATED                                                     2
  AMP PEAK  7(7P11.2) WILD-TYPE                                                   8
D7V8, multiclass
                                                             clus
vv                                                            AMP PEAK  7(7P11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               205
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            AMP PEAK  7(7P11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 272
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
[1] 3 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(7P11.2) MUTATED    35 173
  AMP PEAK  7(7P11.2) WILD-TYPE  44 236
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P11.2) MUTATED     35  173
  AMP PEAK  7(7P11.2) WILD-TYPE   44  236
     clus
vv    AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  NO                           35                            44
  YES                         173                           236
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(7P11.2) MUTATED                                  1     4
  AMP PEAK  7(7P11.2) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7P11.2) MUTATED                          25   173
  AMP PEAK  7(7P11.2) WILD-TYPE                        19   242
D7V12, multiclass
                                  clus
vv                                 AMP PEAK  7(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    173
                                  clus
vv                                 AMP PEAK  7(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      242
[1] 4 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(7P11.2) MUTATED     9 187
  AMP PEAK  7(7P11.2) WILD-TYPE  15 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P11.2) MUTATED      9  187
  AMP PEAK  7(7P11.2) WILD-TYPE   15  244
                        clus
vv                       AMP PEAK  7(7P11.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         187
                        clus
vv                       AMP PEAK  7(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           244
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7Q21.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7Q21.3) MUTATED    86  46
  AMP PEAK  8(7Q21.3) WILD-TYPE 215  67
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                          132                           282 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                           46                            67 
$`AMP PEAK  8(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-BA-A8YP TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 
         142          423         1153         1955          624          799 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1230          392         1250         1960         1330          811 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1045          173         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
        1966          630          933          629          628           98 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A49A 
        1110          224          318          611          429          391 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 
         904          225          484          348          367          317 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CR-5247 
         509         1274         1950         1960          707          358 
TCGA-CR-6478 TCGA-CR-6491 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7388 
        1969          350         1440          105         1954         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         392          907          181         1955          522         1950 
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-5978 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 
         215         1970         1969         1952         1959         1969 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7248 
        1969         3837         1939         1952          797         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7433 
        1976         1099         1955         1957         1947         1984 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CV-A6JZ TCGA-CX-7086 
        1959         1981         1940         1075          714          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK 
         828          773          154          568          128          483 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 
         435          424          338         1081          516          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J 
        1965          575          299          490           92          585 
TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 
           3            6          133            5           37           55 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61O TCGA-MT-A51W 
         111         1057          122          412          360           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T4 
          34          392          112          240         1954         1968 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JS 
         135          157         1663         1043         1894          413 

$`AMP PEAK  8(7Q21.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          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-6869 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF 
        1636         1747          644           63          113          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        1976          314          623          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
         140          133          558          310          536          687 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
         638          428          436            5            4          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1157          142         1151          817          993          642 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 
         395          625         1268         1988         1007         1980 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
        1975          683          290          594          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         432         1970          202          394          735          432 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y 
          46          443          535          645          526          175 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1393         1399          341          129         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1750         1560         1007         1309          877         1353 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
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-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-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
        1036          796          997         1430          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-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 
         911         1472          584         2886         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
         406          701         2641         1478         1840         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 
        1665          641         1899         1948         3835         1948 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1966         1957         1959         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         1945         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7427 
        1095          954         1960         1974         1948         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        1973         1972         1937         1958          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        5480         1960         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1970          906         1959          670          110          646 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 
         606          685         1950          317          321          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         701           77          491          106          539          376 
TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 
         232          368          389         1778         1030          775 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         622          369          368          324          340         1131 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         658           15          384           14           13          407 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
          58          414          403          206            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-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J 
          33          485          441          588          360          440 
TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D 
         351          224          552          378          168           56 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         111          254          910         1726         1559         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-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         218          228          225          387          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D 
         149          135          168         1326         1319         1252 
TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1278          484          735         1497          665          214 

  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                            3                             2 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                         3837                          5480 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                        629.5                         711.0 
[1] "3.0 - 3837.0 (629.5)" "2.0 - 5480.0 (711.0)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  8(7Q21.3) MUTATED         9       22        26        81         6
  AMP PEAK  8(7Q21.3) WILD-TYPE      17       53        48       154         6
                               vv
clus                            STAGE IVC
  AMP PEAK  8(7Q21.3) MUTATED           0
  AMP PEAK  8(7Q21.3) WILD-TYPE         1
D8V3, multiclass
           clus
vv          AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  STAGE I                             9                            17
  STAGE II                           22                            53
  STAGE III                          26                            48
  STAGE IVA                          81                           154
  STAGE IVB                           6                             6
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK  8(7Q21.3) MUTATED      13 33 35 63
  AMP PEAK  8(7Q21.3) WILD-TYPE    34 94 59 99
D8V4, multiclass
       clus
vv      AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  T0+T1                          13                            34
  T2                             33                            94
  T3                             35                            59
  T4                             63                            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
  AMP PEAK  8(7Q21.3) MUTATED    56  18  52   5
  AMP PEAK  8(7Q21.3) WILD-TYPE 114  45 100   3
D8V5, multiclass
    clus
vv   AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  N0                          56                           114
  N1                          18                            45
  N2                          52                           100
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK  8(7Q21.3) MUTATED    46   0  20
  AMP PEAK  8(7Q21.3) WILD-TYPE 121   1  38
D8V6, multiclass
    clus
vv   AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  M0                          46                           121
  M1                           0                             1
  MX                          20                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q21.3) MUTATED    40 122
  AMP PEAK  8(7Q21.3) WILD-TYPE  92 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q21.3) MUTATED     40  122
  AMP PEAK  8(7Q21.3) WILD-TYPE   92  234
        clus
vv       AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  FEMALE                          40                            92
  MALE                           122                           234
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(7Q21.3) MUTATED                                     160
  AMP PEAK  8(7Q21.3) WILD-TYPE                                   317
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  8(7Q21.3) MUTATED                                                             1
  AMP PEAK  8(7Q21.3) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  8(7Q21.3) MUTATED                                                     1
  AMP PEAK  8(7Q21.3) WILD-TYPE                                                   9
D8V8, multiclass
                                                             clus
vv                                                            AMP PEAK  8(7Q21.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               160
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            AMP PEAK  8(7Q21.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 317
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
[1] 3 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(7Q21.3) MUTATED    32 130
  AMP PEAK  8(7Q21.3) WILD-TYPE  47 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q21.3) MUTATED     32  130
  AMP PEAK  8(7Q21.3) WILD-TYPE   47  279
     clus
vv    AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  NO                           32                            47
  YES                         130                           279
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(7Q21.3) MUTATED                                  1     1
  AMP PEAK  8(7Q21.3) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7Q21.3) MUTATED                          24   134
  AMP PEAK  8(7Q21.3) WILD-TYPE                        20   281
D8V12, multiclass
                                  clus
vv                                 AMP PEAK  8(7Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                    134
                                  clus
vv                                 AMP PEAK  8(7Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      281
[1] 4 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(7Q21.3) MUTATED     9 143
  AMP PEAK  8(7Q21.3) WILD-TYPE  15 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q21.3) MUTATED      9  143
  AMP PEAK  8(7Q21.3) WILD-TYPE   15  288
                        clus
vv                       AMP PEAK  8(7Q21.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         143
                        clus
vv                       AMP PEAK  8(7Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           288
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(8P11.23) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8P11.23) MUTATED    98  38
  AMP PEAK  9(8P11.23) WILD-TYPE 203  75
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                           136                            278 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            38                             75 
$`AMP PEAK  9(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-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 
         236          855          622         1976          623          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          278          140          558          310          536 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 
         687         1153          428         1955          624          799 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4739 TCGA-CN-4740 
        1157         1151          392          993         1330          811 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 
        1007         1045         1980          630          629           45 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A63T 
          98          202          394          735          535          225 
TCGA-CN-A63V TCGA-CQ-5324 TCGA-CQ-6229 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-A4C9 
         484         1207         1179         1309         1274          707 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 
         785          391          950         2562         1777         1521 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7364 
        1971          514         1969          345          234         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7382 
        1191         1440          105           30         1036          796 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5440 
         392          907          181         1955          522         1978 
TCGA-CV-5442 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        2327         1665          641         1970         1948         1952 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1957         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7254 
        1936         1959         1987         1095          954         1976 
TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Z 
        1957         1972         1959         1981         5480         1940 
TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7086 
        1954         1977         1075          606          317          237 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         773          154          106          539          376          483 
TCGA-D6-A6EP TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J 
         424         1778          516          548         1965          585 
TCGA-F7-A623 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A634 TCGA-IQ-A61O 
           6          206            5           37           10          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 
         224          552           14           56          112          240 
TCGA-P3-A5QE TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A7J9 
        1559          135          157          168         1663         1043 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         484         1497          665          413 

$`AMP PEAK  9(8P11.23) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          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-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 
         644          384          113          895          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4227 
         351          216          182          314          142          133 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
         423          638          436            5            4          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         142         1230          817          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5360 
         625         1960         1268         1988          173         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         290          933          628          594          629          432 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 
        1970         1110          224          318          611          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
         429           46          443          391          904          645 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         526          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
         985         1959         1959         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
         509          877         1950         1353         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         893          998          303          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
         799         1966         1050         1125          362          311 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7368 
         354          379          350          479         1956         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
        1960         1979          759          889          972         1968 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 
        1954          997         1430         1951          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-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         2886         1958         2437          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-6436 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1899         1969         1959         3835         1948         1966 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        1969         1959         1939         1945         1979         1952 
TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 
        1444          797         1967         1960         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
        1948         1955         1947         1937         1973         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A460 
        1984         1958          851         1945         1960         1946 
TCGA-CV-A464 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1722         1970          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 
         646          714          685         1950          321          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 
         292          701           77          491          568          128 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
         232          435          368          389          338         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         1131          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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 
         378          168           34          392          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1726         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 TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         228          225          387          567          198          149 
TCGA-QK-A8ZA TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA 
         135         1326         1319         1252         1278         1894 
TCGA-UF-A7JD TCGA-UF-A7JJ 
         735          214 

  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                             5                              2 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                          5480                           3835 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                           754                            684 
[1] "5.0 - 5480.0 (754.0)" "2.0 - 3835.0 (684.0)"
[1] "hr=" "1.3"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  9(8P11.23) MUTATED         7       28        27        66         0
  AMP PEAK  9(8P11.23) WILD-TYPE      19       47        47       169        12
                                vv
clus                             STAGE IVC
  AMP PEAK  9(8P11.23) MUTATED           1
  AMP PEAK  9(8P11.23) WILD-TYPE         0
D9V3, multiclass
           clus
vv          AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  STAGE I                              7                             19
  STAGE II                            28                             47
  STAGE III                           27                             47
  STAGE IVA                           66                            169
  STAGE IVB                            0                             12
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK  9(8P11.23) MUTATED      15  48  28  40
  AMP PEAK  9(8P11.23) WILD-TYPE    32  79  66 122
D9V4, multiclass
       clus
vv      AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  T0+T1                           15                             32
  T2                              48                             79
  T3                              28                             66
  T4                              40                            122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  9(8P11.23) MUTATED    52  21  43   0
  AMP PEAK  9(8P11.23) WILD-TYPE 118  42 109   8
D9V5, multiclass
    clus
vv   AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  N0                           52                            118
  N1                           21                             42
  N2                           43                            109
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK  9(8P11.23) MUTATED    49   1  17
  AMP PEAK  9(8P11.23) WILD-TYPE 118   0  41
D9V6, multiclass
    clus
vv   AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  M0                           49                            118
  M1                            1                              0
  MX                           17                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED    38 114
  AMP PEAK  9(8P11.23) WILD-TYPE  94 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED     38  114
  AMP PEAK  9(8P11.23) WILD-TYPE   94  242
        clus
vv       AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  FEMALE                           38                             94
  MALE                            114                            242
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(8P11.23) MUTATED                                     146
  AMP PEAK  9(8P11.23) WILD-TYPE                                   331
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK  9(8P11.23) MUTATED                                                             1
  AMP PEAK  9(8P11.23) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  9(8P11.23) MUTATED                                                     5
  AMP PEAK  9(8P11.23) WILD-TYPE                                                   5
D9V8, multiclass
                                                             clus
vv                                                            AMP PEAK  9(8P11.23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                146
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
                                                             clus
vv                                                            AMP PEAK  9(8P11.23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  331
  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"
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED    27 125
  AMP PEAK  9(8P11.23) WILD-TYPE  52 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED     27  125
  AMP PEAK  9(8P11.23) WILD-TYPE   52  284
     clus
vv    AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  NO                            27                             52
  YES                          125                            284
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8P11.23) MUTATED                                  0     0
  AMP PEAK  9(8P11.23) WILD-TYPE                                2    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8P11.23) MUTATED                          19   128
  AMP PEAK  9(8P11.23) WILD-TYPE                        25   287
D9V12, multiclass
                                  clus
vv                                 AMP PEAK  9(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                     128
                                  clus
vv                                 AMP PEAK  9(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    25
  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"
D9V13, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED     8 130
  AMP PEAK  9(8P11.23) WILD-TYPE  16 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED      8  130
  AMP PEAK  9(8P11.23) WILD-TYPE   16  301
                        clus
vv                       AMP PEAK  9(8P11.23) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          130
                        clus
vv                       AMP PEAK  9(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            301
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(8Q11.21) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(8Q11.21) MUTATED   183  63
  AMP PEAK 10(8Q11.21) WILD-TYPE 118  50
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                           246                            168 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                            63                             50 
$`AMP PEAK 10(8Q11.21) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
         102          283          248          520          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
        1747          190          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DG TCGA-BA-A6DL 
         236          855          622          918         1976          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 
         558          310          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-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 
        1157          142         1151          392          993          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 
         625         1960         1330          811         1988         1007 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1045         1980         1977         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6022 
         683          629          628          594           98          202 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
         224          394          735          432           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
         535          391          904          225          484          348 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-6227 
        1207          654         1422         1393          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
        1274         1950         1353         1960          707          893 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 
         785          391          950         2562         1777         1521 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6484 
        1966         1125          514         1969          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
         234          379         1956         1191         1440         1960 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         105          759          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 
        1954         1430         1951          392          907          181 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
        1077         1955         1950         1438          584         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 
        2886         2327         2437          519         2641         1478 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 
        1840         1665          641         1899         1948         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 
        1959         3835         1948         1969         1966         1969 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7235 
        3837         1959         1970         1970         1987         1952 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7424 TCGA-CV-7428 
        1444          954          797         1976         1947         1973 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 
        1958         1981         5480         1940         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         714          606          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          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          435          424          368          389 
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-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         299         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 
         585            3           13            6           58          133 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 
         414          206            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          552           14 
TCGA-MT-A51X TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-QK-A64Z 
          34          112          240         1726         1559          553 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8ZB 
         357          218          228          225          387          135 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
         168         1326         1663         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          665          214          413 

$`AMP PEAK 10(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          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 
         216          182          314          536          638          428 
TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 
        1230          817          642         1250         1268          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 
        1081         1980          290          630          933          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
          45          432         1970         1110          318          611 
TCGA-CN-6997 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         429          645          526          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         298         1466         1660         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7071 
         129         1253         1000         1057         1959          877 
TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
        1963          998          303          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6491 
         799         1050         1971          362          311          350 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
         479         1435         1245         1979          889           30 
TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         997          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 
         216          156          911         1472          522         3295 
TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 
         546         1958          406          701          215         1315 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 
        1970         1969         1957         1959         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 
        1939         1945         1979         1095         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-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q 
        1972         1937         1984         1959          851         1945 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 
        1960         1946          110          646          685         1950 
TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EM TCGA-D6-A74Q 
         321           77          491          568          232          338 
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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A 
         122          441          360          378          168          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX 
          56          111          254          910         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6V9 
         578         1917         1968          400          245          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-UF-A71B TCGA-UF-A71D 
         198          149          135          157         1319         1252 

  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                             2                              5 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                          5480                           3295 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                         717.5                          645.5 
[1] "2.0 - 5480.0 (717.5)" "5.0 - 3295.0 (645.5)"
[1] "hr=" "1.5"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 10(8Q11.21) MUTATED        17       44        55       133         7
  AMP PEAK 10(8Q11.21) WILD-TYPE       9       31        19       102         5
                                vv
clus                             STAGE IVC
  AMP PEAK 10(8Q11.21) MUTATED           0
  AMP PEAK 10(8Q11.21) WILD-TYPE         1
D10V3, multiclass
           clus
vv          AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  STAGE I                             17                              9
  STAGE II                            44                             31
  STAGE III                           55                             19
  STAGE IVA                          133                            102
  STAGE IVB                            7                              5
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 10(8Q11.21) MUTATED      31 75 63 90
  AMP PEAK 10(8Q11.21) WILD-TYPE    16 52 31 72
D10V4, multiclass
       clus
vv      AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  T0+T1                           31                             16
  T2                              75                             52
  T3                              63                             31
  T4                              90                             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 10(8Q11.21) MUTATED   99 44 90  4
  AMP PEAK 10(8Q11.21) WILD-TYPE 71 19 62  4
D10V5, multiclass
    clus
vv   AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  N0                           99                             71
  N1                           44                             19
  N2                           90                             62
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 10(8Q11.21) MUTATED   107   0  34
  AMP PEAK 10(8Q11.21) WILD-TYPE  60   1  24
D10V6, multiclass
    clus
vv   AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  M0                          107                             60
  M1                            0                              1
  MX                           34                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q11.21) MUTATED    76 215
  AMP PEAK 10(8Q11.21) WILD-TYPE  56 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED     76  215
  AMP PEAK 10(8Q11.21) WILD-TYPE   56  141
        clus
vv       AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  FEMALE                           76                             56
  MALE                            215                            141
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(8Q11.21) MUTATED                                     285
  AMP PEAK 10(8Q11.21) WILD-TYPE                                   192
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 10(8Q11.21) MUTATED                                                             1
  AMP PEAK 10(8Q11.21) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 10(8Q11.21) MUTATED                                                     5
  AMP PEAK 10(8Q11.21) WILD-TYPE                                                   5
D10V8, multiclass
                                                             clus
vv                                                            AMP PEAK 10(8Q11.21) MUTATED
  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
                                                             clus
vv                                                            AMP PEAK 10(8Q11.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  192
  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"
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q11.21) MUTATED    44 247
  AMP PEAK 10(8Q11.21) WILD-TYPE  35 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED     44  247
  AMP PEAK 10(8Q11.21) WILD-TYPE   35  162
     clus
vv    AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  NO                            44                             35
  YES                          247                            162
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(8Q11.21) MUTATED                                  1     7
  AMP PEAK 10(8Q11.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(8Q11.21) MUTATED                          23   247
  AMP PEAK 10(8Q11.21) WILD-TYPE                        21   168
D10V12, multiclass
                                  clus
vv                                 AMP PEAK 10(8Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     247
                                  clus
vv                                 AMP PEAK 10(8Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       168
[1] 4 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(8Q11.21) MUTATED    17 252
  AMP PEAK 10(8Q11.21) WILD-TYPE   7 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED     17  252
  AMP PEAK 10(8Q11.21) WILD-TYPE    7  179
                        clus
vv                       AMP PEAK 10(8Q11.21) MUTATED
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          252
                        clus
vv                       AMP PEAK 10(8Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            179
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(8Q24.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(8Q24.21) MUTATED   218  86
  AMP PEAK 11(8Q24.21) WILD-TYPE  83  27
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           304                            110 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            86                             27 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          283          415          248          722         1288 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
         520          623         1636         1747          190          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
          63          384          113          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         622          918          850          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 
         278          140          133          558          423          687 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
        1153          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         799          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         392          993          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 
         811         1988         1007         1045         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
        1980         1966         1966         1975          683          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         628          594           98          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
          46          443          535          391          904          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 
         526          484          348          298         1207          654 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1393         1399          317          129         1253 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1007          509         1309         1274         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1960          707          893          998          785          391 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
         950         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         1952         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-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1981         1945         5480         1960         1940         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7086 
         670          110          714          606          317          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
         828          773          292          701           77          154 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         106          128          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 
         516         1030          548         1965          575          299 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
        1131          490          658           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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         206            2            5           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 
          24           25           10          111         1057          485 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         588          360          351          360          224          552 
TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A6I9 
         378           14           34           56          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 
         240         1726         1559          578         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          218          228          225          387 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         149          135          168         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1252         1278         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

$`AMP PEAK 11(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          817          642 
TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 
        1250         1268          173         1081          290          630 
TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-A49C 
         933          629           45          432         1970          645 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5333 
         175          367          223         1466         1660          341 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CR-5248 
        1000         1057          877         1963          303         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6492 
        1152          799         1050          362          311          479 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7385 TCGA-CR-7391 
        1435         1245         1979          889          997          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 
         946          908          898          930          156          911 
TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6954 
         546         1958          701         2641         1970         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7250 TCGA-CV-7261 
        1969         1959         1959         1939         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-A45O 
        1974         1948         1957         1972         1937          851 
TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6825 
        1946          646          685         1950          321          491 
TCGA-D6-6827 TCGA-D6-A6EM TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
         568          232          775          622          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-A6C5 
         324          340           15          384          407          403 
TCGA-HD-7754 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 
          25           11           49           33          122          441 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-P3-A5Q5 
         412          440          168          392          111          910 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A8Z7 
        1120         1954         1917          245          567          198 
TCGA-QK-A8ZA TCGA-QK-AA3J 
         135          157 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                             2                             11 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          5480                           2641 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                         710.5                          665.5 
[1] "2.0 - 5480.0 (710.5)"  "11.0 - 2641.0 (665.5)"
[1] "hr=" "1.1"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 11(8Q24.21) MUTATED        19       50        56       181        11
  AMP PEAK 11(8Q24.21) WILD-TYPE       7       25        18        54         1
                                vv
clus                             STAGE IVC
  AMP PEAK 11(8Q24.21) MUTATED           0
  AMP PEAK 11(8Q24.21) WILD-TYPE         1
D11V3, multiclass
           clus
vv          AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  STAGE I                             19                              7
  STAGE II                            50                             25
  STAGE III                           56                             18
  STAGE IVA                          181                             54
  STAGE IVB                           11                              1
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 11(8Q24.21) MUTATED      34  88  75 124
  AMP PEAK 11(8Q24.21) WILD-TYPE    13  39  19  38
D11V4, multiclass
       clus
vv      AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  T0+T1                           34                             13
  T2                              88                             39
  T3                              75                             19
  T4                             124                             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 11(8Q24.21) MUTATED   116  45 125   7
  AMP PEAK 11(8Q24.21) WILD-TYPE  54  18  27   1
D11V5, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  N0                          116                             54
  N1                           45                             18
  N2                          125                             27
  N3                            7                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 11(8Q24.21) MUTATED   129   0  42
  AMP PEAK 11(8Q24.21) WILD-TYPE  38   1  16
D11V6, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  M0                          129                             38
  M1                            0                              1
  MX                           42                             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED    96 265
  AMP PEAK 11(8Q24.21) WILD-TYPE  36  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     96  265
  AMP PEAK 11(8Q24.21) WILD-TYPE   36   91
        clus
vv       AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  FEMALE                           96                             36
  MALE                            265                             91
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(8Q24.21) MUTATED                                     354
  AMP PEAK 11(8Q24.21) WILD-TYPE                                   123
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 11(8Q24.21) MUTATED                                                             1
  AMP PEAK 11(8Q24.21) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 11(8Q24.21) MUTATED                                                     6
  AMP PEAK 11(8Q24.21) WILD-TYPE                                                   4
D11V8, multiclass
                                                             clus
vv                                                            AMP PEAK 11(8Q24.21) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                354
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
                                                             clus
vv                                                            AMP PEAK 11(8Q24.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  123
  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"
D11V9, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED    59 302
  AMP PEAK 11(8Q24.21) WILD-TYPE  20 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     59  302
  AMP PEAK 11(8Q24.21) WILD-TYPE   20  107
     clus
vv    AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  NO                            59                             20
  YES                          302                            107
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(8Q24.21) MUTATED                                  2     9
  AMP PEAK 11(8Q24.21) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8Q24.21) MUTATED                          33   302
  AMP PEAK 11(8Q24.21) WILD-TYPE                        11   113
D11V12, multiclass
                                  clus
vv                                 AMP PEAK 11(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  33
  WHITE                                                     302
                                  clus
vv                                 AMP PEAK 11(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    11
  WHITE                                                       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"
D11V13, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED    21 314
  AMP PEAK 11(8Q24.21) WILD-TYPE   3 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     21  314
  AMP PEAK 11(8Q24.21) WILD-TYPE    3  117
                        clus
vv                       AMP PEAK 11(8Q24.21) MUTATED
  HISPANIC OR LATINO                               21
  NOT HISPANIC OR LATINO                          314
                        clus
vv                       AMP PEAK 11(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            117
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(9P24.1) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(9P24.1) MUTATED    68  24
  AMP PEAK 12(9P24.1) WILD-TYPE 233  89
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                           92                           322 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                           24                            89 
$`AMP PEAK 12(9P24.1) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DJ 
         725          623         1747          113          351          314 
TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5373 
        1153            5         1007         1977         1975          683 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 
         630          933           45         1110          735          432 
TCGA-CN-A499 TCGA-CN-A49C TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 
         535          645          654         1422         1393         1057 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD 
        1179         1750         1309         1353         1960          998 
TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7370 
        1777         1969          234         1956         1440          105 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7399 
        1979          889          796          392          930          181 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         522         3295         1978         2886         2327         1958 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6942 
         519         1840          641         1899         1959         3835 
TCGA-CV-6952 TCGA-CV-7099 TCGA-CV-7254 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 
        1966         1936         1976         1937         1973         1958 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-D6-6516 
        1945         1970          906         1959          714          773 
TCGA-D6-A6EM TCGA-DQ-5625 TCGA-F7-A50G TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8502 
         232         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-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67A 
         588          412          351          378           14          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-QK-A8Z9 
         111          112          254         1120         1917          149 
TCGA-QK-A8ZA TCGA-QK-AA3K 
         135          168 

$`AMP PEAK 12(9P24.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
         248          722         1288         1762          520         1636 
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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
         895          855          622          918          850          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
         182         1976          623          142          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-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-4725 TCGA-CN-4726 
         624            4          799          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1230         1151          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1268         1988         1045          173         1980         1081 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
        1980         1966         1966          290          629          628 
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-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 
         224          318          611          394          429           46 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         443          391          904          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1207         1660         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 
        1253         1000          985         1959         1959         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 
        1007          509         1274          877         1950          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1963          893          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
        2562          358         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-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          345          354          379          350          479 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7374 
        1435         1191         1245         1960          759           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1968         1036         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-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         216          156         1077          911         1472         1955 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 
        1950         1438          584          546         2437          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         701         2641         1478          215         1315         1665 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 
        1970         1948         1969         1952         1948         1969 
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-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1960         1099         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 
        1947         1972         1937         1984         1959         1981 
TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
         851         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1722         1977         1075          670          110          646 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         828          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         435          424          368          389          338         1778 
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-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-A50I TCGA-F7-A50J TCGA-F7-A61V 
        1131          490          658           92          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-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
         206            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-KU-A6H8 
         360          440          360          224          552          168 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          34           56          240          910         1726         1559 
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-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         245          218          228          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         198          135          157         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1252         1278         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                            2                             4 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                         3835                          5480 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                        842.5                         661.5 
[1] "2.0 - 3835.0 (842.5)" "4.0 - 5480.0 (661.5)"
[1] "hr=" "1.3"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 12(9P24.1) MUTATED         8       20        16        56         4
  AMP PEAK 12(9P24.1) WILD-TYPE      18       55        58       179         8
                               vv
clus                            STAGE IVC
  AMP PEAK 12(9P24.1) MUTATED           0
  AMP PEAK 12(9P24.1) WILD-TYPE         1
D12V3, multiclass
           clus
vv          AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  STAGE I                             8                            18
  STAGE II                           20                            55
  STAGE III                          16                            58
  STAGE IVA                          56                           179
  STAGE IVB                           4                             8
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 12(9P24.1) MUTATED      10  28  27  39
  AMP PEAK 12(9P24.1) WILD-TYPE    37  99  67 123
D12V4, multiclass
       clus
vv      AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  T0+T1                          10                            37
  T2                             28                            99
  T3                             27                            67
  T4                             39                           123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 12(9P24.1) MUTATED    36  15  38   4
  AMP PEAK 12(9P24.1) WILD-TYPE 134  48 114   4
D12V5, multiclass
    clus
vv   AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  N0                          36                           134
  N1                          15                            48
  N2                          38                           114
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK 12(9P24.1) MUTATED    33   0  18
  AMP PEAK 12(9P24.1) WILD-TYPE 134   1  40
D12V6, multiclass
    clus
vv   AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  M0                          33                           134
  M1                           0                             1
  MX                          18                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(9P24.1) MUTATED    47  69
  AMP PEAK 12(9P24.1) WILD-TYPE  85 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     47   69
  AMP PEAK 12(9P24.1) WILD-TYPE   85  287
        clus
vv       AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  FEMALE                          47                            85
  MALE                            69                           287
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(9P24.1) MUTATED                                     115
  AMP PEAK 12(9P24.1) WILD-TYPE                                   362
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 12(9P24.1) MUTATED                                                             0
  AMP PEAK 12(9P24.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 12(9P24.1) MUTATED                                                     1
  AMP PEAK 12(9P24.1) WILD-TYPE                                                   9
D12V8, multiclass
                                                             clus
vv                                                            AMP PEAK 12(9P24.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               115
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            AMP PEAK 12(9P24.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 362
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
[1] 3 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(9P24.1) MUTATED    14 102
  AMP PEAK 12(9P24.1) WILD-TYPE  65 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     14  102
  AMP PEAK 12(9P24.1) WILD-TYPE   65  307
     clus
vv    AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  NO                           14                            65
  YES                         102                           307
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(9P24.1) MUTATED                                  0     3
  AMP PEAK 12(9P24.1) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(9P24.1) MUTATED                          11    98
  AMP PEAK 12(9P24.1) WILD-TYPE                        33   317
D12V12, multiclass
                                  clus
vv                                 AMP PEAK 12(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     98
                                  clus
vv                                 AMP PEAK 12(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   33
  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"
D12V13, binary
                               cls
clus                              0   1
  AMP PEAK 12(9P24.1) MUTATED     9 104
  AMP PEAK 12(9P24.1) WILD-TYPE  15 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      9  104
  AMP PEAK 12(9P24.1) WILD-TYPE   15  327
                        clus
vv                       AMP PEAK 12(9P24.1) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         104
                        clus
vv                       AMP PEAK 12(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           327
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(9P23) MUTATION ANALYSIS
D13V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 13(9P23) MUTATED    66  28
  AMP PEAK 13(9P23) WILD-TYPE 235  85
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                         94                         320 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                         28                          85 
$`AMP PEAK 13(9P23) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DJ 
         725          623         1747          113          351          314 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5367 
           5         1157         1007         1980         1977         1966 
TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6994 
        1975          630          933           45         1110          735 
TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49C TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
         432          535          645          654         1422         1393 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 
        1057          985         1179         1750         1309         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-6493 
        1960          998         1777         1969          234         1956 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7399 
         105         1979          796          392          930          181 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1955          522         3295         1978         2886         2327 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6952 
         519         1840          641         1899         1959         1966 
TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7243 TCGA-CV-7254 
        3837         1970         1936         1945          954         1976 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JO 
        1937         1973         1958         1945         1970         1959 
TCGA-CV-A6JZ TCGA-D6-6516 TCGA-D6-A6EM TCGA-DQ-5625 TCGA-DQ-7589 TCGA-F7-A50G 
         714          773          232         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 TCGA-QK-A8Z9 TCGA-QK-AA3K 
         218          387          149          168 

$`AMP PEAK 13(9P23) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
         248          722         1288         1762          520         1636 
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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
         895          855          622          918          850          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
         182         1976          623          142          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-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
        1955          624            4          799          721          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1230         1151          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 
        1268         1988         1045          173         1081         1980 
TCGA-CN-5366 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1966          683          290          629          628          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-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         391          904          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1660         1399          317          341          129         1253 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1000         1959         1959         1560         1007          509 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1274          877         1950          707         1963          893 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         785          391          303          950         2562          358 
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-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971          514          362          311          345 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
         354          379          350          479         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1440         1245         1960          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1968         1036         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-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 
         216          156         1077          911         1472         1950 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
        1438          584          546         1958         2437          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         701         2641         1478          215         1315         1665 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1969         1952         3835         1948 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1969         1957         1969         1959         1959         1970 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1987         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 
        1095          797         1967         1960         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 
        1948         1955         1957         1947         1972         1937 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y 
        1984         1959         1981          851         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JE 
        1940         1946         1954         1722         1977         1075 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
         906          670          110          646          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 
        1950          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-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
         128          539          376          483          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         368          389          338         1778          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
         548         1965          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         1131          490          658 
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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
          58          414          403          206            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-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          34           56          240          910         1726         1559 
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-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         228          225          567          198          135          135 
TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         157         1326         1663         1319         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1043         1894          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                          3                           2 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                       3837                        5480 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                      943.5                       652.0 
[1] "3.0 - 3837.0 (943.5)" "2.0 - 5480.0 (652.0)"
[1] "hr=" "1.3"
D13V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 13(9P23) MUTATED         7       21        17        52         4
  AMP PEAK 13(9P23) WILD-TYPE      19       54        57       183         8
                             vv
clus                          STAGE IVC
  AMP PEAK 13(9P23) MUTATED           0
  AMP PEAK 13(9P23) WILD-TYPE         1
D13V3, multiclass
           clus
vv          AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  STAGE I                           7                          19
  STAGE II                         21                          54
  STAGE III                        17                          57
  STAGE IVA                        52                         183
  STAGE IVB                         4                           8
  STAGE IVC                         0                           1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK 13(9P23) MUTATED       9  30  26  36
  AMP PEAK 13(9P23) WILD-TYPE    38  97  68 126
D13V4, multiclass
       clus
vv      AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  T0+T1                         9                          38
  T2                           30                          97
  T3                           26                          68
  T4                           36                         126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 13(9P23) MUTATED    31  16  38   4
  AMP PEAK 13(9P23) WILD-TYPE 139  47 114   4
D13V5, multiclass
    clus
vv   AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  N0                        31                         139
  N1                        16                          47
  N2                        38                         114
  N3                         4                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1  MX
  AMP PEAK 13(9P23) MUTATED    33   0  17
  AMP PEAK 13(9P23) WILD-TYPE 134   1  41
D13V6, multiclass
    clus
vv   AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  M0                        33                         134
  M1                         0                           1
  MX                        17                          41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                             cls
clus                            0   1
  AMP PEAK 13(9P23) MUTATED    43  71
  AMP PEAK 13(9P23) WILD-TYPE  89 285
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(9P23) MUTATED     43   71
  AMP PEAK 13(9P23) WILD-TYPE   89  285
        clus
vv       AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  FEMALE                        43                          89
  MALE                          71                         285
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(9P23) MUTATED                                     113
  AMP PEAK 13(9P23) WILD-TYPE                                   364
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 13(9P23) MUTATED                                                             0
  AMP PEAK 13(9P23) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 13(9P23) MUTATED                                                     1
  AMP PEAK 13(9P23) WILD-TYPE                                                   9
D13V8, multiclass
                                                             clus
vv                                                            AMP PEAK 13(9P23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             113
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 1
                                                             clus
vv                                                            AMP PEAK 13(9P23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               364
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   9
[1] 3 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(9P23) MUTATED    16  98
  AMP PEAK 13(9P23) WILD-TYPE  63 311
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(9P23) MUTATED     16   98
  AMP PEAK 13(9P23) WILD-TYPE   63  311
     clus
vv    AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  NO                         16                          63
  YES                        98                         311
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(9P23) MUTATED                                  0     3
  AMP PEAK 13(9P23) WILD-TYPE                                2     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(9P23) MUTATED                           9    99
  AMP PEAK 13(9P23) WILD-TYPE                        35   316
D13V12, multiclass
                                  clus
vv                                 AMP PEAK 13(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                9
  WHITE                                                   99
                                  clus
vv                                 AMP PEAK 13(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 35
  WHITE                                                    316
[1] 4 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(9P23) MUTATED     8 103
  AMP PEAK 13(9P23) WILD-TYPE  16 328
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(9P23) MUTATED      8  103
  AMP PEAK 13(9P23) WILD-TYPE   16  328
                        clus
vv                       AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  HISPANIC OR LATINO                             8                          16
  NOT HISPANIC OR LATINO                       103                         328
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(9P13.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(9P13.3) MUTATED    80  29
  AMP PEAK 14(9P13.3) WILD-TYPE 221  84
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          109                           305 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           29                            84 
$`AMP PEAK 14(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-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7870 TCGA-CN-4728 TCGA-CN-4737 
         314          623          278         1153         1151          625 
TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 
        1007         1980         1977         1975          630          933 
TCGA-CN-6012 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 
         629         1110          224          735          432          535 
TCGA-CN-A63T TCGA-CN-A6V3 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-6229 
         225          298         1422         1393          985         1179 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CI 
        1750         1309         1353         1960         1963          950 
TCGA-CR-6467 TCGA-CR-6488 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1777          379         1245          105         1979          759 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7390 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 
         889          972          907          930          181         1077 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
         522         1950         3295          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 
        2327         2437          519          406         1840          641 
TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7180 
        1899         1959         1966         1970         1936         1987 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7254 TCGA-CV-7427 TCGA-CV-7434 TCGA-CV-A45Q 
        1952         1444         1976         1937         1958         1945 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CX-7219 TCGA-D6-6516 
        1977         1970         1959          714          828          773 
TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5629 TCGA-F7-8298 TCGA-F7-A50G 
         232          368         1081          516          490           15 
TCGA-F7-A50I TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-8224 
          92            3          407          133           37           55 
TCGA-HD-8634 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W 
          24           10           33          485          351           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A6SW TCGA-P3-A6T2 
          34          392          111          112         1120         1917 
TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K 
         553          218          198          149          135          168 
TCGA-UF-A71D 
        1252 

$`AMP PEAK 14(9P13.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
         248          722         1288         1762          520         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF 
         190          644          451           63          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          918          850          216          182 
TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        1976          142          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         1157          142         1230          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         817          993          642         1250          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1988         1045          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1081         1980         1966         1966          683          290 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          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-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
          46          443          391          904          645          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5323 
         484          348          175          367          223         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1207          654         1660         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
         129         1253         1000         1057         1959         1959 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1560         1007          509         1274          877         1950 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
         707          893          998          785          391          303 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
        2562          358         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-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 
         362          311          345          354          234          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
         479         1956         1435         1191         1440         1960 
TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
          30         1968         1036          796         1954          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-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         898          216          156          911         1472         1955 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1438          584         1958          701         2641         1478 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
         215         1315         1665         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 
        1952         3835         1948         1969         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 
        1959         3837         1959         1970         1959         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1945         1979         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1960         1099         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
        1947         1973         1972         1937         1984         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1981          851         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU 
        1954         1722         1075          906          670          110 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         646          606          685         1950          317          321 
TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         237          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 
         435          424          389          338         1778         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
         369          368          324          340         1131          658 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
         585          384           14           13            6           58 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HL-7533 
          44           25           11           49          111         1057 
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-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D 
         360          224          552          378          168           56 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX 
         254          240          910         1726         1559         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 TCGA-QK-A6V9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 
         225          387          567          135          157         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1663         1319         1278         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                            3                             2 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                         3295                          5480 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          773                           670 
[1] "3.0 - 3295.0 (773.0)" "2.0 - 5480.0 (670.0)"
[1] "hr=" "1.3"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 14(9P13.3) MUTATED         8       25        16        67         5
  AMP PEAK 14(9P13.3) WILD-TYPE      18       50        58       168         7
                               vv
clus                            STAGE IVC
  AMP PEAK 14(9P13.3) MUTATED           0
  AMP PEAK 14(9P13.3) WILD-TYPE         1
D14V3, multiclass
           clus
vv          AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  STAGE I                             8                            18
  STAGE II                           25                            50
  STAGE III                          16                            58
  STAGE IVA                          67                           168
  STAGE IVB                           5                             7
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK 14(9P13.3) MUTATED      12  36  28  46
  AMP PEAK 14(9P13.3) WILD-TYPE    35  91  66 116
D14V4, multiclass
       clus
vv      AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  T0+T1                          12                            35
  T2                             36                            91
  T3                             28                            66
  T4                             46                           116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 14(9P13.3) MUTATED    43  18  44   4
  AMP PEAK 14(9P13.3) WILD-TYPE 127  45 108   4
D14V5, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  N0                          43                           127
  N1                          18                            45
  N2                          44                           108
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK 14(9P13.3) MUTATED    45   0  16
  AMP PEAK 14(9P13.3) WILD-TYPE 122   1  42
D14V6, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  M0                          45                           122
  M1                           0                             1
  MX                          16                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED    42  87
  AMP PEAK 14(9P13.3) WILD-TYPE  90 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     42   87
  AMP PEAK 14(9P13.3) WILD-TYPE   90  269
        clus
vv       AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  FEMALE                          42                            90
  MALE                            87                           269
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P13.3) MUTATED                                     126
  AMP PEAK 14(9P13.3) WILD-TYPE                                   351
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 14(9P13.3) MUTATED                                                             0
  AMP PEAK 14(9P13.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 14(9P13.3) MUTATED                                                     3
  AMP PEAK 14(9P13.3) WILD-TYPE                                                   7
D14V8, multiclass
                                                             clus
vv                                                            AMP PEAK 14(9P13.3) 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                                                            AMP PEAK 14(9P13.3) 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                                     7
[1] 3 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(9P13.3) MUTATED    20 109
  AMP PEAK 14(9P13.3) WILD-TYPE  59 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     20  109
  AMP PEAK 14(9P13.3) WILD-TYPE   59  300
     clus
vv    AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  NO                           20                            59
  YES                         109                           300
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(9P13.3) MUTATED                                  0     2
  AMP PEAK 14(9P13.3) WILD-TYPE                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(9P13.3) MUTATED                          11   111
  AMP PEAK 14(9P13.3) WILD-TYPE                        33   304
D14V12, multiclass
                                  clus
vv                                 AMP PEAK 14(9P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    111
                                  clus
vv                                 AMP PEAK 14(9P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      304
[1] 4 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(9P13.3) MUTATED    10 113
  AMP PEAK 14(9P13.3) WILD-TYPE  14 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     10  113
  AMP PEAK 14(9P13.3) WILD-TYPE   14  318
                        clus
vv                       AMP PEAK 14(9P13.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         113
                        clus
vv                       AMP PEAK 14(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           318
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(9Q34.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(9Q34.3) MUTATED    94  41
  AMP PEAK 15(9Q34.3) WILD-TYPE 207  72
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                          135                           279 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                           41                            72 
$`AMP PEAK 15(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-BA-A6DJ TCGA-BB-4224 
        1747          451          113          351          314          278 
TCGA-BB-7872 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4731 
         436          624          721         1230         1151          993 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
        1268         1007         1980         1977         1966         1966 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 
         630          933         1970         1110          224          735 
TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63W 
         432          535          391          645          225          348 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6221 
         298         1466          654         1393          317         1000 
TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1057         1179         1750         1309         1353         1960 
TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7368 
         998         1777          514          350         1191         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7402 TCGA-CV-5432 
        1960          105          889         1036          911         1950 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
        3295          584          546         1978         2327         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
         519          406         1840          215          641         1899 
TCGA-CV-6441 TCGA-CV-6952 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7235 
        1970         1966         1936         1959         1987         1952 
TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 
         797         1099         1948         1957         1937         1972 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A468 
        1937         1958         1945         1940         1954         1977 
TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 
        1970          714          317          828          773          701 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 
         128          232          424          368          338         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-MZ-A7D7 
         351           14          392           56          112          240 
TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A6II 
        1120         1917          400          553          218          225 
TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
         149          168         1278         1043         1894          484 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
        1497          665          413 

$`AMP PEAK 15(9Q34.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         102          462          415          276          722         1288 
TCGA-BA-5153 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
        1762         1636          190          644           63          384 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         216          182         1976          623          142          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-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         423          687          638         1153          428         1955 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 
           5            4          799         1157          142          392 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         817          642         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
        1330          811         1988         1045          173         1081 
TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
        1980         1975          683          290          629          628 
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-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-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         904          526          484          175          367          223 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1207         1660         1422         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
        1253          985         1959         1959         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         509         1274          877         1950          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         893          785          391          303          950         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-6478 TCGA-CR-6480 TCGA-CR-6481 
        1050         1125         1971         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
         345          354          234          379          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
        1435         1440         1979          759           30          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968          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-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
         930          216          156          181         1077         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 
        1955          522         1438         2886         1958          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6935 
        2641         1478         1315         1665         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6954 
        1952         1959         3835         1948         1969         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-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1939         1945         1979         1444         1095          954 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7424 
        1967         1960         1976         1974         1955         1947 
TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45R 
        1973         1984         1959         1981          851         5480 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1960         1946         1722         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         670          110          646          606          685         1950 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         321          237          292           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         568          106          539          376          483          435 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         389         1778          516         1030          548         1965 
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-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
         585          384           14           13            6           58 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8634 
         414          403          206            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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 
         552          378          168           34          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 
         910         1726         1559         1954          578         1968 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         357          245          228          387          567          198 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         135          135          157         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A7JD TCGA-UF-A7JJ 
        1252          735          214 

  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                            2                             4 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                         3295                          5480 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                          725                           683 
[1] "2.0 - 3295.0 (725.0)" "4.0 - 5480.0 (683.0)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 15(9Q34.3) MUTATED         7       24        22        91         7
  AMP PEAK 15(9Q34.3) WILD-TYPE      19       51        52       144         5
                               vv
clus                            STAGE IVC
  AMP PEAK 15(9Q34.3) MUTATED           0
  AMP PEAK 15(9Q34.3) WILD-TYPE         1
D15V3, multiclass
           clus
vv          AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  STAGE I                             7                            19
  STAGE II                           24                            51
  STAGE III                          22                            52
  STAGE IVA                          91                           144
  STAGE IVB                           7                             5
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  AMP PEAK 15(9Q34.3) MUTATED      11 34 35 72
  AMP PEAK 15(9Q34.3) WILD-TYPE    36 93 59 90
D15V4, multiclass
       clus
vv      AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  T0+T1                          11                            36
  T2                             34                            93
  T3                             35                            59
  T4                             72                            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
  AMP PEAK 15(9Q34.3) MUTATED    56  21  57   5
  AMP PEAK 15(9Q34.3) WILD-TYPE 114  42  95   3
D15V5, multiclass
    clus
vv   AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  N0                          56                           114
  N1                          21                            42
  N2                          57                            95
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK 15(9Q34.3) MUTATED    52   0  21
  AMP PEAK 15(9Q34.3) WILD-TYPE 115   1  37
D15V6, multiclass
    clus
vv   AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  M0                          52                           115
  M1                           0                             1
  MX                          21                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.3) MUTATED    44 120
  AMP PEAK 15(9Q34.3) WILD-TYPE  88 236
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.3) MUTATED     44  120
  AMP PEAK 15(9Q34.3) WILD-TYPE   88  236
        clus
vv       AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  FEMALE                          44                            88
  MALE                           120                           236
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(9Q34.3) MUTATED                                     161
  AMP PEAK 15(9Q34.3) WILD-TYPE                                   316
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 15(9Q34.3) MUTATED                                                             0
  AMP PEAK 15(9Q34.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 15(9Q34.3) MUTATED                                                     3
  AMP PEAK 15(9Q34.3) WILD-TYPE                                                   7
D15V8, multiclass
                                                             clus
vv                                                            AMP PEAK 15(9Q34.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               161
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
                                                             clus
vv                                                            AMP PEAK 15(9Q34.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 316
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
[1] 3 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(9Q34.3) MUTATED    24 140
  AMP PEAK 15(9Q34.3) WILD-TYPE  55 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.3) MUTATED     24  140
  AMP PEAK 15(9Q34.3) WILD-TYPE   55  269
     clus
vv    AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  NO                           24                            55
  YES                         140                           269
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(9Q34.3) MUTATED                                  0     3
  AMP PEAK 15(9Q34.3) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(9Q34.3) MUTATED                          17   140
  AMP PEAK 15(9Q34.3) WILD-TYPE                        27   275
D15V12, multiclass
                                  clus
vv                                 AMP PEAK 15(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    140
                                  clus
vv                                 AMP PEAK 15(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      275
[1] 4 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(9Q34.3) MUTATED    11 142
  AMP PEAK 15(9Q34.3) WILD-TYPE  13 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.3) MUTATED     11  142
  AMP PEAK 15(9Q34.3) WILD-TYPE   13  289
                        clus
vv                       AMP PEAK 15(9Q34.3) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         142
                        clus
vv                       AMP PEAK 15(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           289
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(11P13) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 16(11P13) MUTATED    55  17
  AMP PEAK 16(11P13) WILD-TYPE 246  96
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          72                          342 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          17                           96 
$`AMP PEAK 16(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-BA-A6DL TCGA-BA-A8YP TCGA-BB-4225 TCGA-BB-7861 TCGA-C9-A47Z 
         850          623          142          140          310            5 
TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5355 
         721          395          625         1960         1988         1007 
TCGA-CN-5363 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5323 TCGA-CQ-5329 
        1977           45          735          225         1466         1422 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7069 
         341          129         1000         1750         1007         1274 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 
        1353         1960          707          785          391          354 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7382 TCGA-CR-7392 
         379         1191         1440          105          796          946 
TCGA-CV-5430 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 
        1955         1978          406         1840         1665          641 
TCGA-CV-6942 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6JZ 
        3835         1976         1099         1946          646          714 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EP TCGA-D6-A74Q 
         828          292          568          128          424          338 
TCGA-DQ-5624 TCGA-DQ-7588 TCGA-F7-A50J TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A67D 
        1778         1965          585          485          351           56 
TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IJ 
        1726         1120         1917         1968          218          387 

$`AMP PEAK 16(11P13) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          520          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG 
        1747          644          451           63          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         622          918          351          216          182         1976 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         314          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         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 
         642         1250         1330          811         1268         1045 
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          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         628          594          629          432           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202         1110          224          318          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         904          645          526          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223          298         1207          654         1660 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
        1393         1399          317         1253         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1179         1560          509         1309 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
         877         1950         1963          893          998          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         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         1952         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-A45R 
        1958         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1940         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 
        1075          906         1959          670          110          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
         685         1950          317          321          237          773 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 
         701           77          491          154          106          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          232          435          368          389 
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-A61S 
        1131          490          658           15           92            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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            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-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         360          224          552          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
          34          392          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T8 TCGA-QK-A64Z 
         910         1559         1954          578          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 
         357          245          228          225          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1663         1319         1252         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          665          214          413 

  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                           5                            2 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                        3835                         5480 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                       717.5                        686.0 
[1] "5.0 - 3835.0 (717.5)" "2.0 - 5480.0 (686.0)"
[1] "hr=" "1.1"
D16V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 16(11P13) MUTATED         4       19        17        40         5
  AMP PEAK 16(11P13) WILD-TYPE      22       56        57       195         7
                              vv
clus                           STAGE IVC
  AMP PEAK 16(11P13) MUTATED           0
  AMP PEAK 16(11P13) WILD-TYPE         1
D16V3, multiclass
           clus
vv          AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  STAGE I                            4                           22
  STAGE II                          19                           56
  STAGE III                         17                           57
  STAGE IVA                         40                          195
  STAGE IVB                          5                            7
  STAGE IVC                          0                            1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 16(11P13) MUTATED       8  27  19  34
  AMP PEAK 16(11P13) WILD-TYPE    39 100  75 128
D16V4, multiclass
       clus
vv      AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  T0+T1                          8                           39
  T2                            27                          100
  T3                            19                           75
  T4                            34                          128
[1] 4 2
[1] TRUE
[1] "dimension 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(11P13) MUTATED    37  10  27   4
  AMP PEAK 16(11P13) WILD-TYPE 133  53 125   4
D16V5, multiclass
    clus
vv   AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  N0                         37                          133
  N1                         10                           53
  N2                         27                          125
  N3                          4                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1  MX
  AMP PEAK 16(11P13) MUTATED    37   0   9
  AMP PEAK 16(11P13) WILD-TYPE 130   1  49
D16V6, multiclass
    clus
vv   AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  M0                         37                          130
  M1                          0                            1
  MX                          9                           49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                              cls
clus                             0   1
  AMP PEAK 16(11P13) MUTATED    23  72
  AMP PEAK 16(11P13) WILD-TYPE 109 284
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED     23   72
  AMP PEAK 16(11P13) WILD-TYPE  109  284
        clus
vv       AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  FEMALE                         23                          109
  MALE                           72                          284
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(11P13) MUTATED                                      94
  AMP PEAK 16(11P13) WILD-TYPE                                   383
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 16(11P13) MUTATED                                                             0
  AMP PEAK 16(11P13) WILD-TYPE                                                           1
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 16(11P13) MUTATED                                                     1
  AMP PEAK 16(11P13) WILD-TYPE                                                   9
D16V8, multiclass
                                                             clus
vv                                                            AMP PEAK 16(11P13) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               94
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  1
                                                             clus
vv                                                            AMP PEAK 16(11P13) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                383
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    9
[1] 3 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(11P13) MUTATED    16  79
  AMP PEAK 16(11P13) WILD-TYPE  63 330
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED     16   79
  AMP PEAK 16(11P13) WILD-TYPE   63  330
     clus
vv    AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  NO                          16                           63
  YES                         79                          330
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(11P13) MUTATED                                  0     4
  AMP PEAK 16(11P13) WILD-TYPE                                2     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(11P13) MUTATED                          10    76
  AMP PEAK 16(11P13) WILD-TYPE                        34   339
D16V12, multiclass
                                  clus
vv                                 AMP PEAK 16(11P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                    76
                                  clus
vv                                 AMP PEAK 16(11P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  34
  WHITE                                                     339
[1] 4 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(11P13) MUTATED     7  82
  AMP PEAK 16(11P13) WILD-TYPE  17 349
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED      7   82
  AMP PEAK 16(11P13) WILD-TYPE   17  349
                        clus
vv                       AMP PEAK 16(11P13) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         82
                        clus
vv                       AMP PEAK 16(11P13) WILD-TYPE
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          349
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(11Q13.3) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(11Q13.3) MUTATED   130  58
  AMP PEAK 17(11Q13.3) WILD-TYPE 171  55
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                           188                            226 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            58                             55 
$`AMP PEAK 17(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-A4II TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DL 
         384          236          918          351         1976          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7870 
         142          187          140          133          310         1153 
TCGA-BB-7871 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 
         428         1955            5          721         1230         1151 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4742 
         993         1250          625         1960         1330         1988 
TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1007         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 
         683          630          933          629          628           45 
TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 
          98          611          394          735          429          443 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CQ-5323 TCGA-CQ-5329 
         391          904          645          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         1179 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1750         1007          509         1274         1353         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5247 
        1963          893          998          785          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         1952          954         1099         1955 
TCGA-CV-7422 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R 
        1957         1937         1984         1959         1981         5480 
TCGA-CV-A460 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-7082 
        1946         1075          906          646          714          317 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-6826 
         237          828          773          292          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6ES 
         568          106          539          376          424          389 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-7848 TCGA-F7-8298 
        1081          548         1965          575         1131          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-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 
         552          168           14           34           56          240 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
        1726         1954         1968          218          228          387 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         149          135          157          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1319         1252         1278         1894          484          735 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

$`AMP PEAK 17(11Q13.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5557 TCGA-BA-5559 
         102          722         1288         1762          623         1747 
TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
         644          113          895          855          622          850 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 
         216          182          314         2878          278          558 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-8601 
         536          423          687          638          436          624 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
           4          799         1157          142          392          817 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 
         642          395          811         1268         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
        1980         1081          290          594          629          432 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 
        1970          202         1110          224          318          432 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
          46          535          225          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223          298         1207          654         1660 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
        1393         1399          317         1253         1057          985 
TCGA-CQ-7064 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CH 
        1560         1309          877         1950          707          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         950         2562         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1966         1050         1125          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7373 
         354          234          479         1435         1245          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
          30          972          796          997         1430          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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
         156         1077          911         1472         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
        1438          584          546         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         519          701          641         1899         1970         1948 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 
        1959         3835         1948         1966         1957         1959 
TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 
        3837         1936         1959         1939         1987         1979 
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-7406 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1974         1948         1947         1937         1973         1972 
TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1958          851         1945         1960         1940         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1722         1977         1970         1959          670          110 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6823 TCGA-D6-6824 
         606          685         1950          321          701           77 
TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A74Q 
         128          483          232          435          368          338 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1778          516         1030          775          622          299 
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-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
           3           14           13            6          407           58 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         414          403          206           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-KU-A6H7 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
         224          378          392          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
         910         1559         1120          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 
         553          357          245          225          567          198 
TCGA-QK-A8ZB TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JH 
         135         1043         1497          665 

  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                             2                              3 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                          5480                           3837 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                         735.0                          667.5 
[1] "2.0 - 5480.0 (735.0)" "3.0 - 3837.0 (667.5)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 17(11Q13.3) MUTATED        15       30        32       112         7
  AMP PEAK 17(11Q13.3) WILD-TYPE      11       45        42       123         5
                                vv
clus                             STAGE IVC
  AMP PEAK 17(11Q13.3) MUTATED           0
  AMP PEAK 17(11Q13.3) WILD-TYPE         1
D17V3, multiclass
           clus
vv          AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  STAGE I                             15                             11
  STAGE II                            30                             45
  STAGE III                           32                             42
  STAGE IVA                          112                            123
  STAGE IVB                            7                              5
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 17(11Q13.3) MUTATED      21 52 45 80
  AMP PEAK 17(11Q13.3) WILD-TYPE    26 75 49 82
D17V4, multiclass
       clus
vv      AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  T0+T1                           21                             26
  T2                              52                             75
  T3                              45                             49
  T4                              80                             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
  AMP PEAK 17(11Q13.3) MUTATED   77 25 81  4
  AMP PEAK 17(11Q13.3) WILD-TYPE 93 38 71  4
D17V5, multiclass
    clus
vv   AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  N0                           77                             93
  N1                           25                             38
  N2                           81                             71
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  AMP PEAK 17(11Q13.3) MUTATED   79  0 21
  AMP PEAK 17(11Q13.3) WILD-TYPE 88  1 37
D17V6, multiclass
    clus
vv   AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  M0                           79                             88
  M1                            0                              1
  MX                           21                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    55 166
  AMP PEAK 17(11Q13.3) WILD-TYPE  77 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     55  166
  AMP PEAK 17(11Q13.3) WILD-TYPE   77  190
        clus
vv       AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  FEMALE                           55                             77
  MALE                            166                            190
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(11Q13.3) MUTATED                                     219
  AMP PEAK 17(11Q13.3) WILD-TYPE                                   258
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 17(11Q13.3) MUTATED                                                             0
  AMP PEAK 17(11Q13.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 17(11Q13.3) MUTATED                                                     2
  AMP PEAK 17(11Q13.3) WILD-TYPE                                                   8
D17V8, multiclass
                                                             clus
vv                                                            AMP PEAK 17(11Q13.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                219
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    2
                                                             clus
vv                                                            AMP PEAK 17(11Q13.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  258
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      8
[1] 3 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(11Q13.3) MUTATED    42 179
  AMP PEAK 17(11Q13.3) WILD-TYPE  37 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     42  179
  AMP PEAK 17(11Q13.3) WILD-TYPE   37  230
     clus
vv    AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  NO                            42                             37
  YES                          179                            230
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(11Q13.3) MUTATED                                  0     3
  AMP PEAK 17(11Q13.3) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(11Q13.3) MUTATED                          23   186
  AMP PEAK 17(11Q13.3) WILD-TYPE                        21   229
D17V12, multiclass
                                  clus
vv                                 AMP PEAK 17(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     186
                                  clus
vv                                 AMP PEAK 17(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    21
  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"
D17V13, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    10 193
  AMP PEAK 17(11Q13.3) WILD-TYPE  14 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     10  193
  AMP PEAK 17(11Q13.3) WILD-TYPE   14  238
                        clus
vv                       AMP PEAK 17(11Q13.3) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          193
                        clus
vv                       AMP PEAK 17(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(12P13.33) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 18(12P13.33) MUTATED    98  33
  AMP PEAK 18(12P13.33) WILD-TYPE 203  80
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                            131                             283 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                             33                              80 
$`AMP PEAK 18(12P13.33) MUTATED`
TCGA-4P-AA8J TCGA-BA-4077 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-6873 
         102         1983          520         1747           63          113 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 
         895          855          622          623          142         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4725 
         278          140          536         1153            5         1157 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         142         1151          392          625         1960         1330 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 
        1980         1977         1966          629          628           45 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A49A 
        1110          224          318          611          735          391 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6221 
         904          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          785         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-CV-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CX-7086 
        1959         1981         5480         1940         1946          237 
TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         828          701          424          389          338         1778 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 
         516         1965          575          622          299         1131 
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          552           14           34          392 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
          56          112          240         1917          400          553 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A71B TCGA-UF-A71E 
         245          218          149          135         1319         1278 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1043          484          735         1497          665 

$`AMP PEAK 18(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-A4II TCGA-BA-A6D8 
         644          451          384          236          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
         351          216          182         1976          314          187 
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-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
         428          436         1955          624            4          799 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         721         1230          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
         395          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
         173         1081         1980         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         290          630          933          594          629          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
          98         1970          202          394          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W 
          46          443          535          645          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1393         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        1253         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1007         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
        1960          707         1963          893          998          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
         303          950         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-6482 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 
         362          311          345          354          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-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
         889           30          972          796          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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 
         930         1077          911         1472         1438          584 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 
         406          701         1478         1840         1315          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-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-7180 
        1970         1970         1936         1959         1939         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7410 TCGA-CV-7424 
        1979         1952         1444         1960         1948         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1973         1937         1984          851         1945 
TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1960         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 
         606          685         1950          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-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7593 
         368         1081         1030          548          775          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          340          490          658           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
          92          384           14           13            6           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-8224 
         133          414          403          206            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-KU-A6H7 
         412          440          351          360          224          378 
TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         168          111          254          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IH 
        1120         1954          578         1968          357          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J 
         225          387          567          198          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JJ 
         168         1326         1663         1252         1894          214 
TCGA-UF-A7JS 
         413 

  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                              3                               2 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                           5480                            3837 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                            735                             687 
[1] "3.0 - 5480.0 (735.0)" "2.0 - 3837.0 (687.0)"
[1] "hr=" "1.4"
D18V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 18(12P13.33) MUTATED         8       22        24        80
  AMP PEAK 18(12P13.33) WILD-TYPE      18       53        50       155
                                 vv
clus                              STAGE IVB STAGE IVC
  AMP PEAK 18(12P13.33) MUTATED           5         0
  AMP PEAK 18(12P13.33) WILD-TYPE         7         1
D18V3, multiclass
           clus
vv          AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  STAGE I                               8                              18
  STAGE II                             22                              53
  STAGE III                            24                              50
  STAGE IVA                            80                             155
  STAGE IVB                             5                               7
  STAGE IVC                             0                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 18(12P13.33) MUTATED      15  40  31  56
  AMP PEAK 18(12P13.33) WILD-TYPE    32  87  63 106
D18V4, multiclass
       clus
vv      AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  T0+T1                            15                              32
  T2                               40                              87
  T3                               31                              63
  T4                               56                             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 18(12P13.33) MUTATED    55  18  54   4
  AMP PEAK 18(12P13.33) WILD-TYPE 115  45  98   4
D18V5, multiclass
    clus
vv   AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  N0                            55                             115
  N1                            18                              45
  N2                            54                              98
  N3                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  AMP PEAK 18(12P13.33) MUTATED    50   0  17
  AMP PEAK 18(12P13.33) WILD-TYPE 117   1  41
D18V6, multiclass
    clus
vv   AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  M0                            50                             117
  M1                             0                               1
  MX                            17                              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                 cls
clus                                0   1
  AMP PEAK 18(12P13.33) MUTATED    34 123
  AMP PEAK 18(12P13.33) WILD-TYPE  98 233
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED     34  123
  AMP PEAK 18(12P13.33) WILD-TYPE   98  233
        clus
vv       AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  FEMALE                            34                              98
  MALE                             123                             233
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(12P13.33) MUTATED                                     154
  AMP PEAK 18(12P13.33) WILD-TYPE                                   323
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 18(12P13.33) MUTATED                                                             0
  AMP PEAK 18(12P13.33) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 18(12P13.33) MUTATED                                                     3
  AMP PEAK 18(12P13.33) WILD-TYPE                                                   7
D18V8, multiclass
                                                             clus
vv                                                            AMP PEAK 18(12P13.33) 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                                     3
                                                             clus
vv                                                            AMP PEAK 18(12P13.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   323
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       7
[1] 3 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(12P13.33) MUTATED    25 132
  AMP PEAK 18(12P13.33) WILD-TYPE  54 277
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED     25  132
  AMP PEAK 18(12P13.33) WILD-TYPE   54  277
     clus
vv    AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  NO                             25                              54
  YES                           132                             277
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(12P13.33) MUTATED                                  1     1
  AMP PEAK 18(12P13.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(12P13.33) MUTATED                          17   134
  AMP PEAK 18(12P13.33) WILD-TYPE                        27   281
D18V12, multiclass
                                  clus
vv                                 AMP PEAK 18(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      134
                                  clus
vv                                 AMP PEAK 18(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        281
[1] 4 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(12P13.33) MUTATED     6 140
  AMP PEAK 18(12P13.33) WILD-TYPE  18 291
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED      6  140
  AMP PEAK 18(12P13.33) WILD-TYPE   18  291
                        clus
vv                       AMP PEAK 18(12P13.33) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           140
                        clus
vv                       AMP PEAK 18(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             291
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(12Q15) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(12Q15) MUTATED    60  19
  AMP PEAK 19(12Q15) WILD-TYPE 241  94
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                          79                          335 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                          19                           94 
$`AMP PEAK 19(12Q15) MUTATED`
TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BB-4223 
        1747          451           63          850          623         2878 
TCGA-BB-4225 TCGA-BB-7870 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 
         140         1153          436            5         1157         1230 
TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-6010 TCGA-CN-6012 
        1151          625         1330         1045          630          629 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A499 TCGA-CN-A49A 
        1110          224          318          611          535          391 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CE 
         904          225          985          509         1963          785 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7383 
         358         1777         1969         1191         1036         1954 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-6935 TCGA-CV-7091 TCGA-CV-7101 
         907         1955         3295         1969         1959         1939 
TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7422 
        1945         1095          954          797         1967         1957 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1973         1972         1981         5480         1960         1940 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A74Q TCGA-DQ-7588 
         773          701          154          376          338         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-7774 
         575          299          368          585            3          407 
TCGA-HD-7753 TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
           5          111          552           14          392           56 
TCGA-MT-A67G TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A8ZA TCGA-UF-A71E TCGA-UF-A7J9 
         112         1968          245          135         1278         1043 
TCGA-UF-A7JH 
         665 

$`AMP PEAK 19(12Q15) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
         623         1636          190          644          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
         236          895          855          622          918          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
         216          182         1976          314          142          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-7866 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 
         687          638          428         1955          624            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         799          721          142          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         642         1250          395         1960          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1988         1007          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          683          290 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
          98         1970          202          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
         429           46          443          645          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         707          893          998          391          303          950 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
        2562         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-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1956         1435         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-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-5431 TCGA-CV-5432 
         181         1077          911         1472          522         1950 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         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-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        1478         1840          215         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1899         1970         1948         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-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 
        3837         1970         1970         1936         1959         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1979         1952         1444         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7432 
        1974         1948         1955         1947         1937         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A460 
        1984         1958         1959          851         1945         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          317          321          237          828 
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-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         539          483          232          435          424          368 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         389         1778         1081          516         1030          548 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         775          622          369          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W 
         490          658           15           92          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          13            6           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         206            2           25           37           55           44 
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-KU-A6H7 
         412          440          351          360          224          378 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         168           34          111          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1726         1559         1120         1954          578         1917 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          357          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
         387          567          198          149          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA 
         168         1326         1663         1319         1252         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          214          413 

  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                           3                            2 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                        5480                         3837 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         797                          683 
[1] "3.0 - 5480.0 (797.0)" "2.0 - 3837.0 (683.0)"
[1] "hr=" "1.4"
D19V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 19(12Q15) MUTATED         9       14        14        43         2
  AMP PEAK 19(12Q15) WILD-TYPE      17       61        60       192        10
                              vv
clus                           STAGE IVC
  AMP PEAK 19(12Q15) MUTATED           0
  AMP PEAK 19(12Q15) WILD-TYPE         1
D19V3, multiclass
           clus
vv          AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  STAGE I                            9                           17
  STAGE II                          14                           61
  STAGE III                         14                           60
  STAGE IVA                         43                          192
  STAGE IVB                          2                           10
  STAGE IVC                          0                            1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 19(12Q15) MUTATED      12  24  15  32
  AMP PEAK 19(12Q15) WILD-TYPE    35 103  79 130
D19V4, multiclass
       clus
vv      AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  T0+T1                         12                           35
  T2                            24                          103
  T3                            15                           79
  T4                            32                          130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 19(12Q15) MUTATED    42   9  24   1
  AMP PEAK 19(12Q15) WILD-TYPE 128  54 128   7
D19V5, multiclass
    clus
vv   AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  N0                         42                          128
  N1                          9                           54
  N2                         24                          128
  N3                          1                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1  MX
  AMP PEAK 19(12Q15) MUTATED    28   0  10
  AMP PEAK 19(12Q15) WILD-TYPE 139   1  48
D19V6, multiclass
    clus
vv   AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  M0                         28                          139
  M1                          0                            1
  MX                         10                           48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED    26  68
  AMP PEAK 19(12Q15) WILD-TYPE 106 288
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED     26   68
  AMP PEAK 19(12Q15) WILD-TYPE  106  288
        clus
vv       AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  FEMALE                         26                          106
  MALE                           68                          288
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(12Q15) MUTATED                                      93
  AMP PEAK 19(12Q15) WILD-TYPE                                   384
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 19(12Q15) MUTATED                                                             0
  AMP PEAK 19(12Q15) WILD-TYPE                                                           1
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 19(12Q15) MUTATED                                                     1
  AMP PEAK 19(12Q15) WILD-TYPE                                                   9
D19V8, multiclass
                                                             clus
vv                                                            AMP PEAK 19(12Q15) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               93
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  1
                                                             clus
vv                                                            AMP PEAK 19(12Q15) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                384
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    9
[1] 3 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(12Q15) MUTATED    19  75
  AMP PEAK 19(12Q15) WILD-TYPE  60 334
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED     19   75
  AMP PEAK 19(12Q15) WILD-TYPE   60  334
     clus
vv    AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  NO                          19                           60
  YES                         75                          334
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(12Q15) MUTATED                                  2     2
  AMP PEAK 19(12Q15) WILD-TYPE                                0     9
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(12Q15) MUTATED                           8    79
  AMP PEAK 19(12Q15) WILD-TYPE                        36   336
D19V12, multiclass
                                  clus
vv                                 AMP PEAK 19(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    79
                                  clus
vv                                 AMP PEAK 19(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                     336
[1] 4 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(12Q15) MUTATED     4  81
  AMP PEAK 19(12Q15) WILD-TYPE  20 350
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED      4   81
  AMP PEAK 19(12Q15) WILD-TYPE   20  350
                        clus
vv                       AMP PEAK 19(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         81
                        clus
vv                       AMP PEAK 19(12Q15) WILD-TYPE
  HISPANIC OR LATINO                               20
  NOT HISPANIC OR LATINO                          350
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(13Q22.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(13Q22.1) MUTATED    53  26
  AMP PEAK 20(13Q22.1) WILD-TYPE 248  87
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                            79                            335 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                            26                             87 
$`AMP PEAK 20(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         1151          392          395          625 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6989 
         811         1268         1988         1975          628          611 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         432          429          904          526          484          348 
TCGA-CN-A63Y TCGA-CQ-6227 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4CH TCGA-CR-5247 
         175         1959         1007         1950          303          358 
TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
        1050          354          379         1191         1440         1960 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 
         105          759           30          907         1955          522 
TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        1978         1665         1970         3837         1970         1970 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7261 
        1959         1945         1987          954         1967         1099 
TCGA-CV-7424 TCGA-CV-7440 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4Z9 
        1947         1981          828          701          128          539 
TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 
         368         1778          516          548         1965          622 
TCGA-DQ-7592 TCGA-F7-A50J TCGA-HD-7753 TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X 
         299          585            5          360           14           34 
TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-UF-A719 TCGA-UF-A7JA TCGA-UF-A7JC 
        1968          228          198         1663         1894          484 
TCGA-UF-A7JH 
         665 

$`AMP PEAK 20(13Q22.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          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-6872 TCGA-BA-6873 
        1636         1747          190          644          384          113 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         236          855          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
         216          182         1976          314          623          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         187         2878          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-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 
        1230          817          993          642         1250         1960 
TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1330         1007         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1977         1980         1966         1966          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          933          629          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         318          394          735           46          443          535 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         391          645          225          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        1057          985         1959         1179         1750         1560 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309         1274          877         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         707         1963          893          998          785          391 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         2562         1663         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-6487 TCGA-CR-6491 TCGA-CR-6492 
         362          311          345          234          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 
        1956         1435         1245         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-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-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1472         1950         3295         1438          584          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-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-6935 TCGA-CV-6936 TCGA-CV-6941 
         641         1899         1948         1969         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-7091 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 
        1959         1959         1936         1939         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 
        1444         1095          797         1960         1976         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1957         1937         1973         1972 
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-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
         317          321          237          773          292           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EK 
         491          154          568          106          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
         232          435          424          389          338         1081 
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-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
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-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
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-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-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         392           56          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1726         1559         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-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         225          387          567          149          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         157          168         1326         1319         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1043          735         1497          214          413 

  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                             5                              2 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                          3837                           5480 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                           628                            714 
[1] "5.0 - 3837.0 (628.0)" "2.0 - 5480.0 (714.0)"
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 20(13Q22.1) MUTATED         3       16        14        49         2
  AMP PEAK 20(13Q22.1) WILD-TYPE      23       59        60       186        10
                                vv
clus                             STAGE IVC
  AMP PEAK 20(13Q22.1) MUTATED           0
  AMP PEAK 20(13Q22.1) WILD-TYPE         1
D20V3, multiclass
           clus
vv          AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  STAGE I                              3                             23
  STAGE II                            16                             59
  STAGE III                           14                             60
  STAGE IVA                           49                            186
  STAGE IVB                            2                             10
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 20(13Q22.1) MUTATED       5  24  23  33
  AMP PEAK 20(13Q22.1) WILD-TYPE    42 103  71 129
D20V4, multiclass
       clus
vv      AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  T0+T1                            5                             42
  T2                              24                            103
  T3                              23                             71
  T4                              33                            129
[1] 4 2
[1] TRUE
[1] "dimension 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(13Q22.1) MUTATED    31  12  33   0
  AMP PEAK 20(13Q22.1) WILD-TYPE 139  51 119   8
D20V5, multiclass
    clus
vv   AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  N0                           31                            139
  N1                           12                             51
  N2                           33                            119
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 20(13Q22.1) MUTATED    29   0  10
  AMP PEAK 20(13Q22.1) WILD-TYPE 138   1  48
D20V6, multiclass
    clus
vv   AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  M0                           29                            138
  M1                            0                              1
  MX                           10                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q22.1) MUTATED    25  75
  AMP PEAK 20(13Q22.1) WILD-TYPE 107 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED     25   75
  AMP PEAK 20(13Q22.1) WILD-TYPE  107  281
        clus
vv       AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  FEMALE                           25                            107
  MALE                             75                            281
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(13Q22.1) MUTATED                                      99
  AMP PEAK 20(13Q22.1) WILD-TYPE                                   378
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 20(13Q22.1) MUTATED                                                             0
  AMP PEAK 20(13Q22.1) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 20(13Q22.1) MUTATED                                                     1
  AMP PEAK 20(13Q22.1) WILD-TYPE                                                   9
D20V8, multiclass
                                                             clus
vv                                                            AMP PEAK 20(13Q22.1) 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                                                            AMP PEAK 20(13Q22.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  378
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      9
[1] 3 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(13Q22.1) MUTATED    22  78
  AMP PEAK 20(13Q22.1) WILD-TYPE  57 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED     22   78
  AMP PEAK 20(13Q22.1) WILD-TYPE   57  331
     clus
vv    AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  NO                            22                             57
  YES                           78                            331
[1] 2 2
[1] FALSE
D20V10, continuous
D20V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(13Q22.1) MUTATED                                  1     4
  AMP PEAK 20(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(13Q22.1) MUTATED                           9    82
  AMP PEAK 20(13Q22.1) WILD-TYPE                        35   333
D20V12, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      82
                                  clus
vv                                 AMP PEAK 20(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       333
[1] 4 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(13Q22.1) MUTATED     7  84
  AMP PEAK 20(13Q22.1) WILD-TYPE  17 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED      7   84
  AMP PEAK 20(13Q22.1) WILD-TYPE   17  347
                        clus
vv                       AMP PEAK 20(13Q22.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       AMP PEAK 20(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(13Q34) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(13Q34) MUTATED    52  23
  AMP PEAK 21(13Q34) WILD-TYPE 249  90
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                          75                          339 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                          23                           90 
$`AMP PEAK 21(13Q34) MUTATED`
TCGA-BA-4075 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-4225 
         283          451          895          623          278          140 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5358 
         142         1151          392          625         1988          173 
TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6997 
        1975          628           98          611          432          429 
TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5329 TCGA-CQ-6228 
         904          484          348          175         1422         1959 
TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1950         1960          707         1963          303          950 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 
         358         1663         1777          354          379         1191 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7392 
        1440          105          759         1951          907          946 
TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6961 TCGA-CV-7090 
         522         1978          519         1665         1959         3837 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7243 TCGA-CV-7424 TCGA-CV-7440 TCGA-CV-A45R 
        1970         1970          954         1947         1981         5480 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A6EQ TCGA-D6-A6ES 
         828          292          701          128          368          389 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J TCGA-HD-8314 TCGA-IQ-7630 
         516          548         1965          585           44          485 
TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8ZA 
         360           14           34         1968          228          135 
TCGA-UF-A719 TCGA-UF-A7JC TCGA-UF-A7JH 
        1663          484          665 

$`AMP PEAK 21(13Q34) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          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-6871 TCGA-BA-6872 
        1636         1747          190          644           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         113          236          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP 
         351          216          182         1976          314          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         187         2878          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 
        1955          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1157         1230          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
         395         1960         1330          811         1268         1007 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1045         1980         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1966          683          290          630          933          629 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
         594          629           45          432         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6998 
        1110          224          318          394          735           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          535          391          645          225          526 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
        1253         1000         1057          985         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1750         1560         1007          509         1309         1274 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         877         1353          893          998          785          391 
TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        2562         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-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         345          234          350          479         1956         1435 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1245         1960         1979          889           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-7389 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         392          913          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-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-5970 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958         2437          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840          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-6954 TCGA-CV-6960 TCGA-CV-7091 
        1948         1969         1966         1957         1969         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-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1952         1444         1095          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         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-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1959          851         1945         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
         685         1950          317          321          237          773 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
          77          491          154          568          106          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q 
         376          483          232          435          424          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1778         1081         1030          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         1131 
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-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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            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-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
          10          111           33         1057          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-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         552          378          168          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         112          254          240          910         1726         1559 
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 TCGA-QK-A6V9 
         357          245          218          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         198          149          135          157          168         1326 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
        1319         1252         1278         1043         1894          735 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          214          413 

  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                          14                            2 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                        5480                         3835 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                         625                          722 
[1] "14.0 - 5480.0 (625.0)" "2.0 - 3835.0 (722.0)" 
[1] "hr=" "1"  
D21V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 21(13Q34) MUTATED         2       18        21        42         2
  AMP PEAK 21(13Q34) WILD-TYPE      24       57        53       193        10
                              vv
clus                           STAGE IVC
  AMP PEAK 21(13Q34) MUTATED           0
  AMP PEAK 21(13Q34) WILD-TYPE         1
D21V3, multiclass
           clus
vv          AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  STAGE I                            2                           24
  STAGE II                          18                           57
  STAGE III                         21                           53
  STAGE IVA                         42                          193
  STAGE IVB                          2                           10
  STAGE IVC                          0                            1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 21(13Q34) MUTATED       6  30  23  27
  AMP PEAK 21(13Q34) WILD-TYPE    41  97  71 135
D21V4, multiclass
       clus
vv      AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  T0+T1                          6                           41
  T2                            30                           97
  T3                            23                           71
  T4                            27                          135
[1] 4 2
[1] TRUE
[1] "dimension 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(13Q34) MUTATED    32  18  29   0
  AMP PEAK 21(13Q34) WILD-TYPE 138  45 123   8
D21V5, multiclass
    clus
vv   AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  N0                         32                          138
  N1                         18                           45
  N2                         29                          123
  N3                          0                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1  MX
  AMP PEAK 21(13Q34) MUTATED    33   0  11
  AMP PEAK 21(13Q34) WILD-TYPE 134   1  47
D21V6, multiclass
    clus
vv   AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  M0                         33                          134
  M1                          0                            1
  MX                         11                           47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(13Q34) MUTATED    22  75
  AMP PEAK 21(13Q34) WILD-TYPE 110 281
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(13Q34) MUTATED     22   75
  AMP PEAK 21(13Q34) WILD-TYPE  110  281
        clus
vv       AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  FEMALE                         22                          110
  MALE                           75                          281
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(13Q34) MUTATED                                      95
  AMP PEAK 21(13Q34) WILD-TYPE                                   382
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 21(13Q34) MUTATED                                                             0
  AMP PEAK 21(13Q34) WILD-TYPE                                                           1
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 21(13Q34) MUTATED                                                     2
  AMP PEAK 21(13Q34) WILD-TYPE                                                   8
D21V8, multiclass
                                                             clus
vv                                                            AMP PEAK 21(13Q34) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               95
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  2
                                                             clus
vv                                                            AMP PEAK 21(13Q34) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                382
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
[1] 3 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(13Q34) MUTATED    19  78
  AMP PEAK 21(13Q34) WILD-TYPE  60 331
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(13Q34) MUTATED     19   78
  AMP PEAK 21(13Q34) WILD-TYPE   60  331
     clus
vv    AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  NO                          19                           60
  YES                         78                          331
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(13Q34) MUTATED                                  0     3
  AMP PEAK 21(13Q34) WILD-TYPE                                2     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(13Q34) MUTATED                           7    81
  AMP PEAK 21(13Q34) WILD-TYPE                        37   334
D21V12, multiclass
                                  clus
vv                                 AMP PEAK 21(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    81
                                  clus
vv                                 AMP PEAK 21(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  37
  WHITE                                                     334
[1] 4 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(13Q34) MUTATED     8  83
  AMP PEAK 21(13Q34) WILD-TYPE  16 348
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(13Q34) MUTATED      8   83
  AMP PEAK 21(13Q34) WILD-TYPE   16  348
                        clus
vv                       AMP PEAK 21(13Q34) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         83
                        clus
vv                       AMP PEAK 21(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          348
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(15Q26.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(15Q26.3) MUTATED    55  24
  AMP PEAK 22(15Q26.3) WILD-TYPE 246  89
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            79                            335 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            24                             89 
$`AMP PEAK 22(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          850 
TCGA-BA-A8YP TCGA-BB-7861 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4729 
         142          310         1955            5         1151          392 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5365 
         625         1330          811         1045         1980         1980 
TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6022 TCGA-CN-6992 TCGA-CQ-6228 
        1966          630          628          202          394         1959 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 
         509         1274          707          950          358         1971 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 
         514          354          350         1435         1191          105 
TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-7090 
          30         1036          907         1665         1948         3837 
TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 
        1939         1952         1095         1976         1099         1955 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-A6JD TCGA-CV-A6K2 TCGA-D6-6516 
        1947         1937         1984         1970         1950          773 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
         128          232          516          548         1965          575 
TCGA-F7-7848 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A633 
        1131           58            5           37           55           49 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-MT-A67A TCGA-MT-A67G 
         111           33          441          412          392          112 
TCGA-P3-A5QA TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-UF-A71E TCGA-UF-A7JF 
        1726          228          198          157         1278         1497 
TCGA-UF-A7JH 
         665 

$`AMP PEAK 22(15Q26.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         102          462          415          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-7269 TCGA-BA-A4IF 
        1747          190          644          384          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          918          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        1976          314          623          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         140          133          558          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A480 
         638         1153          428          436          624            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 
         799          721         1157          142         1230          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 
         993          642         1250          395         1960         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5367 
        1988         1007          173         1081         1977         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
        1975          683          290          933          629          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
         629           45          432           98         1970         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         224          318          611          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
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-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
        1253         1000         1057          985         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 
        1750         1560         1007         1309          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1353         1960         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         391          303         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-6487 TCGA-CR-6488 TCGA-CR-6492 
         362          311          345          234          379          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        1956         1440         1245         1960         1979          759 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         889          972         1968          796         1954          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-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         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-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1970         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
        1969         1966         1957         1969         1959         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 
        1970         1970         1936         1959         1945         1987 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1979         1444          954          797         1967         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1974         1948         1957         1973         1972         1937 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1958         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1960         1940         1946         1954         1722         1977 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         714          606          685          317          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         828          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         568          106          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1030          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         324          340          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-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
         407          133          414          403          206            2 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
          25           44           24           25           11           10 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J 
        1057          485          122          588          360          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-MZ-A7D7 
          14           34           56          111          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1559         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 TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         225          387          567          149          135          135 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 
         168         1326         1663         1319         1252         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          484          735          214          413 

  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                             5                              2 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                          3837                           5480 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           665                            701 
[1] "5.0 - 3837.0 (665.0)" "2.0 - 5480.0 (701.0)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 22(15Q26.3) MUTATED         6       14        13        49         4
  AMP PEAK 22(15Q26.3) WILD-TYPE      20       61        61       186         8
                                vv
clus                             STAGE IVC
  AMP PEAK 22(15Q26.3) MUTATED           0
  AMP PEAK 22(15Q26.3) WILD-TYPE         1
D22V3, multiclass
           clus
vv          AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  STAGE I                              6                             20
  STAGE II                            14                             61
  STAGE III                           13                             61
  STAGE IVA                           49                            186
  STAGE IVB                            4                              8
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 22(15Q26.3) MUTATED       9  24  12  41
  AMP PEAK 22(15Q26.3) WILD-TYPE    38 103  82 121
D22V4, multiclass
       clus
vv      AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  T0+T1                            9                             38
  T2                              24                            103
  T3                              12                             82
  T4                              41                            121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 22(15Q26.3) MUTATED    32  13  28   2
  AMP PEAK 22(15Q26.3) WILD-TYPE 138  50 124   6
D22V5, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  N0                           32                            138
  N1                           13                             50
  N2                           28                            124
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 22(15Q26.3) MUTATED    32   0  11
  AMP PEAK 22(15Q26.3) WILD-TYPE 135   1  47
D22V6, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  M0                           32                            135
  M1                            0                              1
  MX                           11                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED    29  69
  AMP PEAK 22(15Q26.3) WILD-TYPE 103 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED     29   69
  AMP PEAK 22(15Q26.3) WILD-TYPE  103  287
        clus
vv       AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  FEMALE                           29                            103
  MALE                             69                            287
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(15Q26.3) MUTATED                                      94
  AMP PEAK 22(15Q26.3) WILD-TYPE                                   383
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 22(15Q26.3) MUTATED                                                             0
  AMP PEAK 22(15Q26.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 22(15Q26.3) MUTATED                                                     4
  AMP PEAK 22(15Q26.3) WILD-TYPE                                                   6
D22V8, multiclass
                                                             clus
vv                                                            AMP PEAK 22(15Q26.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 94
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            AMP PEAK 22(15Q26.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  383
  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"
D22V9, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED    17  81
  AMP PEAK 22(15Q26.3) WILD-TYPE  62 328
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED     17   81
  AMP PEAK 22(15Q26.3) WILD-TYPE   62  328
     clus
vv    AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  NO                            17                             62
  YES                           81                            328
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(15Q26.3) MUTATED                                  0     3
  AMP PEAK 22(15Q26.3) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(15Q26.3) MUTATED                          11    79
  AMP PEAK 22(15Q26.3) WILD-TYPE                        33   336
D22V12, multiclass
                                  clus
vv                                 AMP PEAK 22(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      79
                                  clus
vv                                 AMP PEAK 22(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    33
  WHITE                                                       336
[1] 4 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(15Q26.3) MUTATED     4  85
  AMP PEAK 22(15Q26.3) WILD-TYPE  20 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED      4   85
  AMP PEAK 22(15Q26.3) WILD-TYPE   20  346
                        clus
vv                       AMP PEAK 22(15Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       AMP PEAK 22(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            346
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(17Q12) MUTATION ANALYSIS
D23V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 23(17Q12) MUTATED    50  17
  AMP PEAK 23(17Q12) WILD-TYPE 251  96
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          67                          347 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          17                           96 
$`AMP PEAK 23(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         1045         1966         1110          318          611 
TCGA-CN-6994 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-6228 TCGA-CQ-7069 
         735          645          526          348         1959         1274 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 
        1950          707          785          358         1777         1969 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7399 
         379         1191          105         1954          907          181 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 
        1955          522         1950         1978          406         1840 
TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7248 
        1665         1959         1969         1939         1945         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7424 TCGA-CV-A45R TCGA-CV-A6JZ 
        1960         1976         1099         1947         5480          714 
TCGA-D6-8569 TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
         128          424          389          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 TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71E 
          56          218          198          168         1663         1278 
TCGA-UF-A7JH 
         665 

$`AMP PEAK 23(17Q12) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
          63          113          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 
         142          187         2878          278          558          310 
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-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         436         1955            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988         1007          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1081         1977         1980         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         629           45          432           98         1970          202 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         224          394          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
         535          391          904          225          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877         1353         1960         1963          893          998 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         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         1952         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-A45Y TCGA-CV-A45Z 
        1959         1981          851         1945         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 
         906         1959          670          110          646          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          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-D6-A6EK TCGA-D6-A6EM 
         568          106          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         435          368          338         1778         1081         1030 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         548          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         324          340         1131          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-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         224          552          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392          111          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1726         1559         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
        1968          400          553          357          245          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         225          387          567          149          135          135 
TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA 
         157         1326         1319         1252         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          214          413 

  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                           5                            2 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                        5480                         3837 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                         707                          701 
[1] "5.0 - 5480.0 (707.0)" "2.0 - 3837.0 (701.0)"
[1] "hr=" "1"  
D23V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 23(17Q12) MUTATED         3       13        18        38         0
  AMP PEAK 23(17Q12) WILD-TYPE      23       62        56       197        12
                              vv
clus                           STAGE IVC
  AMP PEAK 23(17Q12) MUTATED           1
  AMP PEAK 23(17Q12) WILD-TYPE         0
D23V3, multiclass
           clus
vv          AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  STAGE I                            3                           23
  STAGE II                          13                           62
  STAGE III                         18                           56
  STAGE IVA                         38                          197
  STAGE IVB                          0                           12
  STAGE IVC                          1                            0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  AMP PEAK 23(17Q12) MUTATED       4  23  21  25
  AMP PEAK 23(17Q12) WILD-TYPE    43 104  73 137
D23V4, multiclass
       clus
vv      AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  T0+T1                          4                           43
  T2                            23                          104
  T3                            21                           73
  T4                            25                          137
[1] 4 2
[1] TRUE
[1] "dimension 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(17Q12) MUTATED    30  12  28   0
  AMP PEAK 23(17Q12) WILD-TYPE 140  51 124   8
D23V5, multiclass
    clus
vv   AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  N0                         30                          140
  N1                         12                           51
  N2                         28                          124
  N3                          0                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1  MX
  AMP PEAK 23(17Q12) MUTATED    30   1   9
  AMP PEAK 23(17Q12) WILD-TYPE 137   0  49
D23V6, multiclass
    clus
vv   AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  M0                         30                          137
  M1                          1                            0
  MX                          9                           49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                              cls
clus                             0   1
  AMP PEAK 23(17Q12) MUTATED    17  68
  AMP PEAK 23(17Q12) WILD-TYPE 115 288
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED     17   68
  AMP PEAK 23(17Q12) WILD-TYPE  115  288
        clus
vv       AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  FEMALE                         17                          115
  MALE                           68                          288
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(17Q12) MUTATED                                      82
  AMP PEAK 23(17Q12) WILD-TYPE                                   395
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 23(17Q12) MUTATED                                                             1
  AMP PEAK 23(17Q12) WILD-TYPE                                                           0
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 23(17Q12) MUTATED                                                     2
  AMP PEAK 23(17Q12) WILD-TYPE                                                   8
D23V8, multiclass
                                                             clus
vv                                                            AMP PEAK 23(17Q12) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               82
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  2
                                                             clus
vv                                                            AMP PEAK 23(17Q12) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                395
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
[1] 3 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(17Q12) MUTATED    12  73
  AMP PEAK 23(17Q12) WILD-TYPE  67 336
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED     12   73
  AMP PEAK 23(17Q12) WILD-TYPE   67  336
     clus
vv    AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  NO                          12                           67
  YES                         73                          336
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(17Q12) MUTATED                                  0     2
  AMP PEAK 23(17Q12) WILD-TYPE                                2     9
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(17Q12) MUTATED                           9    71
  AMP PEAK 23(17Q12) WILD-TYPE                        35   344
D23V12, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 9
  WHITE                                                    71
                                  clus
vv                                 AMP PEAK 23(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  35
  WHITE                                                     344
[1] 4 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(17Q12) MUTATED     8  71
  AMP PEAK 23(17Q12) WILD-TYPE  16 360
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED      8   71
  AMP PEAK 23(17Q12) WILD-TYPE   16  360
                        clus
vv                       AMP PEAK 23(17Q12) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         71
                        clus
vv                       AMP PEAK 23(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          360
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(18P11.31) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(18P11.31) MUTATED    85  37
  AMP PEAK 24(18P11.31) WILD-TYPE 216  76
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                            122                             292 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                             37                              76 
$`AMP PEAK 24(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-BA-A4IG TCGA-BA-A6DL 
         644           63          384          113          855          623 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          278          140          558          310          536 
TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 
        1153          624            5         1157         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5363 TCGA-CN-5366 
         392          817          395          625         1977         1966 
TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
        1966          629           98          202          224          318 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6227 
         225          526          348          367          317         1959 
TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 
         509         1950          707          391          358         1777 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
        1971         1969          345         1956         1435         1191 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         105          759          907          181         1077          911 
TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1472         1950         3295          546         1978         2886 
TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 
         519         2641         1840         1315          641         1970 
TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1969         1959         1969         1939         1945         1987 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7434 
        1952          954          797         1955         1957         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Z TCGA-CV-A461 TCGA-CX-7086 TCGA-D6-6823 
        1959         1981         1940         1954          237          701 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5631 
         106          128          435          424          338          548 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7595 TCGA-F7-8298 TCGA-F7-A623 TCGA-H7-8502 
        1965          775          324          490            6          133 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ 
         403          206           25           44           10          111 
TCGA-IQ-A61G TCGA-KU-A66S TCGA-KU-A66T TCGA-MZ-A7D7 TCGA-QK-A8Z7 TCGA-QK-A8ZA 
         360          224          552          240          198          135 
TCGA-QK-A8ZB TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
         135         1663         1252         1278         1894          735 
TCGA-UF-A7JF TCGA-UF-A7JS 
        1497          413 

$`AMP PEAK 24(18P11.31) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 
         102          462         1983          276          248         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 
        1762          725          623          190          451          236 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4227 
         182         1976          314          142          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 
        1250         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1007         1045          173         1980         1081         1980 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1975          683          290          630          933          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
         594          629           45          432         1970         1110 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V 
         443          535          391          904          645          484 
TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         175          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422         1393         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000         1057          985         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1750         1560         1007         1309         1274          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1353         1960         1963          893          998          785 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          950         2562         1663         1152          799 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 
        1521         1966         1050         1125          514          362 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          354          234          379          350          479 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
        1440         1245         1960         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-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-CV-5430 TCGA-CV-5431 
         898          930          216          156         1955          522 
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-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6934 
         701         1478          215         1665         1899         1948 
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-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 
        1959         1979         1444         1095         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 
        1976         1099         1974         1948         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q 
        1973         1972         1937         1984          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        5480         1960         1946         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          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-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ 
         568          539          376          483          232          368 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 
         389         1778         1081          516         1030          575 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 
         622          299          369          368          340         1131 
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-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-HD-7229 
          14           13          407           58          414            2 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
           5           37           55           24           25           11 
TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          49           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 
         588          412          440          351          360          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           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         1726         1559         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          387 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B 
         567          149          157          168         1326         1319 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JJ 
        1043          484          665          214 

  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                              5                               2 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                           3295                            5480 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                          642.5                           717.5 
[1] "5.0 - 3295.0 (642.5)" "2.0 - 5480.0 (717.5)"
[1] "hr=" "1.1"
D24V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 24(18P11.31) MUTATED         4       16        26        73
  AMP PEAK 24(18P11.31) WILD-TYPE      22       59        48       162
                                 vv
clus                              STAGE IVB STAGE IVC
  AMP PEAK 24(18P11.31) MUTATED           2         1
  AMP PEAK 24(18P11.31) WILD-TYPE        10         0
D24V3, multiclass
           clus
vv          AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  STAGE I                               4                              22
  STAGE II                             16                              59
  STAGE III                            26                              48
  STAGE IVA                            73                             162
  STAGE IVB                             2                              10
  STAGE IVC                             1                               0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  AMP PEAK 24(18P11.31) MUTATED      12  30  36  47
  AMP PEAK 24(18P11.31) WILD-TYPE    35  97  58 115
D24V4, multiclass
       clus
vv      AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  T0+T1                            12                              35
  T2                               30                              97
  T3                               36                              58
  T4                               47                             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
  AMP PEAK 24(18P11.31) MUTATED    44  20  51   2
  AMP PEAK 24(18P11.31) WILD-TYPE 126  43 101   6
D24V5, multiclass
    clus
vv   AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  N0                            44                             126
  N1                            20                              43
  N2                            51                             101
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  AMP PEAK 24(18P11.31) MUTATED    40   1  18
  AMP PEAK 24(18P11.31) WILD-TYPE 127   0  40
D24V6, multiclass
    clus
vv   AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  M0                            40                             127
  M1                             1                               0
  MX                            18                              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(18P11.31) MUTATED    23 121
  AMP PEAK 24(18P11.31) WILD-TYPE 109 235
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(18P11.31) MUTATED     23  121
  AMP PEAK 24(18P11.31) WILD-TYPE  109  235
        clus
vv       AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  FEMALE                            23                             109
  MALE                             121                             235
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(18P11.31) MUTATED                                     140
  AMP PEAK 24(18P11.31) WILD-TYPE                                   337
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 24(18P11.31) MUTATED                                                             0
  AMP PEAK 24(18P11.31) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 24(18P11.31) MUTATED                                                     4
  AMP PEAK 24(18P11.31) WILD-TYPE                                                   6
D24V8, multiclass
                                                             clus
vv                                                            AMP PEAK 24(18P11.31) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 140
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
                                                             clus
vv                                                            AMP PEAK 24(18P11.31) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   337
  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"
D24V9, binary
                                 cls
clus                                0   1
  AMP PEAK 24(18P11.31) MUTATED    21 123
  AMP PEAK 24(18P11.31) WILD-TYPE  58 286
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(18P11.31) MUTATED     21  123
  AMP PEAK 24(18P11.31) WILD-TYPE   58  286
     clus
vv    AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  NO                             21                              58
  YES                           123                             286
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(18P11.31) MUTATED                                  0     1
  AMP PEAK 24(18P11.31) WILD-TYPE                                2    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(18P11.31) MUTATED                          17   121
  AMP PEAK 24(18P11.31) WILD-TYPE                        27   294
D24V12, multiclass
                                  clus
vv                                 AMP PEAK 24(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      121
                                  clus
vv                                 AMP PEAK 24(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        294
[1] 4 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(18P11.31) MUTATED     5 128
  AMP PEAK 24(18P11.31) WILD-TYPE  19 303
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(18P11.31) MUTATED      5  128
  AMP PEAK 24(18P11.31) WILD-TYPE   19  303
                        clus
vv                       AMP PEAK 24(18P11.31) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           128
                        clus
vv                       AMP PEAK 24(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                  19
  NOT HISPANIC OR LATINO                             303
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(18Q11.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(18Q11.2) MUTATED    62  22
  AMP PEAK 25(18Q11.2) WILD-TYPE 239  91
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            84                            330 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            22                             91 
$`AMP PEAK 25(18Q11.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 
         102          462          283          415          722          520 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DL 
        1636         1747          895          855          918          623 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
         142         2878          278          140          558          310 
TCGA-CN-4723 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5367 TCGA-CN-6012 
         721          817          395          625         1966          629 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-7064 
          98          202          224          348          367         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6482 TCGA-CR-7367 
        1007          509          358         1777          345         1440 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7398 
         105          759           30         1954          907          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 
         181         1077         1472         1950         3295          546 
TCGA-CV-5440 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6941 TCGA-CV-6954 
        1978         1840         1315          641         1959         1957 
TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7406 TCGA-CV-7418 
        3837         1970         1939         1987         1974         1955 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CX-7219 TCGA-D6-A6EO TCGA-D6-A6ES TCGA-DQ-7589 
        1940         1954          828          435          389          575 
TCGA-DQ-7590 TCGA-H7-A76A TCGA-HD-7917 TCGA-HD-A634 TCGA-IQ-7630 TCGA-IQ-A61O 
         775          206           37           10          485          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-QK-A64Z TCGA-QK-A6IG 
         224          552           34          240          553          218 
TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
         198          135         1319         1278         1043         1894 

$`AMP PEAK 25(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-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         113          236          622          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7862 
         182         1976          314          187          133          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-4725 
        1955          624            5            4          799         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
         142         1230         1151          392          993          642 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
        1250         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1007         1045          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1980         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          628          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1970         1110          318          611          394          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         904          645          225          526          484          175 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1179         1750         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1353         1960          707         1963          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         785          391          303          950         2562         1663 
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-6484 
        1971          514         1969          362          311          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-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 
        1191         1245         1960         1979          889          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-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
         216          911         1955          522         1438          584 
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-5978 TCGA-CV-6003 TCGA-CV-6436 
         701         2641         1478          215         1665         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1969         1952         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1969         1966         1969         1959         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1936         1959         1945         1979         1952         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-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1099         1948         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A464 
         851         1945         5480         1960         1946         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         317          321          237          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-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ 
         539          376          483          232          424          368 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         338         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
        1965          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          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-H7-A6C5 TCGA-HD-7229 
         407           58          133          414          403            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
           5           25           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          11           49          111           33         1057          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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         378          168           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         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 
        1954          578         1917         1968          400          357 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 
         245          228          225          387          567          149 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D 
         135          157          168         1326         1663         1252 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          665          214          413 

  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            10                              2 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                          3837                           5480 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                         627.0                          710.5 
[1] "10.0 - 3837.0 (627.0)" "2.0 - 5480.0 (710.5)" 
[1] "hr=" "1"  
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 25(18Q11.2) MUTATED         4       15        10        51         1
  AMP PEAK 25(18Q11.2) WILD-TYPE      22       60        64       184        11
                                vv
clus                             STAGE IVC
  AMP PEAK 25(18Q11.2) MUTATED           1
  AMP PEAK 25(18Q11.2) WILD-TYPE         0
D25V3, multiclass
           clus
vv          AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  STAGE I                              4                             22
  STAGE II                            15                             60
  STAGE III                           10                             64
  STAGE IVA                           51                            184
  STAGE IVB                            1                             11
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 25(18Q11.2) MUTATED      11  27  14  33
  AMP PEAK 25(18Q11.2) WILD-TYPE    36 100  80 129
D25V4, multiclass
       clus
vv      AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  T0+T1                           11                             36
  T2                              27                            100
  T3                              14                             80
  T4                              33                            129
[1] 4 2
[1] TRUE
[1] "dimension 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(18Q11.2) MUTATED    30  11  32   1
  AMP PEAK 25(18Q11.2) WILD-TYPE 140  52 120   7
D25V5, multiclass
    clus
vv   AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  N0                           30                            140
  N1                           11                             52
  N2                           32                            120
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 25(18Q11.2) MUTATED    28   1  13
  AMP PEAK 25(18Q11.2) WILD-TYPE 139   0  45
D25V6, multiclass
    clus
vv   AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  M0                           28                            139
  M1                            1                              0
  MX                           13                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(18Q11.2) MUTATED    18  82
  AMP PEAK 25(18Q11.2) WILD-TYPE 114 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED     18   82
  AMP PEAK 25(18Q11.2) WILD-TYPE  114  274
        clus
vv       AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  FEMALE                           18                            114
  MALE                             82                            274
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                                      96
  AMP PEAK 25(18Q11.2) WILD-TYPE                                   381
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 25(18Q11.2) MUTATED                                                             1
  AMP PEAK 25(18Q11.2) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 25(18Q11.2) MUTATED                                                     3
  AMP PEAK 25(18Q11.2) WILD-TYPE                                                   7
D25V8, multiclass
                                                             clus
vv                                                            AMP PEAK 25(18Q11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 96
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            AMP PEAK 25(18Q11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  381
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      7
[1] 3 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(18Q11.2) MUTATED    14  86
  AMP PEAK 25(18Q11.2) WILD-TYPE  65 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED     14   86
  AMP PEAK 25(18Q11.2) WILD-TYPE   65  323
     clus
vv    AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  NO                            14                             65
  YES                           86                            323
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(18Q11.2) MUTATED                                  0     1
  AMP PEAK 25(18Q11.2) WILD-TYPE                                2    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(18Q11.2) MUTATED                          15    83
  AMP PEAK 25(18Q11.2) WILD-TYPE                        29   332
D25V12, multiclass
                                  clus
vv                                 AMP PEAK 25(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      83
                                  clus
vv                                 AMP PEAK 25(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       332
[1] 4 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(18Q11.2) MUTATED     3  91
  AMP PEAK 25(18Q11.2) WILD-TYPE  21 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED      3   91
  AMP PEAK 25(18Q11.2) WILD-TYPE   21  340
                        clus
vv                       AMP PEAK 25(18Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       AMP PEAK 25(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            340
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(19P13.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(19P13.2) MUTATED    35  10
  AMP PEAK 26(19P13.2) WILD-TYPE 266 103
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            45                            369 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            10                            103 
$`AMP PEAK 26(19P13.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-4223 
         102         1747          190          895          182         2878 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-6013 TCGA-CN-6021 
         140          310          428          624          628         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A63V TCGA-CQ-7067 TCGA-CR-6467 
        1110          224          611          484          509         1777 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5431 
         234          379          105          392         1472          522 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-7235 TCGA-CV-7254 
        1978         2327         1840         1970         1952         1976 
TCGA-CV-7261 TCGA-CV-7428 TCGA-CV-A45Z TCGA-CV-A6K2 TCGA-CX-7086 TCGA-CX-7219 
        1099         1973         1940         1950          237          828 
TCGA-DQ-5629 TCGA-F7-8298 TCGA-H7-A76A TCGA-HL-7533 TCGA-MT-A67G TCGA-P3-A5QA 
         516          490          206         1057          112         1726 
TCGA-QK-A6V9 TCGA-QK-AA3J TCGA-UF-A718 
         567          157         1326 

$`AMP PEAK 26(19P13.2) 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-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
        1636          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         236          855          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         216         1976          314          623          142          187 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         278          133          558          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 
         638         1153          436         1955            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         799          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1007         1045          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          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          933          629          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
         432           98          202          318          394          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
         904          645          225          526          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959         1179         1750         1560         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 
        1969          362          311          345          354          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-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-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-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
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-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2886         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        2641         1478          215         1315         1665          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-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         1959         1970         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1939         1945         1987         1979         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 
         954          797         1967         1960         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1947         1937         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-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        5480         1960         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 
         646          714          606          685          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-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         232          435          424          368          389          338 
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-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         340         1131          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-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-IQ-7630 
          11           49           10          111           33          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-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 
          14           34          392           56          111          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         240          910         1559         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 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         218          228          225          387          198          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         135          135          168         1663         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1278         1043         1894          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                           102                              2 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                          2878                           5480 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                           624                            707 
[1] "102.0 - 2878.0 (624.0)" "2.0 - 5480.0 (707.0)"  
[1] "hr=" "1.5"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 26(19P13.2) MUTATED         5        6         7        22         0
  AMP PEAK 26(19P13.2) WILD-TYPE      21       69        67       213        12
                                vv
clus                             STAGE IVC
  AMP PEAK 26(19P13.2) MUTATED           0
  AMP PEAK 26(19P13.2) WILD-TYPE         1
D26V3, multiclass
           clus
vv          AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  STAGE I                              5                             21
  STAGE II                             6                             69
  STAGE III                            7                             67
  STAGE IVA                           22                            213
  STAGE IVB                            0                             12
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  AMP PEAK 26(19P13.2) MUTATED       8   8  10  14
  AMP PEAK 26(19P13.2) WILD-TYPE    39 119  84 148
D26V4, multiclass
       clus
vv      AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  T0+T1                            8                             39
  T2                               8                            119
  T3                              10                             84
  T4                              14                            148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 26(19P13.2) MUTATED    15   5  18   0
  AMP PEAK 26(19P13.2) WILD-TYPE 155  58 134   8
D26V5, multiclass
    clus
vv   AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  N0                           15                            155
  N1                            5                             58
  N2                           18                            134
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  AMP PEAK 26(19P13.2) MUTATED    13   0   8
  AMP PEAK 26(19P13.2) WILD-TYPE 154   1  50
D26V6, multiclass
    clus
vv   AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  M0                           13                            154
  M1                            0                              1
  MX                            8                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(19P13.2) MUTATED     9  44
  AMP PEAK 26(19P13.2) WILD-TYPE 123 312
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19P13.2) MUTATED      9   44
  AMP PEAK 26(19P13.2) WILD-TYPE  123  312
        clus
vv       AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  FEMALE                            9                            123
  MALE                             44                            312
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(19P13.2) MUTATED                                      52
  AMP PEAK 26(19P13.2) WILD-TYPE                                   425
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  AMP PEAK 26(19P13.2) MUTATED                                                             0
  AMP PEAK 26(19P13.2) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 26(19P13.2) MUTATED                                                     1
  AMP PEAK 26(19P13.2) WILD-TYPE                                                   9
D26V8, multiclass
                                                             clus
vv                                                            AMP PEAK 26(19P13.2) 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                                    1
                                                             clus
vv                                                            AMP PEAK 26(19P13.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  425
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      9
[1] 3 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(19P13.2) MUTATED     9  44
  AMP PEAK 26(19P13.2) WILD-TYPE  70 365
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19P13.2) MUTATED      9   44
  AMP PEAK 26(19P13.2) WILD-TYPE   70  365
     clus
vv    AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  NO                             9                             70
  YES                           44                            365
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(19P13.2) MUTATED                                  0     0
  AMP PEAK 26(19P13.2) WILD-TYPE                                2    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19P13.2) MUTATED                           7    45
  AMP PEAK 26(19P13.2) WILD-TYPE                        37   370
D26V12, multiclass
                                  clus
vv                                 AMP PEAK 26(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      45
                                  clus
vv                                 AMP PEAK 26(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       370
[1] 4 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(19P13.2) MUTATED     3  48
  AMP PEAK 26(19P13.2) WILD-TYPE  21 383
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19P13.2) MUTATED      3   48
  AMP PEAK 26(19P13.2) WILD-TYPE   21  383
                        clus
vv                       AMP PEAK 26(19P13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       AMP PEAK 26(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            383
[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   111  38
  AMP PEAK 27(20P12.2) WILD-TYPE 190  75
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           149                            265 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                            38                             75 
$`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-BA-A6DG TCGA-BB-4224 TCGA-BB-4225 
         384          236          216         1976          278          140 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 
         310          536          436            5         1151          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          642          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 
         811         1268         1988         1045         1980         1081 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
        1977         1966          290          629          628           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A63T 
         202         1110          224          318          611          225 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 
        1422         1393         1057          985         1179         1560 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
         509         1274         1353         1960          707          893 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6484 
         785          950         2562          358         1777          354 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7377 
         379         1191         1440          105          759         1968 
TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5431 
         392          946          216          181         1077          522 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
        3295         1438          584         2327         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
         406          701         2641         1840          215         1665 
TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7180 
        1952         1969         1957         3837         1970         1987 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7430 
        1952         1095          954          797         1967         1972 
TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A464 TCGA-CV-A6JE 
        1959         5480         1960         1940         1722         1075 
TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 
         906          110          646          714          606          317 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EP 
         773          292          491          128          376          424 
TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S 
         368         1778         1965          299          585            3 
TCGA-H7-8501 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7632 
          58           44           10          111          485          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A67A TCGA-MT-A67D 
         588          360          351          552          392           56 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 
         112          254         1726          578         1968          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZA 
         245          218          225          387          198          135 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ 
        1278         1043         1894         1497          214 

$`AMP PEAK 27(20P12.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 
         102          462          283          415         1983         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
        1762          520          623         1636          644          451 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
          63          113          895          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
         850          351          182          314          623          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 
         187         2878          133          558          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 
         638         1153          428         1955          624            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
         799          721         1157          142         1230          392 
TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 
        1250         1007          173         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         683          630          933          594          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         432         1970          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         526          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 
         298         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         1253         1000         1959 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 
        1959         1750         1007         1309          877         1950 
TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
        1963          998          391          303         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-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-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 
        1979          889           30          972         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
        1954          997         1430         1951          907          913 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 
         908          898          930          156          911         1472 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
        1955         1950          546         1978         2886         1958 
TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1478         1315          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1969         1959         3835         1948         1966         1969 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1959         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1945         1979         1444         1960         1976         1099 
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-A460 TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO 
        1945         1946         1954         1977         1970         1959 
TCGA-CV-A6JT TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         670          685         1950          321          237          828 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
         701           77          154          568          106          539 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
         483          232          435          389          338         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         1131          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-H7-A76A 
           6          407          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 
           2            5           25           37           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-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
         412          440          360          224          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
          14           34          111          240          910         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH 
        1120         1954         1917          400          553          228 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         567          149          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        1663         1319         1252          484          735          665 
TCGA-UF-A7JS 
         413 

  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 
                          5480                           3835 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           707                            687 
[1] "3.0 - 5480.0 (707.0)" "2.0 - 3835.0 (687.0)"
[1] "hr=" "1.4"
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 27(20P12.2) MUTATED        10       25        35        86         5
  AMP PEAK 27(20P12.2) WILD-TYPE      16       50        39       149         7
                                vv
clus                             STAGE IVC
  AMP PEAK 27(20P12.2) MUTATED           0
  AMP PEAK 27(20P12.2) WILD-TYPE         1
D27V3, multiclass
           clus
vv          AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  STAGE I                             10                             16
  STAGE II                            25                             50
  STAGE III                           35                             39
  STAGE IVA                           86                            149
  STAGE IVB                            5                              7
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  AMP PEAK 27(20P12.2) MUTATED      20 44 35 63
  AMP PEAK 27(20P12.2) WILD-TYPE    27 83 59 99
D27V4, multiclass
       clus
vv      AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  T0+T1                           20                             27
  T2                              44                             83
  T3                              35                             59
  T4                              63                             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
  AMP PEAK 27(20P12.2) MUTATED    60  32  55   3
  AMP PEAK 27(20P12.2) WILD-TYPE 110  31  97   5
D27V5, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  N0                           60                            110
  N1                           32                             31
  N2                           55                             97
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  AMP PEAK 27(20P12.2) MUTATED   69  0 17
  AMP PEAK 27(20P12.2) WILD-TYPE 98  1 41
D27V6, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  M0                           69                             98
  M1                            0                              1
  MX                           17                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    50 131
  AMP PEAK 27(20P12.2) WILD-TYPE  82 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     50  131
  AMP PEAK 27(20P12.2) WILD-TYPE   82  225
        clus
vv       AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  FEMALE                           50                             82
  MALE                            131                            225
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                     177
  AMP PEAK 27(20P12.2) WILD-TYPE                                   300
                                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                                                     4
  AMP PEAK 27(20P12.2) WILD-TYPE                                                   6
D27V8, multiclass
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                177
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) WILD-TYPE
  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                                      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"
D27V9, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    33 148
  AMP PEAK 27(20P12.2) WILD-TYPE  46 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     33  148
  AMP PEAK 27(20P12.2) WILD-TYPE   46  261
     clus
vv    AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  NO                            33                             46
  YES                          148                            261
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(20P12.2) MUTATED                                  2     4
  AMP PEAK 27(20P12.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20P12.2) MUTATED                          15   151
  AMP PEAK 27(20P12.2) WILD-TYPE                        29   264
D27V12, multiclass
                                  clus
vv                                 AMP PEAK 27(20P12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     151
                                  clus
vv                                 AMP PEAK 27(20P12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       264
[1] 4 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    14 151
  AMP PEAK 27(20P12.2) WILD-TYPE  10 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     14  151
  AMP PEAK 27(20P12.2) WILD-TYPE   10  280
                        clus
vv                       AMP PEAK 27(20P12.2) MUTATED
  HISPANIC OR LATINO                               14
  NOT HISPANIC OR LATINO                          151
                        clus
vv                       AMP PEAK 27(20P12.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            280
[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   135  40
  AMP PEAK 28(20Q11.22) WILD-TYPE 166  73
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            175                             239 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                             40                              73 
$`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-BA-A6DG TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         216         1976         2878          278          140          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A47Z 
         310          536          687          638          436            5 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        1157         1151          817          993          642          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 
        1045         1980         1977         1966          290          933 
TCGA-CN-6013 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         628          202         1110          318          611          394 
TCGA-CN-6994 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6V3 TCGA-CQ-5329 
         735          391          225          526          298         1422 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 
        1393         1057          985         1179         1560          509 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
        1274         1950         1353         1960          707          785 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6474 
         391         2562          358         1777         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 
         514         1969          354          379         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 
        1191         1440          105          759          889         1968 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7401 
        1036         1954          392          946          216         1077 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
         911         1955         1950         3295         1438          584 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 
        2327         1958         2437          406          701         1840 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 
         215         1665          641         1952         1969         1957 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 
        1969         3837         1970         1987         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A464 
         797         1967         1976         5480         1940         1722 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1075          906          110          646          714          606 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A6EP 
         237          773          701          491          128          424 
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-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X 
         588          351          552          378           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6T0 
         392           56          112          240         1726          578 
TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
        1968          357          218          387          567          198 
TCGA-QK-A8Z9 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
         149         1252         1278         1043         1894         1497 
TCGA-UF-A7JJ 
         214 

$`AMP PEAK 28(20Q11.22) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5153 
         102          462          415         1983         1288         1762 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG 
         520          623         1636          644           63          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DJ 
         622          918          850          351          182          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7870 
         623          142          187          133          423         1153 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         428         1955          624            4          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 
         142         1230          392         1250         1007          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1081         1980         1966         1975          683          630 
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-6024 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
        1970          224          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         535          904          645          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223         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         1253         1000 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 
        1959         1959         1750         1007         1309          877 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 
        1963          893          998          303          950         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6480 
        1152          799         1521         1966         1050          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7368 
         311          345          234          350          479         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 
        1960         1979           30          972          796          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-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5439 
         930          156          181         1472          522          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
        1978         2886          519         2641         1478         1315 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 
        1899         1970         1948         1969         1959         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        1948         1966         1959         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1945         1979         1952         1444 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1960         1099         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-A45Y 
        1958         1959         1981          851         1945         1960 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT 
        1946         1954         1977         1970         1959          670 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 
         685         1950          317          321          828          292 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
          77          154          568          106          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         483          232          435          368          389          338 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 
        1081          516         1030          775          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         324          340         1131          658           15           92 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C4 
         384           14           13          407          133          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8634 
         403          206            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-KU-A6H8 
         360          412          440          360          224          168 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         111          254          910         1559         1120         1954 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
        1917          400          553          245          228          225 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         135          135          157          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS 
        1319          484          735          665          413 

  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 
                           5480                            3835 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            707                             683 
[1] "3.0 - 5480.0 (707.0)" "2.0 - 3835.0 (683.0)"
[1] "hr=" "1.6"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 28(20Q11.22) MUTATED        15       31        37        95
  AMP PEAK 28(20Q11.22) WILD-TYPE      11       44        37       140
                                 vv
clus                              STAGE IVB STAGE IVC
  AMP PEAK 28(20Q11.22) MUTATED           7         0
  AMP PEAK 28(20Q11.22) WILD-TYPE         5         1
D28V3, multiclass
           clus
vv          AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  STAGE I                              15                              11
  STAGE II                             31                              44
  STAGE III                            37                              37
  STAGE IVA                            95                             140
  STAGE IVB                             7                               5
  STAGE IVC                             0                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  AMP PEAK 28(20Q11.22) MUTATED      26 50 41 69
  AMP PEAK 28(20Q11.22) WILD-TYPE    21 77 53 93
D28V4, multiclass
       clus
vv      AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  T0+T1                            26                              21
  T2                               50                              77
  T3                               41                              53
  T4                               69                              93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2 N3
  AMP PEAK 28(20Q11.22) MUTATED   75 28 63  4
  AMP PEAK 28(20Q11.22) WILD-TYPE 95 35 89  4
D28V5, multiclass
    clus
vv   AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  N0                            75                              95
  N1                            28                              35
  N2                            63                              89
  N3                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 MX
  AMP PEAK 28(20Q11.22) MUTATED   77  0 20
  AMP PEAK 28(20Q11.22) WILD-TYPE 90  1 38
D28V6, multiclass
    clus
vv   AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  M0                            77                              90
  M1                             0                               1
  MX                            20                              38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.22) MUTATED    56 157
  AMP PEAK 28(20Q11.22) WILD-TYPE  76 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     56  157
  AMP PEAK 28(20Q11.22) WILD-TYPE   76  199
        clus
vv       AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  FEMALE                            56                              76
  MALE                             157                             199
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.22) MUTATED                                     210
  AMP PEAK 28(20Q11.22) WILD-TYPE                                   267
                                 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                                                     3
  AMP PEAK 28(20Q11.22) WILD-TYPE                                                   7
D28V8, multiclass
                                                             clus
vv                                                            AMP PEAK 28(20Q11.22) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 210
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     3
                                                             clus
vv                                                            AMP PEAK 28(20Q11.22) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   267
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       7
[1] 3 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    39 174
  AMP PEAK 28(20Q11.22) WILD-TYPE  40 235
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     39  174
  AMP PEAK 28(20Q11.22) WILD-TYPE   40  235
     clus
vv    AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  NO                             39                              40
  YES                           174                             235
[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                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q11.22) MUTATED                          22   177
  AMP PEAK 28(20Q11.22) WILD-TYPE                        22   238
D28V12, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      177
                                  clus
vv                                 AMP PEAK 28(20Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                        238
[1] 4 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    13 183
  AMP PEAK 28(20Q11.22) WILD-TYPE  11 248
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     13  183
  AMP PEAK 28(20Q11.22) WILD-TYPE   11  248
                        clus
vv                       AMP PEAK 28(20Q11.22) MUTATED
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           183
                        clus
vv                       AMP PEAK 28(20Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             248
[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    73  33
  AMP PEAK 29(XQ28) WILD-TYPE 228  80
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        106                         308 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         33                          80 
$`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-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
         351          623          142         2878          140          133 
TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
        1955         1157         1151          395          625         1960 
TCGA-CN-4742 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6023 
        1988         1966          630          629          628         1110 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63Y TCGA-CQ-5327 
         318          611          432          904          175         1660 
TCGA-CQ-5329 TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7072 
        1422         1253         1959         1179          509         1950 
TCGA-CQ-A4C7 TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6477 
        1960          391          358         1663         1777          514 
TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 
         234         1956         1954          907          216          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-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6433 
        2327         2437          406         1478         1840          641 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 
        1969         1952         1970         1939         1945         1952 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-A45Q 
         954          797         1960         1947         1937         1945 
TCGA-CV-A6JE TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6827 
        1075          646          237          773          701          568 
TCGA-D6-8568 TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
         106          483         1081          516          548         1965 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50G TCGA-H7-A6C5 TCGA-HD-7754 TCGA-HD-7917 
         299         1131           15          403           25           37 
TCGA-HD-8635 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A51X 
          25           33          485          360          552           34 
TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-P3-A6T4 TCGA-QK-A8Z9 TCGA-UF-A719 TCGA-UF-A71B 
         254         1559         1968          149         1663         1319 
TCGA-UF-A71E TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS 
        1278          735          665          413 

$`AMP PEAK 29(XQ28) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         102          462          415          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-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG 
         644          451           63          113          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         622          918          850          216          182         1976 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         314          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 
        1230          392          817          993          642         1250 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1007         1045          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 
         683          290          933          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-A499 TCGA-CN-A49A 
         735          429           46          443          535          391 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 
         645          225          526          484          348          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5330 
         223          298         1466         1207          654         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          317          341          129         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
         985         1959         1750         1560         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1274          877         1353          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5249 
         998          785          303          950         2562         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-6488 
        1969          362          311          345          354          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         350          479         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-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
         972         1968         1036          796          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-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 
         930          156         1077          911         1472          584 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
        1978         2886         1958          519          701         2641 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         215         1315         1665         1899         1970         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-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        1969         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-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         1974         1948         1955         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-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1981          851         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO 
        1954         1722         1977         1970          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         670          110          714          606          685         1950 
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-D6-A6EM TCGA-D6-A6EO 
         154          128          539          376          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 
         424          368          389          338         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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 
         133          414          206            2            5           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-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
        1057          122          441          588          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         351          360          224          378          168           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392           56          111          112          240          910 
TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
        1726         1120         1954          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 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         387          567          198          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
         168         1326         1252         1043         1894          484 
TCGA-UF-A7JF TCGA-UF-A7JJ 
        1497          214 

  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                        5480 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        754                         686 
[1] "15.0 - 3295.0 (754.0)" "2.0 - 5480.0 (686.0)" 
[1] "hr=" "1.1"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 29(XQ28) MUTATED         6       18        19        69         3
  AMP PEAK 29(XQ28) WILD-TYPE      20       57        55       166         9
                             vv
clus                          STAGE IVC
  AMP PEAK 29(XQ28) MUTATED           1
  AMP PEAK 29(XQ28) WILD-TYPE         0
D29V3, multiclass
           clus
vv          AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  STAGE I                           6                          20
  STAGE II                         18                          57
  STAGE III                        19                          55
  STAGE IVA                        69                         166
  STAGE IVB                         3                           9
  STAGE IVC                         1                           0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK 29(XQ28) MUTATED      10  28  35  45
  AMP PEAK 29(XQ28) WILD-TYPE    37  99  59 117
D29V4, multiclass
       clus
vv      AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T0+T1                        10                          37
  T2                           28                          99
  T3                           35                          59
  T4                           45                         117
[1] 4 2
[1] TRUE
[1] "dimension 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    41  17  49   2
  AMP PEAK 29(XQ28) WILD-TYPE 129  46 103   6
D29V5, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  N0                        41                         129
  N1                        17                          46
  N2                        49                         103
  N3                         2                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1  MX
  AMP PEAK 29(XQ28) MUTATED    37   1  13
  AMP PEAK 29(XQ28) WILD-TYPE 130   0  45
D29V6, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  M0                        37                         130
  M1                         1                           0
  MX                        13                          45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    33 100
  AMP PEAK 29(XQ28) WILD-TYPE  99 256
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     33  100
  AMP PEAK 29(XQ28) WILD-TYPE   99  256
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        33                          99
  MALE                         100                         256
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                     131
  AMP PEAK 29(XQ28) WILD-TYPE                                   346
                             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                                                     2
  AMP PEAK 29(XQ28) WILD-TYPE                                                   8
D29V8, multiclass
                                                             clus
vv                                                            AMP PEAK 29(XQ28) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             131
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 2
                                                             clus
vv                                                            AMP PEAK 29(XQ28) 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                                   8
[1] 3 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    29 104
  AMP PEAK 29(XQ28) WILD-TYPE  50 305
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     29  104
  AMP PEAK 29(XQ28) WILD-TYPE   50  305
     clus
vv    AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  NO                         29                          50
  YES                       104                         305
[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                                1     9
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(XQ28) MUTATED                          11   115
  AMP PEAK 29(XQ28) WILD-TYPE                        33   300
D29V12, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                  115
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                    300
[1] 4 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     8 117
  AMP PEAK 29(XQ28) WILD-TYPE  16 314
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      8  117
  AMP PEAK 29(XQ28) WILD-TYPE   16  314
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             8                          16
  NOT HISPANIC OR LATINO                       117                         314
[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    53  28
  DEL PEAK  1(1P36.21) WILD-TYPE 248  85
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            81                            333 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            28                             85 
$`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-BA-A6DL TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7871 
         236          850          623          558          536          428 
TCGA-BB-8601 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6012 TCGA-CN-6018 
         624         1007         1045         1081          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         432         1970          224          611          394          735 
TCGA-CN-6997 TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-7072 
         429          225          317         1000         1959         1950 
TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7365 
         707          950         1521         1050          354         1191 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CV-5432 
         105         1979          759          889           30         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6003 
        3295         1438          546         1978          215         1665 
TCGA-CV-6935 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7254 TCGA-CV-7261 
        1969         1970         1970         1939         1976         1099 
TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7440 TCGA-CV-A6JE 
        1974         1955         1947         1972         1981         1075 
TCGA-D6-6516 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7589 
         773          232          424          338          516          575 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-8489 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A6HZ 
         622          299          658           44           24          111 
TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-QK-A8Z7 TCGA-UF-A71D 
         360          351          224           14          198         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD 
        1278         1043          735 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          415         1983          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-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
         644          384          113          895          855          622 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         918          351          216          182         1976          314 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
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-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        1955            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
         811         1268         1988          173         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 
         630          933          628          594          629           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
         202         1110          318          432           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
         535          391          904          645          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         341          129         1253         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1274          877         1353         1960         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 
         998          785          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         1952         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-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1959          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
        1946         1954         1722         1977         1970          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          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-D6-A6EK TCGA-D6-A6EO 
         106          128          539          376          483          435 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         368          389         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 
        1131          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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          25           37           55           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-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 
         588          412          440          360          552          378 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         168           34          392           56          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         254          240          910         1726         1559         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          387 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         567          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
        1326         1663         1319         1894          484         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  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                           5480 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                           629                            714 
[1] "14.0 - 3295.0 (629.0)" "2.0 - 5480.0 (714.0)" 
[1] "hr=" "1.3"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.21) MUTATED         4       11        18        38         3
  DEL PEAK  1(1P36.21) WILD-TYPE      22       64        56       197         9
                                vv
clus                             STAGE IVC
  DEL PEAK  1(1P36.21) MUTATED           0
  DEL PEAK  1(1P36.21) WILD-TYPE         1
D30V3, multiclass
           clus
vv          DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  STAGE I                              4                             22
  STAGE II                            11                             64
  STAGE III                           18                             56
  STAGE IVA                           38                            197
  STAGE IVB                            3                              9
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK  1(1P36.21) MUTATED       8  18  20  30
  DEL PEAK  1(1P36.21) WILD-TYPE    39 109  74 132
D30V4, multiclass
       clus
vv      DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  T0+T1                            8                             39
  T2                              18                            109
  T3                              20                             74
  T4                              30                            132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.21) MUTATED    29  12  24   2
  DEL PEAK  1(1P36.21) WILD-TYPE 141  51 128   6
D30V5, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  N0                           29                            141
  N1                           12                             51
  N2                           24                            128
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK  1(1P36.21) MUTATED    27   0   6
  DEL PEAK  1(1P36.21) WILD-TYPE 140   1  52
D30V6, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  M0                           27                            140
  M1                            0                              1
  MX                            6                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    21  68
  DEL PEAK  1(1P36.21) WILD-TYPE 111 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     21   68
  DEL PEAK  1(1P36.21) WILD-TYPE  111  288
        clus
vv       DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           21                            111
  MALE                             68                            288
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                      84
  DEL PEAK  1(1P36.21) WILD-TYPE                                   393
                                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                                                     5
  DEL PEAK  1(1P36.21) WILD-TYPE                                                   5
D30V8, multiclass
                                                             clus
vv                                                            DEL PEAK  1(1P36.21) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 84
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
                                                             clus
vv                                                            DEL PEAK  1(1P36.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  393
  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"
D30V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    22  67
  DEL PEAK  1(1P36.21) WILD-TYPE  57 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     22   67
  DEL PEAK  1(1P36.21) WILD-TYPE   57  342
     clus
vv    DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  NO                            22                             57
  YES                           67                            342
[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                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.21) MUTATED                          10    73
  DEL PEAK  1(1P36.21) WILD-TYPE                        34   342
D30V12, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      73
                                  clus
vv                                 DEL PEAK  1(1P36.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       342
[1] 4 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  77
  DEL PEAK  1(1P36.21) WILD-TYPE  20 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED      4   77
  DEL PEAK  1(1P36.21) WILD-TYPE   20  354
                        clus
vv                       DEL PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       DEL PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            354
[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    73  32
  DEL PEAK  2(1P13.2) WILD-TYPE 228  81
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          105                           309 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           32                            81 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-6870 TCGA-BA-6871 
         102          283          415         1288          451           63 
TCGA-BA-7269 TCGA-BA-A6DE TCGA-BB-7862 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 
         236          182          536          624            5          721 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 
         392          993          625         1007         1980         1081 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
         630          629           45         1970          202          224 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63W 
         394          735          429           46          225          348 
TCGA-CN-A6V3 TCGA-CQ-5332 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CA 
         298          317         1560          509         1950         1963 
TCGA-CQ-A4CI TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 
         950         1969          311         1191          105         1979 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
         759           30          181         1955         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5973 
        1438          584          546         1978         2437         2641 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 
        1840          215         1665          641         1969         1952 
TCGA-CV-6941 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1959         1959         1970         1939         1945         1987 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7424 
        1095          797         1976         1099         1955         1947 
TCGA-CV-7435 TCGA-CV-A461 TCGA-CV-A6JT TCGA-CX-7082 TCGA-D6-6516 TCGA-D6-A4ZB 
        1959         1954          670          317          773          376 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-F7-8489 
         232          435          424          338          516          658 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-8634 
          92            3            6            5           44           24 
TCGA-HD-8635 TCGA-IQ-A61H TCGA-IQ-A61L TCGA-KU-A66T TCGA-P3-A5QE TCGA-P3-A6T8 
          25          412          351          552         1559          400 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E 
         149          135         1326         1663         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        1043          484          735 

$`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-A4IG TCGA-BA-A4IH 
         644          384          113          895          855          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ 
         918          850          351          216         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         623          142          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-C9-A480 TCGA-CN-4722 
        1153          428          436         1955            4          799 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 
        1157          142         1230         1151          817          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
        1250          395         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1988         1045          173         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 
        1966         1975          683          290          933          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6988 
         594          629          432           98         1110          318 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         611          432          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         645          526          484          175          367          223 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959         1179         1750         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309         1274          877         1353         1960          707 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
         893          998          785          391          303         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-6477 TCGA-CR-6480 
        1966         1050         1125         1971          514          362 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7373 
        1956         1435         1440         1245         1960          889 
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-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         911         1472          522         2886         2327         1958 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 
         519          406          701         1478         1315         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1970         1948         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-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 
        1959         1979         1952         1444          954         1967 
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-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-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 
        1945         5480         1960         1940         1946         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU 
        1977         1970         1075          906         1959          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
         646          714          606          685         1950          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-A6EK 
         154          568          106          128          539          483 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         368          389         1778         1081         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-A50G 
         368          324          340         1131          490           15 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 
         585          384           14           13          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
         133          414          403          206            2           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          37           55           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-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
         360          440          360          224          378          168 
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-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX 
         254          240          910         1726         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1917         1968          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         218          228          225          387          567          198 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JF 
         135          157          168         1319         1894         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  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                          5480 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          630                           722 
[1] "3.0 - 3295.0 (630.0)" "2.0 - 5480.0 (722.0)"
[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       18        21        64         2
  DEL PEAK  2(1P13.2) WILD-TYPE      20       57        53       171        10
                               vv
clus                            STAGE IVC
  DEL PEAK  2(1P13.2) MUTATED           1
  DEL PEAK  2(1P13.2) WILD-TYPE         0
D31V3, multiclass
           clus
vv          DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                             6                            20
  STAGE II                           18                            57
  STAGE III                          21                            53
  STAGE IVA                          64                           171
  STAGE IVB                           2                            10
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  2(1P13.2) MUTATED       9  30  29  44
  DEL PEAK  2(1P13.2) WILD-TYPE    38  97  65 118
D31V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                           9                            38
  T2                             30                            97
  T3                             29                            65
  T4                             44                           118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  2(1P13.2) MUTATED    46  17  40   2
  DEL PEAK  2(1P13.2) WILD-TYPE 124  46 112   6
D31V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          46                           124
  N1                          17                            46
  N2                          40                           112
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  2(1P13.2) MUTATED    40   1  12
  DEL PEAK  2(1P13.2) WILD-TYPE 127   0  46
D31V6, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  M0                          40                           127
  M1                           1                             0
  MX                          12                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    33  90
  DEL PEAK  2(1P13.2) WILD-TYPE  99 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     33   90
  DEL PEAK  2(1P13.2) WILD-TYPE   99  266
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          33                            99
  MALE                            90                           266
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED                                     119
  DEL PEAK  2(1P13.2) WILD-TYPE                                   358
                               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                                                     4
  DEL PEAK  2(1P13.2) WILD-TYPE                                                   6
D31V8, multiclass
                                                             clus
vv                                                            DEL PEAK  2(1P13.2) 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                                   4
                                                             clus
vv                                                            DEL PEAK  2(1P13.2) 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"
D31V9, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    17 106
  DEL PEAK  2(1P13.2) WILD-TYPE  62 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     17  106
  DEL PEAK  2(1P13.2) WILD-TYPE   62  303
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                           17                            62
  YES                         106                           303
[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                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.2) MUTATED                          14   102
  DEL PEAK  2(1P13.2) WILD-TYPE                        30   313
D31V12, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    102
                                  clus
vv                                 DEL PEAK  2(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   30
  WHITE                                                      313
[1] 4 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     7 105
  DEL PEAK  2(1P13.2) WILD-TYPE  17 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7  105
  DEL PEAK  2(1P13.2) WILD-TYPE   17  326
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         105
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           326
[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    26  12
  DEL PEAK  3(1Q44) WILD-TYPE 275 101
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         38                         376 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         12                         101 
$`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         1007 
TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5330 TCGA-CQ-5333 
          45          735          225          348         1393          341 
TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7372 
        1253         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          906 
TCGA-CV-A6JT TCGA-D6-6517 TCGA-D6-A4Z9 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-8489 
         670          292          539         1965          575          658 
TCGA-F7-A61S TCGA-F7-A61W TCGA-HD-8634 TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-P3-A6T8 
           3           14           24          351          378          400 
TCGA-UF-A7J9 TCGA-UF-A7JC 
        1043          484 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          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-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         113          236          895          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         850          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         623          142          187         2878          278          140 
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-C9-A480 
         638         1153          428          436         1955            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         799          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
         392          817          993          642         1250          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988         1045 
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-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         629          628          594          629          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         394          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         391          904          645          526          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6221 
        1660         1422         1399          317          129         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        1057          985         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1007          509         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1353          707         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         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-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971          514          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-7370 TCGA-CR-7371 
        1435         1440         1245         1960          105         1979 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         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-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-5440 
         522         1950         3295         1438          584         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-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-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-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        3835         1948         1966         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        3837         1959         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
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-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        1959          110          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
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-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         128          376          483          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
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-F7-8298 TCGA-F7-A50G 
         368          324          340         1131          490           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
          92          585          384           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
           5           25           37           55           44           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-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
         485          122          441          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W 
         440          360          224          552          168           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-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         240          910         1726         1559         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1917         1968          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         218          228          225          387          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
        1663         1319         1252         1278         1894          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  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                        5480 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      641.0                       710.5 
[1] "3.0 - 2886.0 (641.0)" "2.0 - 5480.0 (710.5)"
[1] "hr=" "1.3"
D32V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  3(1Q44) MUTATED         2        5         8        25         0
  DEL PEAK  3(1Q44) WILD-TYPE      24       70        66       210        12
                             vv
clus                          STAGE IVC
  DEL PEAK  3(1Q44) MUTATED           0
  DEL PEAK  3(1Q44) WILD-TYPE         1
D32V3, multiclass
           clus
vv          DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                           2                          24
  STAGE II                          5                          70
  STAGE III                         8                          66
  STAGE IVA                        25                         210
  STAGE IVB                         0                          12
  STAGE IVC                         0                           1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  DEL PEAK  3(1Q44) MUTATED       3  12  13  13
  DEL PEAK  3(1Q44) WILD-TYPE    44 115  81 149
D32V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         3                          44
  T2                           12                         115
  T3                           13                          81
  T4                           13                         149
[1] 4 2
[1] TRUE
[1] "dimension 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    17   4  17   0
  DEL PEAK  3(1Q44) WILD-TYPE 153  59 135   8
D32V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                        17                         153
  N1                         4                          59
  N2                        17                         135
  N3                         0                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1  MX
  DEL PEAK  3(1Q44) MUTATED    17   0   6
  DEL PEAK  3(1Q44) WILD-TYPE 150   1  52
D32V6, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  M0                        17                         150
  M1                         0                           1
  MX                         6                          52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    15  30
  DEL PEAK  3(1Q44) WILD-TYPE 117 326
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     15   30
  DEL PEAK  3(1Q44) WILD-TYPE  117  326
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        15                         117
  MALE                          30                         326
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(1Q44) MUTATED                                      45
  DEL PEAK  3(1Q44) WILD-TYPE                                   432
                             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                                                  10
D32V8, multiclass
                                                             clus
vv                                                            DEL PEAK  3(1Q44) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                              45
  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                                               432
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  10
[1] 3 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  38
  DEL PEAK  3(1Q44) WILD-TYPE  72 371
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      7   38
  DEL PEAK  3(1Q44) WILD-TYPE   72  371
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                          7                          72
  YES                        38                         371
[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                                2     9
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q44) MUTATED                           2    40
  DEL PEAK  3(1Q44) WILD-TYPE                        42   375
D32V12, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   40
                                  clus
vv                                 DEL PEAK  3(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 42
  WHITE                                                    375
[1] 4 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     4  39
  DEL PEAK  3(1Q44) WILD-TYPE  20 392
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      4   39
  DEL PEAK  3(1Q44) WILD-TYPE   20  392
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             4                          20
  NOT HISPANIC OR LATINO                        39                         392
[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    52  13
  DEL PEAK  4(2Q21.2) WILD-TYPE 249 100
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           65                           349 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           13                           100 
$`DEL PEAK  4(2Q21.2) MUTATED`
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A8YP 
         415          722         1288          190          113          142 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 
         310          536          423            5          721          395 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6018 
        1980         1977          683          290          933           45 
TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63V 
         224          735          443          535          904          484 
TCGA-CN-A6V3 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4CB 
         298         1399          129         1560         1274          893 
TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5973 
        1050          354          930          181          911         2641 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7235 TCGA-CV-A45R 
        1665         1899         1959         1970         1952         5480 
TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-D6-6826 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-7593 
         646         1950          154          232          424          369 
TCGA-F7-A50J TCGA-F7-A620 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61E 
         585           13            5           37          111          588 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-KU-A6H7 TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IH 
         351          552          378         1968          218          228 
TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A71E TCGA-UF-A7JF 
         198          135          168         1278         1497 

$`DEL PEAK  4(2Q21.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          283         1983          276          248 
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-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451           63          384          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
         182         1976          314          623          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7864 TCGA-BB-7866 
         278          140          133          558          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 
        1153          428          436         1955          624            4 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         799         1157          142         1230         1151          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
         817          993          642         1250          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
         173         1081         1980         1966         1966         1975 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         630          629          628          594          629          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
          98         1970          202         1110          318          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A49C 
         394          432          429           46          391          645 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         225          526          348          175          367          223 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         317          341         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1959         1179         1750         1007          509 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1963          998          785          391          303          950 
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-6477 TCGA-CR-6478 
        1521         1966         1125         1971          514         1969 
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-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-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-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 
         908          898          216          156         1077         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-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         519          406          701         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1315          641         1970         1948         1969         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-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         3837         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1939         1945         1987         1979         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
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-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1981          851         1945         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        1959          670          110          714          606          685 
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-D6-8569 
         701           77          491          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         539          376          483          435          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         338         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
        1965          575          775          622          299          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 
          92            3          384           14            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            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-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         441          360          412          440          360          224 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         112          254          240          910         1726         1559 
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 TCGA-QK-A6V9 TCGA-QK-A8Z9 
         357          245          225          387          567          149 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         135          157         1326         1663         1319         1252 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ 
        1043         1894          484          735          665          214 
TCGA-UF-A7JS 
         413 

  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 
                         5480                          3837 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                          535                           773 
[1] "5.0 - 5480.0 (535.0)" "2.0 - 3837.0 (773.0)"
[1] "hr=" "1.2"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  4(2Q21.2) MUTATED         3        9        18        33         3
  DEL PEAK  4(2Q21.2) WILD-TYPE      23       66        56       202         9
                               vv
clus                            STAGE IVC
  DEL PEAK  4(2Q21.2) MUTATED           0
  DEL PEAK  4(2Q21.2) WILD-TYPE         1
D33V3, multiclass
           clus
vv          DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  STAGE I                             3                            23
  STAGE II                            9                            66
  STAGE III                          18                            56
  STAGE IVA                          33                           202
  STAGE IVB                           3                             9
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  4(2Q21.2) MUTATED       6  18  16  28
  DEL PEAK  4(2Q21.2) WILD-TYPE    41 109  78 134
D33V4, multiclass
       clus
vv      DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  T0+T1                           6                            41
  T2                             18                           109
  T3                             16                            78
  T4                             28                           134
[1] 4 2
[1] TRUE
[1] "dimension 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    30  13  18   2
  DEL PEAK  4(2Q21.2) WILD-TYPE 140  50 134   6
D33V5, multiclass
    clus
vv   DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  N0                          30                           140
  N1                          13                            50
  N2                          18                           134
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  4(2Q21.2) MUTATED    30   0  11
  DEL PEAK  4(2Q21.2) WILD-TYPE 137   1  47
D33V6, multiclass
    clus
vv   DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  M0                          30                           137
  M1                           0                             1
  MX                          11                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED    30  43
  DEL PEAK  4(2Q21.2) WILD-TYPE 102 313
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     30   43
  DEL PEAK  4(2Q21.2) WILD-TYPE  102  313
        clus
vv       DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  FEMALE                          30                           102
  MALE                            43                           313
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q21.2) MUTATED                                      71
  DEL PEAK  4(2Q21.2) WILD-TYPE                                   406
                               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                                                     2
  DEL PEAK  4(2Q21.2) WILD-TYPE                                                   8
D33V8, multiclass
                                                             clus
vv                                                            DEL PEAK  4(2Q21.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                71
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            DEL PEAK  4(2Q21.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 406
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
[1] 3 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  66
  DEL PEAK  4(2Q21.2) WILD-TYPE  72 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED      7   66
  DEL PEAK  4(2Q21.2) WILD-TYPE   72  343
     clus
vv    DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  NO                            7                            72
  YES                          66                           343
[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                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q21.2) MUTATED                           8    60
  DEL PEAK  4(2Q21.2) WILD-TYPE                        36   355
D33V12, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     60
                                  clus
vv                                 DEL PEAK  4(2Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      355
[1] 4 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     6  63
  DEL PEAK  4(2Q21.2) WILD-TYPE  18 368
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED      6   63
  DEL PEAK  4(2Q21.2) WILD-TYPE   18  368
                        clus
vv                       DEL PEAK  4(2Q21.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK  4(2Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           368
[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    69  23
  DEL PEAK  5(2Q22.1) WILD-TYPE 232  90
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           92                           322 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           23                            90 
$`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-BA-A4IH TCGA-BB-7861 TCGA-BB-7862 TCGA-C9-A47Z TCGA-CN-4723 
         236          622          310          536            5          721 
TCGA-CN-4736 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6010 
         395         1045         1980         1977          290          630 
TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6997 
         933           45           98         1110          735          429 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A641 TCGA-CQ-5327 TCGA-CQ-7064 
         535          391          904          367         1660         1560 
TCGA-CQ-7069 TCGA-CQ-A4CD TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6484 
        1274          998          358         1050         1971          354 
TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7402 
        1440         1979         1430          907          181          911 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6945 
        1438          584         2886         2641          215         1969 
TCGA-CV-7091 TCGA-CV-7235 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-A45Q TCGA-CV-A45R 
        1959         1952         1947         1937         1945         5480 
TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-D6-6516 TCGA-D6-6826 
         906          110          646         1950          773          154 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-5624 
         106          539          376          232          424         1778 
TCGA-DQ-5629 TCGA-DQ-7593 TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 
         516          369          585          384           13            6 
TCGA-H7-7774 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L 
         407           55          111          588          412          351 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A7D7 TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A8Z7 
         552          378          240          400          228          198 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC 
         135          135          168         1278         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF 
         735         1497 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         102          462          283          276          248          722 
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-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II 
         644          451          384          895          855          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         850          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         623          142          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         133          558          423          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 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          642         1250          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
         811         1268         1988         1007          173         1081 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
        1980         1966         1966         1975          683          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
         628          594          629          432         1970          202 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 
         224          318          611          394          432           46 
TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         443          645          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         175          223          298         1466         1207          654 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
        1179         1750         1007          509         1309          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353         1960          707         1963          893 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         785          391          303          950         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-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
         514         1969          362          311          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-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960          105          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-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-7401 TCGA-CR-7404 TCGA-CV-5430 
         930          216          156         1077         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
         522         1950         3295          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-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-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-7095 
        1966         1957         1969         1959         3837         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-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1979         1444         1095          954          797         1967 
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-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1957         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1959         1981          851         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO 
        1954         1722         1977         1970         1075         1959 
TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 
         670          714          606          685          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-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         568          128          483          435          368          389 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
         338         1081         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         775          622          299          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S 
        1131          490          658           15           92            3 
TCGA-F7-A61W TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
          14           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
           2            5           25           37           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-A61J TCGA-IQ-A61O 
         485          122          441          360          440          360 
TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          168           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         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z 
        1120         1954          578         1917         1968          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         357          245          218          225          387          567 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         149          157         1326         1663         1319         1252 
TCGA-UF-A7J9 TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1043          665          214          413 

  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 
                         5480                          3837 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          568                           767 
[1] "5.0 - 5480.0 (568.0)" "2.0 - 3837.0 (767.0)"
[1] "hr=" "1"  
D34V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  5(2Q22.1) MUTATED         2       14        18        61         6
  DEL PEAK  5(2Q22.1) WILD-TYPE      24       61        56       174         6
                               vv
clus                            STAGE IVC
  DEL PEAK  5(2Q22.1) MUTATED           1
  DEL PEAK  5(2Q22.1) WILD-TYPE         0
D34V3, multiclass
           clus
vv          DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                             2                            24
  STAGE II                           14                            61
  STAGE III                          18                            56
  STAGE IVA                          61                           174
  STAGE IVB                           6                             6
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  5(2Q22.1) MUTATED       5  25  24  49
  DEL PEAK  5(2Q22.1) WILD-TYPE    42 102  70 113
D34V4, multiclass
       clus
vv      DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T0+T1                           5                            42
  T2                             25                           102
  T3                             24                            70
  T4                             49                           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  5(2Q22.1) MUTATED    39  16  38   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 131  47 114   5
D34V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          39                           131
  N1                          16                            47
  N2                          38                           114
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  5(2Q22.1) MUTATED    49   1  13
  DEL PEAK  5(2Q22.1) WILD-TYPE 118   0  45
D34V6, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  M0                          49                           118
  M1                           1                             0
  MX                          13                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    39  75
  DEL PEAK  5(2Q22.1) WILD-TYPE  93 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     39   75
  DEL PEAK  5(2Q22.1) WILD-TYPE   93  281
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          39                            93
  MALE                            75                           281
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                                     111
  DEL PEAK  5(2Q22.1) WILD-TYPE                                   366
                               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                                                     3
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                   7
D34V8, multiclass
                                                             clus
vv                                                            DEL PEAK  5(2Q22.1) 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                                   3
                                                             clus
vv                                                            DEL PEAK  5(2Q22.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 366
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
[1] 3 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  97
  DEL PEAK  5(2Q22.1) WILD-TYPE  62 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     17   97
  DEL PEAK  5(2Q22.1) WILD-TYPE   62  312
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           17                            62
  YES                          97                           312
[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                                2     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q22.1) MUTATED                          11    95
  DEL PEAK  5(2Q22.1) WILD-TYPE                        33   320
D34V12, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     95
                                  clus
vv                                 DEL PEAK  5(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      320
[1] 4 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     7  98
  DEL PEAK  5(2Q22.1) WILD-TYPE  17 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      7   98
  DEL PEAK  5(2Q22.1) WILD-TYPE   17  333
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          98
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           333
[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    90  41
  DEL PEAK  6(2Q36.2) WILD-TYPE 211  72
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          131                           283 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                           41                            72 
$`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-A4IG TCGA-BA-A6D8 
        1747          190           63          113          855          850 
TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 
         182          314          142          133          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
         423          687          624            5            4          721 
TCGA-CN-4727 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1230          395          811         1268         1988         1045 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
        1081         1977         1975          290          933          629 
TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A499 
          45         1970          224          735          429          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5327 
         391          904          348          298         1466         1660 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-7064 TCGA-CQ-A4CI TCGA-CR-6472 TCGA-CR-6477 
         317         1253         1560          950         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-A45R TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JY TCGA-D6-6826 
        1981         5480         1075          906          646          154 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7592 
         376          232          424          516          575          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A620 TCGA-F7-A623 
         369          368           15          585           13            6 
TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E 
         403            5           55           49          111          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A6I9 
         360          412          351          552          378          254 
TCGA-MZ-A7D7 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZB 
         240          400          218          387          198          135 
TCGA-QK-AA3K TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JH TCGA-UF-A7JJ 
         168         1252         1278          665          214 

$`DEL PEAK  6(2Q36.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         102          462          276          248          722         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
         725          623          644          451          384          236 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG 
         895          622          918          351          216         1976 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         623          187         2878          278          140          558 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-CN-4722 
         638         1153          428          436         1955          799 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        1157          142         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5355 
         642         1250          625         1960         1330         1007 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 
         173         1980         1980         1966         1966          683 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         630          628          594          629          432           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
         202         1110          318          611          394          432 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
          46          443          645          225          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 
         175          367          223         1207          654         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 
        1393         1399          341          129         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959         1179         1750         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
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-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
         799         1777         1521         1966         1125         1971 
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-7365 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7376 
         350          479         1191         1245          759          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-7401 TCGA-CV-5430 
         898          930          216          156         1077         1955 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
        1950         1438          546         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
        2437          406          701         1478         1840         1315 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6952 
        1899         1970         1948         1952         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1957         1969         3837         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 
         954          797         1960         1948         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O 
        1972         1937         1984         1958         1959          851 
TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        1945         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
        1977         1970         1959          670          110          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          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-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EO 
         568          106          128          539          483          435 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         368          389          338         1778         1081         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-DQ-7596 
         548         1965          775          622          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
        1131          490          658           92            3          384 
TCGA-F7-A61W TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A 
          14          407           58          133          414          206 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
           2           25           37           44           24           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-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
         441          440          360          224          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 
          34          392           56          111          112          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1726         1559         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
        1968          553          357          245          228          225 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 
         567          149          135          157         1326         1663 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1319         1043         1894          484          735         1497 
TCGA-UF-A7JS 
         413 

  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 
                         5480                          3837 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          585                           773 
[1] "4.0 - 5480.0 (585.0)" "2.0 - 3837.0 (773.0)"
[1] "hr=" "1"  
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  6(2Q36.2) MUTATED         3       17        30        70         6
  DEL PEAK  6(2Q36.2) WILD-TYPE      23       58        44       165         6
                               vv
clus                            STAGE IVC
  DEL PEAK  6(2Q36.2) MUTATED           0
  DEL PEAK  6(2Q36.2) WILD-TYPE         1
D35V3, multiclass
           clus
vv          DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  STAGE I                             3                            23
  STAGE II                           17                            58
  STAGE III                          30                            44
  STAGE IVA                          70                           165
  STAGE IVB                           6                             6
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  6(2Q36.2) MUTATED       7  28  38  55
  DEL PEAK  6(2Q36.2) WILD-TYPE    40  99  56 107
D35V4, multiclass
       clus
vv      DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  T0+T1                           7                            40
  T2                             28                            99
  T3                             38                            56
  T4                             55                           107
[1] 4 2
[1] TRUE
[1] "dimension 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    49  22  42   4
  DEL PEAK  6(2Q36.2) WILD-TYPE 121  41 110   4
D35V5, multiclass
    clus
vv   DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  N0                          49                           121
  N1                          22                            41
  N2                          42                           110
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  6(2Q36.2) MUTATED    51   0  17
  DEL PEAK  6(2Q36.2) WILD-TYPE 116   1  41
D35V6, multiclass
    clus
vv   DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  M0                          51                           116
  M1                           0                             1
  MX                          17                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    43 105
  DEL PEAK  6(2Q36.2) WILD-TYPE  89 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     43  105
  DEL PEAK  6(2Q36.2) WILD-TYPE   89  251
        clus
vv       DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  FEMALE                          43                            89
  MALE                           105                           251
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(2Q36.2) MUTATED                                     145
  DEL PEAK  6(2Q36.2) WILD-TYPE                                   332
                               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                                                     3
  DEL PEAK  6(2Q36.2) WILD-TYPE                                                   7
D35V8, multiclass
                                                             clus
vv                                                            DEL PEAK  6(2Q36.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               145
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
                                                             clus
vv                                                            DEL PEAK  6(2Q36.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 332
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
[1] 3 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    21 127
  DEL PEAK  6(2Q36.2) WILD-TYPE  58 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     21  127
  DEL PEAK  6(2Q36.2) WILD-TYPE   58  282
     clus
vv    DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  NO                           21                            58
  YES                         127                           282
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(2Q36.2) MUTATED                                  1     6
  DEL PEAK  6(2Q36.2) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q36.2) MUTATED                          20   116
  DEL PEAK  6(2Q36.2) WILD-TYPE                        24   299
D35V12, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q36.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                    116
                                  clus
vv                                 DEL PEAK  6(2Q36.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   24
  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"
D35V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    12 127
  DEL PEAK  6(2Q36.2) WILD-TYPE  12 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     12  127
  DEL PEAK  6(2Q36.2) WILD-TYPE   12  304
                        clus
vv                       DEL PEAK  6(2Q36.2) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         127
                        clus
vv                       DEL PEAK  6(2Q36.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           304
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  7(3P26.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.2) MUTATED   195  86
  DEL PEAK  7(3P26.2) WILD-TYPE 106  27
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          281                           133 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           86                            27 
$`DEL PEAK  7(3P26.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
         102          462          283          415          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-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
          63          384          895          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 
         216          182          623          142          278          133 
TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         536         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         1157          142         1151          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         817          993         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1988         1007         1045          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          683          630          933          629          628 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 
         594           45          432           98         1970          224 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          391          904          645          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5332 
         348          367          298          654         1393          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
        1179         1560         1007          509         1274         1950 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
         950         2562          358         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
        1969          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-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 
        1960         1979          759          889         1968         1036 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
        1954         1430          392          907          216          156 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077          911         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 
        1438          584          546         1978         2886         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         519          406         2641         1478         1840          215 
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-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1959         1969         1966         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         1959         1970         1970         1936         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-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 
         797         1967         1976         1099         1948         1955 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1947         1973         1937         1984         1958         1959 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 
        1075          906          670          110          714          685 
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-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EM 
         491          154          106          128          376          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         435          424          368          389          338         1778 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
         516         1030          548         1965          575          622 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         299          324         1131          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-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
           6          133          414          403            2            5 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E 
          24           25           49          111          485          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T 
         360          412          440          351          360          552 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX 
          14           34           56          240         1726         1954 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ 
        1968          400          553          357          228          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         567          198          149          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
         168         1326         1663         1319         1278         1043 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         484          735         1497          665          413 

$`DEL PEAK  7(3P26.2) 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-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DJ 
         113          236          855          622         1976          314 
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-A480 TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4733 
         687          638            4          799         1230          642 
TCGA-CN-4741 TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
        1268          290          629          202         1110          318 
TCGA-CN-A499 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 
         535          484          175          223         1466         1207 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 
        1660         1422         1399          341          129         1750 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 
        1309          877         1353          391          303         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-6480 TCGA-CR-6481 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 
         362          311          105           30          972          796 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         997         1951          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
         930          181         1472         2327         1958          701 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-7183 TCGA-CV-7235 
         641         1899         3835         1948         1979         1952 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7440 
        1960         1974         1957         1937         1972         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JY 
         851         1945         1977         1970         1959          646 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 
         606         1950          321           77          568          539 
TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
         483         1081          775          369          368          340 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         407           58          206           25           37           55 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          44           11           10           33         1057          122 
TCGA-IQ-7632 TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
         441          224          378          168          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         112          254          910         1559         1120          578 
TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-UF-A71D TCGA-UF-A7JA 
        1917          245          218          225         1252         1894 
TCGA-UF-A7JJ 
         214 

  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                            2                             4 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                         5480                          3835 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          701                           701 
[1] "2.0 - 5480.0 (701.0)" "4.0 - 3835.0 (701.0)"
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  7(3P26.2) MUTATED        18       47        53       168        10
  DEL PEAK  7(3P26.2) WILD-TYPE       8       28        21        67         2
                               vv
clus                            STAGE IVC
  DEL PEAK  7(3P26.2) MUTATED           1
  DEL PEAK  7(3P26.2) WILD-TYPE         0
D36V3, multiclass
           clus
vv          DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  STAGE I                            18                             8
  STAGE II                           47                            28
  STAGE III                          53                            21
  STAGE IVA                         168                            67
  STAGE IVB                          10                             2
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  7(3P26.2) MUTATED      29  80  74 117
  DEL PEAK  7(3P26.2) WILD-TYPE    18  47  20  45
D36V4, multiclass
       clus
vv      DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  T0+T1                          29                            18
  T2                             80                            47
  T3                             74                            20
  T4                            117                            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  7(3P26.2) MUTATED   114  43 117   6
  DEL PEAK  7(3P26.2) WILD-TYPE  56  20  35   2
D36V5, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  N0                         114                            56
  N1                          43                            20
  N2                         117                            35
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  7(3P26.2) MUTATED   115   1  36
  DEL PEAK  7(3P26.2) WILD-TYPE  52   0  22
D36V6, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  M0                         115                            52
  M1                           1                             0
  MX                          36                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    75 257
  DEL PEAK  7(3P26.2) WILD-TYPE  57  99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     75  257
  DEL PEAK  7(3P26.2) WILD-TYPE   57   99
        clus
vv       DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  FEMALE                          75                            57
  MALE                           257                            99
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P26.2) MUTATED                                     327
  DEL PEAK  7(3P26.2) WILD-TYPE                                   150
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  7(3P26.2) MUTATED                                                             1
  DEL PEAK  7(3P26.2) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  7(3P26.2) MUTATED                                                     4
  DEL PEAK  7(3P26.2) WILD-TYPE                                                   6
D36V8, multiclass
                                                             clus
vv                                                            DEL PEAK  7(3P26.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               327
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
                                                             clus
vv                                                            DEL PEAK  7(3P26.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 150
  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"
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    57 275
  DEL PEAK  7(3P26.2) WILD-TYPE  22 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     57  275
  DEL PEAK  7(3P26.2) WILD-TYPE   22  134
     clus
vv    DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  NO                           57                            22
  YES                         275                           134
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P26.2) MUTATED                                  2     6
  DEL PEAK  7(3P26.2) WILD-TYPE                                0     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P26.2) MUTATED                          40   274
  DEL PEAK  7(3P26.2) WILD-TYPE                         4   141
D36V12, multiclass
                                  clus
vv                                 DEL PEAK  7(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 40
  WHITE                                                    274
                                  clus
vv                                 DEL PEAK  7(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                      141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    17 290
  DEL PEAK  7(3P26.2) WILD-TYPE   7 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     17  290
  DEL PEAK  7(3P26.2) WILD-TYPE    7  141
                        clus
vv                       DEL PEAK  7(3P26.2) MUTATED
  HISPANIC OR LATINO                              17
  NOT HISPANIC OR LATINO                         290
                        clus
vv                       DEL PEAK  7(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           141
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  8(3P24.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P24.1) MUTATED   206  90
  DEL PEAK  8(3P24.1) WILD-TYPE  95  23
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          296                           118 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                           90                            23 
$`DEL PEAK  8(3P24.1) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         248          520         1636         1747          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4II 
         451           63          384          236          895          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP 
         850          351          216          182          623          142 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 
         278          133          558          536          687         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 
         428          436         1955          624            5          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        1157          142         1151          392          817          993 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          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          683 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
         630          933          629          628          594           45 
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-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          391          904          645          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 
         348          367          298         1393          317         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959         1179 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1560         1007          509         1274         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6473 
         950         2562          358         1663          799         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
        1971          514         1969          362          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-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-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 
         759          889         1968         1036         1954         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
        1951          392          907          216          156         1077 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         911         1955          522         1950         3295         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-5978 TCGA-CV-5979 
         406         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1665         1970         1948         1969         1952         1959 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1969         1966         1957         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-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1945         1987         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1967         1976         1099         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1947         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        1959         5480         1940         1946         1954         1722 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 
        1075          906          670          110          714          685 
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-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EM 
         491          154          106          128          376          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         435          424          368          389          338         1778 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
         516         1030          548         1965          575          622 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         299          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
          15           92          585            3          384           14 
TCGA-F7-A620 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          13          133          414          403            2            5 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ 
          37           55           24           25           49          111 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         485          588          360          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
         360          552          378           14           34           56 
TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
         240         1726         1954         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         357          228          387          567          198          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         135          135          157          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1319         1278         1043          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JS 
         665          413 

$`DEL PEAK  8(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-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
         855          622         1976          314          187         2878 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-C9-A480 TCGA-CN-4722 
         140          310          423          638            4          799 
TCGA-CN-4727 TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-6023 
        1230          642         1268          290          629         1110 
TCGA-CN-A499 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 
         535          484          175          223         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 
        1750         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 
        1952         1960         1974         1937         1981          851 
TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JY 
        1945         1960         1977         1970         1959          646 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 
         606         1950          321           77          568          539 
TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-A623 
         483         1081          775          369          368            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 
         407           58          206           25           44           11 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A66S 
          10           33         1057          122          441          224 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         168          392          111          112          254          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG 
        1559         1120          578         1917          245          218 
TCGA-QK-A6II TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JJ 
         225         1252         1894          214 

  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                            2                             4 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                         5480                          3835 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                        686.0                         723.5 
[1] "2.0 - 5480.0 (686.0)" "4.0 - 3835.0 (723.5)"
[1] "hr=" "1.3"
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  8(3P24.1) MUTATED        17       50        55       176        10
  DEL PEAK  8(3P24.1) WILD-TYPE       9       25        19        59         2
                               vv
clus                            STAGE IVC
  DEL PEAK  8(3P24.1) MUTATED           1
  DEL PEAK  8(3P24.1) WILD-TYPE         0
D37V3, multiclass
           clus
vv          DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  STAGE I                            17                             9
  STAGE II                           50                            25
  STAGE III                          55                            19
  STAGE IVA                         176                            59
  STAGE IVB                          10                             2
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  8(3P24.1) MUTATED      27  86  76 123
  DEL PEAK  8(3P24.1) WILD-TYPE    20  41  18  39
D37V4, multiclass
       clus
vv      DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  T0+T1                          27                            20
  T2                             86                            41
  T3                             76                            18
  T4                            123                            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(3P24.1) MUTATED   116  46 122   6
  DEL PEAK  8(3P24.1) WILD-TYPE  54  17  30   2
D37V5, multiclass
    clus
vv   DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  N0                         116                            54
  N1                          46                            17
  N2                         122                            30
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  8(3P24.1) MUTATED   119   1  36
  DEL PEAK  8(3P24.1) WILD-TYPE  48   0  22
D37V6, multiclass
    clus
vv   DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  M0                         119                            48
  M1                           1                             0
  MX                          36                            22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED    81 270
  DEL PEAK  8(3P24.1) WILD-TYPE  51  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     81  270
  DEL PEAK  8(3P24.1) WILD-TYPE   51   86
        clus
vv       DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  FEMALE                          81                            51
  MALE                           270                            86
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P24.1) MUTATED                                     346
  DEL PEAK  8(3P24.1) WILD-TYPE                                   131
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  8(3P24.1) MUTATED                                                             1
  DEL PEAK  8(3P24.1) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  8(3P24.1) MUTATED                                                     4
  DEL PEAK  8(3P24.1) WILD-TYPE                                                   6
D37V8, multiclass
                                                             clus
vv                                                            DEL PEAK  8(3P24.1) MUTATED
  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                                   4
                                                             clus
vv                                                            DEL PEAK  8(3P24.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 131
  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"
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED    58 293
  DEL PEAK  8(3P24.1) WILD-TYPE  21 116
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     58  293
  DEL PEAK  8(3P24.1) WILD-TYPE   21  116
     clus
vv    DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  NO                           58                            21
  YES                         293                           116
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3P24.1) MUTATED                                  1     7
  DEL PEAK  8(3P24.1) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P24.1) MUTATED                          41   292
  DEL PEAK  8(3P24.1) WILD-TYPE                         3   123
D37V12, multiclass
                                  clus
vv                                 DEL PEAK  8(3P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 41
  WHITE                                                    292
                                  clus
vv                                 DEL PEAK  8(3P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                      123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED    17 308
  DEL PEAK  8(3P24.1) WILD-TYPE   7 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     17  308
  DEL PEAK  8(3P24.1) WILD-TYPE    7  123
                        clus
vv                       DEL PEAK  8(3P24.1) MUTATED
  HISPANIC OR LATINO                              17
  NOT HISPANIC OR LATINO                         308
                        clus
vv                       DEL PEAK  8(3P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           123
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  9(3P14.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P14.2) MUTATED   208  90
  DEL PEAK  9(3P14.2) WILD-TYPE  93  23
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          298                           116 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                           90                            23 
$`DEL PEAK  9(3P14.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
         248         1762          520          623         1636         1747 
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-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         895          918          850          351          216          182 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 
         623          142          278          133          536          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-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           5          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         392          817          993          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1988         1007         1045          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          683          630          933          629          628 
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          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         429           46          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 
         645          225          526          348          367          298 
TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1466         1393          317         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
         985         1959         1959         1179         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
         509         1274         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
        1963          893          785          950         2562          358 
TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1663          799         1777         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-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 
          30         1968         1036         1954         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         392          907          216          156          181         1077 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         911         1955          522         1950         3295         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-5978 TCGA-CV-5979 
         406         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1665         1970         1948         1969         1952         1959 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
        1969         1966         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-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A6JE 
        1981         5480         1940         1946         1954         1075 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 
         670          110          714          685          317          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 
         828          773          292          701          491          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         128          539          376          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         368          389          338         1778          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 
         548         1965          575          622          299          324 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
        1131          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 
           3           14           13            6          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-8635 
         403            2            5           37           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-KU-A6H7 TCGA-MT-A51W 
         440          351          360          552          378           14 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
          34           56          240         1726         1954         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
         400          553          357          228          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         198          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
        1326         1663         1319         1278         1043          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         735         1497          665          413 

$`DEL PEAK  9(3P14.2) WILD-TYPE`
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH 
         722         1288          725          113          855          622 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 
        1976          314          187         2878          140          558 
TCGA-BB-7861 TCGA-BB-7863 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4735 
         310          423            4          799          642         1250 
TCGA-CN-4741 TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-6023 TCGA-CN-A63V TCGA-CN-A63Y 
        1268          290          629         1110          484          175 
TCGA-CN-A6V1 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
         223         1207          654         1660         1422         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CD 
         341          129         1750         1309          877          998 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
         391          303         1152         1521         1966         1050 
TCGA-CR-6481 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 
         311          972          796          997          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5442 TCGA-CV-5443 
         908          898          930         1472         2327         1958 
TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-7090 
         701          641         1899         3835         1948         3837 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7427 TCGA-CV-A45O 
        1979         1952         1960         1974         1937          851 
TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
        1945         1960         1722         1977         1970          906 
TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6824 
        1959          646          606         1950          321           77 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 
         154          568          483         1081          775          369 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
         368          340          384          407           58          206 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
          25           55           44           11           10           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A67A 
        1057          122          441          224          168          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910         1559         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-UF-A71D 
         578         1917          245          218          225         1252 
TCGA-UF-A7JA TCGA-UF-A7JJ 
        1894          214 

  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                            2                             4 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                         5480                          3837 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          684                           750 
[1] "2.0 - 5480.0 (684.0)" "4.0 - 3837.0 (750.0)"
[1] "hr=" "1.3"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  9(3P14.2) MUTATED        18       50        55       177        10
  DEL PEAK  9(3P14.2) WILD-TYPE       8       25        19        58         2
                               vv
clus                            STAGE IVC
  DEL PEAK  9(3P14.2) MUTATED           1
  DEL PEAK  9(3P14.2) WILD-TYPE         0
D38V3, multiclass
           clus
vv          DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  STAGE I                            18                             8
  STAGE II                           50                            25
  STAGE III                          55                            19
  STAGE IVA                         177                            58
  STAGE IVB                          10                             2
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK  9(3P14.2) MUTATED      30  89  73 123
  DEL PEAK  9(3P14.2) WILD-TYPE    17  38  21  39
D38V4, multiclass
       clus
vv      DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  T0+T1                          30                            17
  T2                             89                            38
  T3                             73                            21
  T4                            123                            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  9(3P14.2) MUTATED   116  48 123   6
  DEL PEAK  9(3P14.2) WILD-TYPE  54  15  29   2
D38V5, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  N0                         116                            54
  N1                          48                            15
  N2                         123                            29
  N3                           6                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  9(3P14.2) MUTATED   119   1  38
  DEL PEAK  9(3P14.2) WILD-TYPE  48   0  20
D38V6, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  M0                         119                            48
  M1                           1                             0
  MX                          38                            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    84 270
  DEL PEAK  9(3P14.2) WILD-TYPE  48  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     84  270
  DEL PEAK  9(3P14.2) WILD-TYPE   48   86
        clus
vv       DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  FEMALE                          84                            48
  MALE                           270                            86
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P14.2) MUTATED                                     349
  DEL PEAK  9(3P14.2) WILD-TYPE                                   128
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK  9(3P14.2) MUTATED                                                             1
  DEL PEAK  9(3P14.2) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                     4
  DEL PEAK  9(3P14.2) WILD-TYPE                                                   6
D38V8, multiclass
                                                             clus
vv                                                            DEL PEAK  9(3P14.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               349
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
                                                             clus
vv                                                            DEL PEAK  9(3P14.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 128
  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"
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    62 292
  DEL PEAK  9(3P14.2) WILD-TYPE  17 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     62  292
  DEL PEAK  9(3P14.2) WILD-TYPE   17  117
     clus
vv    DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  NO                           62                            17
  YES                         292                           117
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(3P14.2) MUTATED                                  1     7
  DEL PEAK  9(3P14.2) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P14.2) MUTATED                          41   294
  DEL PEAK  9(3P14.2) WILD-TYPE                         3   121
D38V12, multiclass
                                  clus
vv                                 DEL PEAK  9(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 41
  WHITE                                                    294
                                  clus
vv                                 DEL PEAK  9(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                      121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    18 310
  DEL PEAK  9(3P14.2) WILD-TYPE   6 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     18  310
  DEL PEAK  9(3P14.2) WILD-TYPE    6  121
                        clus
vv                       DEL PEAK  9(3P14.2) MUTATED
  HISPANIC OR LATINO                              18
  NOT HISPANIC OR LATINO                         310
                        clus
vv                       DEL PEAK  9(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           121
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 10(3P12.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(3P12.1) MUTATED   189  86
  DEL PEAK 10(3P12.1) WILD-TYPE 112  27
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          275                           139 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                           86                            27 
$`DEL PEAK 10(3P12.1) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
         248         1762          520          623         1636         1747 
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-A4II TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP 
         895          918          850          182          623          142 
TCGA-BB-4224 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         278          687         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         624            5          721         1157          142         1230 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         392          817          993         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1960         1330          811         1007         1045          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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         683          630          933          629          628          594 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
          45          432           98         1970         1110          224 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          535          904          645          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-5332 
         348          367          298         1466         1393          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
        1179         1560         1007          509         1274         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1353         1960          707         1963          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 
         785          950         2562          358         1777         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
         514         1969          362          345          354          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-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7388 
         889           30         1968         1036         1954         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
         392          907          216          156         1077          911 
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-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 
         546         1978         2437          519          406         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 
        1478         1840         1315         1665         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 
        1969         1952         1959         1969         1957         1969 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         1959         1970         1970         1936         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-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 
         797         1967         1976         1099         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
        1957         1947         1973         1972         1937         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A6JE 
        1959         1981         1940         1946         1954         1075 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 
         906          670          110          714          685          317 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8568 
         237          828          773          292          154          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         128          539          376          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
         368          338         1778          516         1030         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         575          299          324         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 
          15           92          585            3           14           13 
TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8224 
           6          133          414          403           37           55 
TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G 
          25           49          111          485          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          552 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX 
          14           34           56          240         1726         1954 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A6V9 
        1968          400          553          357          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         198          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1326         1663         1319         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         484          735         1497          665          413 

$`DEL PEAK 10(3P12.1) WILD-TYPE`
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH 
         722         1288          725          113          855          622 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
         351          216         1976          314          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-7866 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4741 
         638            4          799         1151          642         1268 
TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6988 
        1988         1975          290          629          202          318 
TCGA-CN-A49A TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5324 TCGA-CQ-5325 
         391          484          175          223         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         1750 
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         1952 
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-A45R TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO 
        5480         1960         1722         1977         1970         1959 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6823 TCGA-D6-6824 
         646          606         1950          321          701           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5631 
         491          568          483          389         1081          548 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A61V 
         775          622          369          368          340          384 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         407           58          206            2            5           25 
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-7631 TCGA-IQ-7632 TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
         122          441          378          168          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         112          254          910         1559         1120          578 
TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-UF-A71D 
        1917          245          218          228          225         1252 
TCGA-UF-A7JJ 
         214 

  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                            3                             2 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                         3295                          5480 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          721                           646 
[1] "3.0 - 3295.0 (721.0)" "2.0 - 5480.0 (646.0)"
[1] "hr=" "1.8"
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 10(3P12.1) MUTATED        14       48        53       166         7
  DEL PEAK 10(3P12.1) WILD-TYPE      12       27        21        69         5
                               vv
clus                            STAGE IVC
  DEL PEAK 10(3P12.1) MUTATED           1
  DEL PEAK 10(3P12.1) WILD-TYPE         0
D39V3, multiclass
           clus
vv          DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  STAGE I                            14                            12
  STAGE II                           48                            27
  STAGE III                          53                            21
  STAGE IVA                         166                            69
  STAGE IVB                           7                             5
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 10(3P12.1) MUTATED      27  85  69 112
  DEL PEAK 10(3P12.1) WILD-TYPE    20  42  25  50
D39V4, multiclass
       clus
vv      DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  T0+T1                          27                            20
  T2                             85                            42
  T3                             69                            25
  T4                            112                            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 10(3P12.1) MUTATED   108  47 112   5
  DEL PEAK 10(3P12.1) WILD-TYPE  62  16  40   3
D39V5, multiclass
    clus
vv   DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  N0                         108                            62
  N1                          47                            16
  N2                         112                            40
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 10(3P12.1) MUTATED   109   1  37
  DEL PEAK 10(3P12.1) WILD-TYPE  58   0  21
D39V6, multiclass
    clus
vv   DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  M0                         109                            58
  M1                           1                             0
  MX                          37                            21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED    77 249
  DEL PEAK 10(3P12.1) WILD-TYPE  55 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     77  249
  DEL PEAK 10(3P12.1) WILD-TYPE   55  107
        clus
vv       DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  FEMALE                          77                            55
  MALE                           249                           107
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3P12.1) MUTATED                                     320
  DEL PEAK 10(3P12.1) WILD-TYPE                                   157
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 10(3P12.1) MUTATED                                                             1
  DEL PEAK 10(3P12.1) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 10(3P12.1) MUTATED                                                     5
  DEL PEAK 10(3P12.1) WILD-TYPE                                                   5
D39V8, multiclass
                                                             clus
vv                                                            DEL PEAK 10(3P12.1) MUTATED
  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                                   5
                                                             clus
vv                                                            DEL PEAK 10(3P12.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 157
  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"
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED    57 269
  DEL PEAK 10(3P12.1) WILD-TYPE  22 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     57  269
  DEL PEAK 10(3P12.1) WILD-TYPE   22  140
     clus
vv    DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  NO                           57                            22
  YES                         269                           140
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(3P12.1) MUTATED                                  1     7
  DEL PEAK 10(3P12.1) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3P12.1) MUTATED                          39   268
  DEL PEAK 10(3P12.1) WILD-TYPE                         5   147
D39V12, multiclass
                                  clus
vv                                 DEL PEAK 10(3P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 39
  WHITE                                                    268
                                  clus
vv                                 DEL PEAK 10(3P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                      147
[1] 4 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(3P12.1) MUTATED    16 284
  DEL PEAK 10(3P12.1) WILD-TYPE   8 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     16  284
  DEL PEAK 10(3P12.1) WILD-TYPE    8  147
                        clus
vv                       DEL PEAK 10(3P12.1) MUTATED
  HISPANIC OR LATINO                              16
  NOT HISPANIC OR LATINO                         284
                        clus
vv                       DEL PEAK 10(3P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           147
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4P15.2) MUTATED   119  53
  DEL PEAK 11(4P15.2) WILD-TYPE 182  60
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          172                           242 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           53                            60 
$`DEL PEAK 11(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-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DL 
          63          895          855          850          216          623 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7871 
         142         2878          278          133          310          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
        1955          624            5            4          721         1157 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 
         142         1151          817         1250         1330         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6010 
        1007          173         1081         1977          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
         933          629           45          432         1970         1110 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         224          611          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
          46          535          391          904          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6223 
         348          367          298         1466          317         1057 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CD 
        1959         1560          509         1950          707          998 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6487 
         950          358         1663         1050         1971          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
         379          350         1191         1440         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 
        1979          759          889           30         1954         1951 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         907          156         1472          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6934 
        1438          584         1978         2437          215         1948 
TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 
        1969         1959         3835         1959         1959         1970 
TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 
        1939         1952         1444         1095          797         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7430 
        1976         1099         1974         1955         1957         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-D6-6516 
        1937         1984         1959         1981          317          773 
TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         701          539          376          232          435          424 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-8298 
         338          516         1965          575          324          490 
TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7753 
          15          384           14          133          403            5 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E 
          37           55           44           49          111          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         360          412          440          112          254          240 
TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A8Z7 
        1726         1120         1954         1968          400          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A7J9 
         149          135          157          168         1319         1043 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         735         1497          665          413 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6869 
         102         1288         1762          725         1747          644 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
         384          113          236          622          918          351 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4228 
         182         1976          314          187          140          558 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
         536          423          687          638         1153          436 
TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
         799         1230          392          993          642          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5359 
         625         1960          811         1268         1045         1980 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 
        1980         1966         1966         1975          683          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-A498 
         594          629           98          202          318          443 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5324 TCGA-CQ-5325 
         645          484          175          223         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422         1393         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
        1253         1000          985         1959         1179         1750 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309         1274          877         1353         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
        1963          893          785          391          303         2562 
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-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7376 TCGA-CR-7377 
         479         1956         1435         1245          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 
        1036          796          997         1430          392          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-CV-5430 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
        1077          911         1955          546         2886         2327 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958          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-6936 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1952         1948         1969         1966         1957         1969 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 
        3837         1970         1936         1959         1945         1987 
TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 
        1979          954         1960         1948         1947         1937 
TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1973         1958          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
         714          606          685         1950          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         828          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
         106          128          483          368          389         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         1131          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-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-8635 
         414          206            2           25           24           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-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         441          351          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 
         910         1559          578         1917          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         245          218          228          225          387          567 
TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA 
         135         1326         1663         1252         1278         1894 
TCGA-UF-A7JC TCGA-UF-A7JJ 
         484          214 

  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                            4                             2 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         3835                          5480 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                        626.5                         780.0 
[1] "4.0 - 3835.0 (626.5)" "2.0 - 5480.0 (780.0)"
[1] "hr=" "1.1"
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 11(4P15.2) MUTATED        13       29        28       100         6
  DEL PEAK 11(4P15.2) WILD-TYPE      13       46        46       135         6
                               vv
clus                            STAGE IVC
  DEL PEAK 11(4P15.2) MUTATED           0
  DEL PEAK 11(4P15.2) WILD-TYPE         1
D40V3, multiclass
           clus
vv          DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  STAGE I                            13                            13
  STAGE II                           29                            46
  STAGE III                          28                            46
  STAGE IVA                         100                           135
  STAGE IVB                           6                             6
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 11(4P15.2) MUTATED      20 46 45 67
  DEL PEAK 11(4P15.2) WILD-TYPE    27 81 49 95
D40V4, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T0+T1                          20                            27
  T2                             46                            81
  T3                             45                            49
  T4                             67                            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 11(4P15.2) MUTATED    68  23  70   5
  DEL PEAK 11(4P15.2) WILD-TYPE 102  40  82   3
D40V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                          68                           102
  N1                          23                            40
  N2                          70                            82
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 11(4P15.2) MUTATED    59   0  27
  DEL PEAK 11(4P15.2) WILD-TYPE 108   1  31
D40V6, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  M0                          59                           108
  M1                           0                             1
  MX                          27                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    43 155
  DEL PEAK 11(4P15.2) WILD-TYPE  89 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     43  155
  DEL PEAK 11(4P15.2) WILD-TYPE   89  201
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          43                            89
  MALE                           155                           201
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P15.2) MUTATED                                     193
  DEL PEAK 11(4P15.2) WILD-TYPE                                   284
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 11(4P15.2) MUTATED                                                             0
  DEL PEAK 11(4P15.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 11(4P15.2) MUTATED                                                     5
  DEL PEAK 11(4P15.2) WILD-TYPE                                                   5
D40V8, multiclass
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               193
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) 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                                     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(4P15.2) MUTATED    36 162
  DEL PEAK 11(4P15.2) WILD-TYPE  43 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     36  162
  DEL PEAK 11(4P15.2) WILD-TYPE   43  247
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  NO                           36                            43
  YES                         162                           247
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4P15.2) MUTATED                                  0     3
  DEL PEAK 11(4P15.2) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P15.2) MUTATED                          23   165
  DEL PEAK 11(4P15.2) WILD-TYPE                        21   250
D40V12, multiclass
                                  clus
vv                                 DEL PEAK 11(4P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 23
  WHITE                                                    165
                                  clus
vv                                 DEL PEAK 11(4P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      250
[1] 4 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(4P15.2) MUTATED    10 176
  DEL PEAK 11(4P15.2) WILD-TYPE  14 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     10  176
  DEL PEAK 11(4P15.2) WILD-TYPE   14  255
                        clus
vv                       DEL PEAK 11(4P15.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         176
                        clus
vv                       DEL PEAK 11(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           255
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 12(4Q21.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q21.3) MUTATED    91  34
  DEL PEAK 12(4Q21.3) WILD-TYPE 210  79
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                          125                           289 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                           34                            79 
$`DEL PEAK 12(4Q21.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 
         102          283          276          520          451          113 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DL TCGA-BA-A8YP 
         895          855          850          216          623          142 
TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         133          428         1955          624            5            4 
TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5360 
        1157          392         1250          625         1330         1081 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         630          933          629           45          432         1970 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         224          611          735          429           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5334 
         535          904          225          348         1466          129 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 
         985         1959         1560          509         1950          707 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6487 
         303          950         1663         1050          354          234 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
         379         1956         1191          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7404 
         889           30         1954          946          156         1472 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
         522         1950         3295         1438          546         1978 
TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 
        2437         1665         1970         1959         3835         1957 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7261 TCGA-CV-7418 
        1959         1970         1939         1987         1099         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45R 
        1957         1947         1959         1981         1945         5480 
TCGA-CV-A460 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EP 
        1946          701          539          376          232          424 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A50G 
         338          516         1965          575          299           15 
TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-A61H 
         585            3          403           24          111          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
         440          351          112         1726         1954         1968 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A8ZA TCGA-QK-AA3K 
         357          245          218          225          135          168 
TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1663         1252          484          735         1497 

$`DEL PEAK 12(4Q21.3) 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-A4IH TCGA-BA-A4II 
         644           63          384          236          622          918 
TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
         351          182         1976          314          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-7872 TCGA-CN-4722 TCGA-CN-4723 
         687          638         1153          436          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142         1230         1151          817          993          642 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         395         1960          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1045          173         1980         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 
        1966         1975          683          290          628          594 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 
         629           98          202         1110          318          394 
TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         432          391          645          526          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223          298         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 
        1422         1393         1399          317          341         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
        1000         1057         1959         1179         1750         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
        1309         1274          877         1353         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 
         893          998          785          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-7367 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1435         1440         1245         1960 
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-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
        1951          392          907          913          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
         930          216          181         1077          911         1955 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
         584         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-6935 TCGA-CV-6936 TCGA-CV-6943 
         641         1899         1948         1969         1952         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 
        1969         1966         1969         1959         3837         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1936         1959         1945         1979         1952         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-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-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1984         1958          851         1960         1940         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
         670          110          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          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-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
         128          483          435          368          389         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
        1081         1030          548          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          206            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 
          25           37           55           44           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-A61O TCGA-KU-A66S TCGA-KU-A66T 
         441          588          360          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          254          240          910         1559         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
         578         1917          400          553          228          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 
         567          198          149          135          157         1326 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JJ 
        1319         1278         1043         1894          665          214 
TCGA-UF-A7JS 
         413 

  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                            3                             2 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                         5480                          3837 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                          629                           721 
[1] "3.0 - 5480.0 (629.0)" "2.0 - 3837.0 (721.0)"
[1] "hr=" "1.1"
D41V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 12(4Q21.3) MUTATED         9       22        30        62         2
  DEL PEAK 12(4Q21.3) WILD-TYPE      17       53        44       173        10
                               vv
clus                            STAGE IVC
  DEL PEAK 12(4Q21.3) MUTATED           0
  DEL PEAK 12(4Q21.3) WILD-TYPE         1
D41V3, multiclass
           clus
vv          DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  STAGE I                             9                            17
  STAGE II                           22                            53
  STAGE III                          30                            44
  STAGE IVA                          62                           173
  STAGE IVB                           2                            10
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 12(4Q21.3) MUTATED      15  39  36  37
  DEL PEAK 12(4Q21.3) WILD-TYPE    32  88  58 125
D41V4, multiclass
       clus
vv      DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  T0+T1                          15                            32
  T2                             39                            88
  T3                             36                            58
  T4                             37                           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"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 12(4Q21.3) MUTATED    46  21  45   2
  DEL PEAK 12(4Q21.3) WILD-TYPE 124  42 107   6
D41V5, multiclass
    clus
vv   DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  N0                          46                           124
  N1                          21                            42
  N2                          45                           107
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 12(4Q21.3) MUTATED    46   0  20
  DEL PEAK 12(4Q21.3) WILD-TYPE 121   1  38
D41V6, multiclass
    clus
vv   DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  M0                          46                           121
  M1                           0                             1
  MX                          20                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q21.3) MUTATED    40 103
  DEL PEAK 12(4Q21.3) WILD-TYPE  92 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q21.3) MUTATED     40  103
  DEL PEAK 12(4Q21.3) WILD-TYPE   92  253
        clus
vv       DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  FEMALE                          40                            92
  MALE                           103                           253
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4Q21.3) MUTATED                                     142
  DEL PEAK 12(4Q21.3) WILD-TYPE                                   335
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 12(4Q21.3) MUTATED                                                             0
  DEL PEAK 12(4Q21.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 12(4Q21.3) MUTATED                                                     1
  DEL PEAK 12(4Q21.3) WILD-TYPE                                                   9
D41V8, multiclass
                                                             clus
vv                                                            DEL PEAK 12(4Q21.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               142
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
                                                             clus
vv                                                            DEL PEAK 12(4Q21.3) 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                                     9
[1] 3 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(4Q21.3) MUTATED    24 119
  DEL PEAK 12(4Q21.3) WILD-TYPE  55 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q21.3) MUTATED     24  119
  DEL PEAK 12(4Q21.3) WILD-TYPE   55  290
     clus
vv    DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  NO                           24                            55
  YES                         119                           290
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(4Q21.3) MUTATED                                  1     5
  DEL PEAK 12(4Q21.3) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q21.3) MUTATED                          15   115
  DEL PEAK 12(4Q21.3) WILD-TYPE                        29   300
D41V12, multiclass
                                  clus
vv                                 DEL PEAK 12(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    115
                                  clus
vv                                 DEL PEAK 12(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      300
[1] 4 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(4Q21.3) MUTATED    10 124
  DEL PEAK 12(4Q21.3) WILD-TYPE  14 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q21.3) MUTATED     10  124
  DEL PEAK 12(4Q21.3) WILD-TYPE   14  307
                        clus
vv                       DEL PEAK 12(4Q21.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         124
                        clus
vv                       DEL PEAK 12(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           307
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 13(4Q22.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q22.1) MUTATED    94  40
  DEL PEAK 13(4Q22.1) WILD-TYPE 207  73
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                          134                           280 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                           40                            73 
$`DEL PEAK 13(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-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4227 
         855          850          216          623          142          133 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
        1153          428         1955          624            5            4 
TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5360 
        1157          392         1250          625         1330         1081 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
        1966          630          933          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6997 
          98         1970          224          611          735          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W 
          46          443          535          904          225          348 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 
        1466         1000          985         1959         1560          509 
TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 
        1950         1960          707          303          950         1663 
TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 
        1050          354          234          379         1956         1191 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1440          105         1979          759          889           30 
TCGA-CR-7383 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
        1954          946          156         1472          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5976 
        3295         1438          546         1978         2437         1478 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
        1665         1970         1969         1959         3835         1969 
TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7245 
        1957         1959         1970         1939         1987          797 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 
        1099         1974         1955         1957         1947         1972 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A460 TCGA-CX-7086 TCGA-D6-6516 
        1959         1981         1945         1946          237          773 
TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q 
         701          539          376          232          424          338 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S 
         516         1965          575          299          585            3 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
         403           24          111          588          360          412 
TCGA-IQ-A61J TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
         440          112          240         1726         1954         1968 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A7JC 
         245          218          149          135         1663          484 
TCGA-UF-A7JD TCGA-UF-A7JF 
         735         1497 

$`DEL PEAK 13(4Q22.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          462          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-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH 
         190          644           63          384          236          622 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
         918          351          182         1976          314          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          278          140          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-CN-4722 TCGA-CN-4723 
         423          687          638          436          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142         1230         1151          817          993          642 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         395         1960          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1045          173         1980         1977         1980         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        1975          683          290          628          594          629 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-A49A 
         202         1110          318          394          432          391 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         645          526          484          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
         298         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
        1399          317          341          129         1253         1057 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1959         1179         1750         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         877         1353         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         391         2562          358         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-6491 TCGA-CR-6492 TCGA-CR-7364 
         362          311          345          350          479         1435 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1245         1960          972         1968         1036          796 
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-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-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         911         1955          584         2886         2327         1958 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 
         519          406          701         2641         1840          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 
        1315          641         1899         1948         1952         1948 
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-7242 
        1959         1945         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7410 TCGA-CV-7427 
         954         1967         1960         1976         1948         1937 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45R 
        1973         1937         1984         1958          851         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1940         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         828          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         106          128          483          435          368          389 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
        1778         1081         1030          548          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          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-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A 
           6          407           58          133          414          206 
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-A6I0 TCGA-HL-7533 
          25           11           49           10           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         485          122          441          351          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         552          378          168           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         1559         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
         578         1917          400          553          357          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J 
         225          387          567          198          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         168         1326         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          665          214          413 

  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                            3                             2 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                         3835                          5480 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                        747.0                         676.5 
[1] "3.0 - 3835.0 (747.0)" "2.0 - 5480.0 (676.5)"
[1] "hr=" "1"  
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 13(4Q22.1) MUTATED        10       23        30        71         2
  DEL PEAK 13(4Q22.1) WILD-TYPE      16       52        44       164        10
                               vv
clus                            STAGE IVC
  DEL PEAK 13(4Q22.1) MUTATED           0
  DEL PEAK 13(4Q22.1) WILD-TYPE         1
D42V3, multiclass
           clus
vv          DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  STAGE I                            10                            16
  STAGE II                           23                            52
  STAGE III                          30                            44
  STAGE IVA                          71                           164
  STAGE IVB                           2                            10
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 13(4Q22.1) MUTATED      15  40  37  47
  DEL PEAK 13(4Q22.1) WILD-TYPE    32  87  57 115
D42V4, multiclass
       clus
vv      DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  T0+T1                          15                            32
  T2                             40                            87
  T3                             37                            57
  T4                             47                           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 13(4Q22.1) MUTATED    51  22  50   2
  DEL PEAK 13(4Q22.1) WILD-TYPE 119  41 102   6
D42V5, multiclass
    clus
vv   DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  N0                          51                           119
  N1                          22                            41
  N2                          50                           102
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 13(4Q22.1) MUTATED    47   0  21
  DEL PEAK 13(4Q22.1) WILD-TYPE 120   1  37
D42V6, multiclass
    clus
vv   DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  M0                          47                           120
  M1                           0                             1
  MX                          21                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q22.1) MUTATED    40 115
  DEL PEAK 13(4Q22.1) WILD-TYPE  92 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     40  115
  DEL PEAK 13(4Q22.1) WILD-TYPE   92  241
        clus
vv       DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  FEMALE                          40                            92
  MALE                           115                           241
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q22.1) MUTATED                                     154
  DEL PEAK 13(4Q22.1) WILD-TYPE                                   323
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 13(4Q22.1) MUTATED                                                             0
  DEL PEAK 13(4Q22.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 13(4Q22.1) MUTATED                                                     1
  DEL PEAK 13(4Q22.1) WILD-TYPE                                                   9
D42V8, multiclass
                                                             clus
vv                                                            DEL PEAK 13(4Q22.1) 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                                   1
                                                             clus
vv                                                            DEL PEAK 13(4Q22.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 323
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
[1] 3 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(4Q22.1) MUTATED    27 128
  DEL PEAK 13(4Q22.1) WILD-TYPE  52 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     27  128
  DEL PEAK 13(4Q22.1) WILD-TYPE   52  281
     clus
vv    DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  NO                           27                            52
  YES                         128                           281
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(4Q22.1) MUTATED                                  1     5
  DEL PEAK 13(4Q22.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q22.1) MUTATED                          16   125
  DEL PEAK 13(4Q22.1) WILD-TYPE                        28   290
D42V12, multiclass
                                  clus
vv                                 DEL PEAK 13(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    125
                                  clus
vv                                 DEL PEAK 13(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  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"
D42V13, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q22.1) MUTATED    10 136
  DEL PEAK 13(4Q22.1) WILD-TYPE  14 295
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     10  136
  DEL PEAK 13(4Q22.1) WILD-TYPE   14  295
                        clus
vv                       DEL PEAK 13(4Q22.1) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         136
                        clus
vv                       DEL PEAK 13(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           295
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 14(4Q35.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(4Q35.2) MUTATED   124  47
  DEL PEAK 14(4Q35.2) WILD-TYPE 177  66
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          171                           243 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                           47                            66 
$`DEL PEAK 14(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-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB 
         384          113          895          855          850          216 
TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         142         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 
           5            4          799          721         1157          392 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 
         395          625         1330         1988         1007         1980 
TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1081         1966         1975          630          933          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
          45          432          202          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T 
         429           46          443          535          904          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6228 TCGA-CQ-7064 
         526          348         1422         1393         1959         1560 
TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 
         509         1950         1960          707          950         1663 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7364 
        1050         1971          354          234          379         1435 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1191          105         1979          759          889           30 
TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
         392          946          156          181         1077         1472 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
         522         1950         3295         1438          546         1978 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 
        2327         1958         2437          519         2641         1478 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         215         1665         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        1959         3835         1957         1959         1970         1939 
TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
        1987         1095          954         1967         1976         1099 
TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45Q TCGA-CV-A460 
        1957         1972         1984         1959         1945         1946 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-A4Z9 
         110          714          237          828          701          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         376          483          232          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
         389          338          516          548         1965          575 
TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         299          490          658           15           92          585 
TCGA-F7-A61S TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-8634 TCGA-HD-8635 
           3          414          403            2           24           25 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
          49           10          111          588          412          440 
TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX 
         351          378          112          254         1726         1954 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A8Z7 
         400          553          245          218          228          198 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC 
         135          135         1326         1252         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
         735         1497          665 

$`DEL PEAK 14(4Q35.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          462          415         1983          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
        1288         1762          725         1747          190          644 
TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE 
          63          236          622          918          351          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        1976          314          623          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         1230         1151          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         993          642         1250         1960          811         1268 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5373 
        1045          173         1977         1980         1966          683 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6021 
         290          628          594          629           98         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A49A TCGA-CN-A49C 
        1110          224          318          611          391          645 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1207          654         1660         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1179         1750         1007         1309         1274          877 
TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1353         1963          893          998          785          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         303         2562          358         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1521         1966         1125          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 
         311          345          350          479         1956         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1245         1960          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
        1954          997         1430         1951          907          913 
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-5436 TCGA-CV-5441 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5979 
         584         2886          406          701         1840         1315 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 
         641         1899         1948         1969         1966         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1959         3837         1970         1936         1959         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7406 
        1979         1952         1444          797         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
        1948         1955         1947         1937         1973         1937 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1958         1981          851         5480         1960         1940 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        1959          670          646          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         317          321          773          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-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
        1030          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
         340         1131          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 
         407           58          133          206            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-HL-7533 
          37           55           44           11           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61O TCGA-KU-A66S 
         485          122          441          360          360          224 
TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         552          168           14           34          392           56 
TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         111          240          910         1559         1120          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
        1917         1968          357          225          387          567 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E 
         149          157          168         1663         1319         1278 
TCGA-UF-A7J9 TCGA-UF-A7JJ TCGA-UF-A7JS 
        1043          214          413 

  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                            2                             5 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                         3835                          5480 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          625                           785 
[1] "2.0 - 3835.0 (625.0)" "5.0 - 5480.0 (785.0)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 14(4Q35.2) MUTATED        11       26        41        94         6
  DEL PEAK 14(4Q35.2) WILD-TYPE      15       49        33       141         6
                               vv
clus                            STAGE IVC
  DEL PEAK 14(4Q35.2) MUTATED           1
  DEL PEAK 14(4Q35.2) WILD-TYPE         0
D43V3, multiclass
           clus
vv          DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  STAGE I                            11                            15
  STAGE II                           26                            49
  STAGE III                          41                            33
  STAGE IVA                          94                           141
  STAGE IVB                           6                             6
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 14(4Q35.2) MUTATED      18 45 50 68
  DEL PEAK 14(4Q35.2) WILD-TYPE    29 82 44 94
D43V4, multiclass
       clus
vv      DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  T0+T1                          18                            29
  T2                             45                            82
  T3                             50                            44
  T4                             68                            94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 14(4Q35.2) MUTATED    68  32  61   3
  DEL PEAK 14(4Q35.2) WILD-TYPE 102  31  91   5
D43V5, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  N0                          68                           102
  N1                          32                            31
  N2                          61                            91
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK 14(4Q35.2) MUTATED   68  1 24
  DEL PEAK 14(4Q35.2) WILD-TYPE 99  0 34
D43V6, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  M0                          68                            99
  M1                           1                             0
  MX                          24                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    65 136
  DEL PEAK 14(4Q35.2) WILD-TYPE  67 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     65  136
  DEL PEAK 14(4Q35.2) WILD-TYPE   67  220
        clus
vv       DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  FEMALE                          65                            67
  MALE                           136                           220
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q35.2) MUTATED                                     199
  DEL PEAK 14(4Q35.2) WILD-TYPE                                   278
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 14(4Q35.2) MUTATED                                                             0
  DEL PEAK 14(4Q35.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 14(4Q35.2) MUTATED                                                     2
  DEL PEAK 14(4Q35.2) WILD-TYPE                                                   8
D43V8, multiclass
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               199
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) WILD-TYPE
  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                                     8
[1] 3 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(4Q35.2) MUTATED    32 169
  DEL PEAK 14(4Q35.2) WILD-TYPE  47 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     32  169
  DEL PEAK 14(4Q35.2) WILD-TYPE   47  240
     clus
vv    DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  NO                           32                            47
  YES                         169                           240
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(4Q35.2) MUTATED                                  1     4
  DEL PEAK 14(4Q35.2) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(4Q35.2) MUTATED                          22   166
  DEL PEAK 14(4Q35.2) WILD-TYPE                        22   249
D43V12, multiclass
                                  clus
vv                                 DEL PEAK 14(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    166
                                  clus
vv                                 DEL PEAK 14(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      249
[1] 4 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(4Q35.2) MUTATED    10 178
  DEL PEAK 14(4Q35.2) WILD-TYPE  14 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     10  178
  DEL PEAK 14(4Q35.2) WILD-TYPE   14  253
                        clus
vv                       DEL PEAK 14(4Q35.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         178
                        clus
vv                       DEL PEAK 14(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 15(5Q12.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q12.1) MUTATED   130  44
  DEL PEAK 15(5Q12.1) WILD-TYPE 171  69
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          174                           240 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                           44                            69 
$`DEL PEAK 15(5Q12.1) 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-A4IG TCGA-BA-A4IH 
          63          384          113          236          855          622 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP 
         850          351          216          182          623          142 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8596 
         187          278          133          536          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
         624            5         1157         1230          392          817 
TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
         993          625         1330         1988         1007         1045 
TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 
        1081         1966          630          933          629          432 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A499 TCGA-CN-A63U 
         224          318          394          429          535          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6227 
         348          367         1393          317          985         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
        1179         1560         1007          509         1274         1950 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 
         707          785          950          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         1952         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-A45R TCGA-CV-A45Z TCGA-CV-A460 
        1947         1972         1959         5480         1940         1946 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 
        1075          906          685          317          237          701 
TCGA-D6-6825 TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         491          368          338          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         1131 
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          552           56 
TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 
         240         1726         1954         1968          400          357 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         218          228          387          149          135          135 
TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         157         1663         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
        1894          484          735         1497          665          413 

$`DEL PEAK 15(5Q12.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
        1762          725          623         1636         1747          644 
TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4223 TCGA-BB-4225 
         895          918         1976          314         2878          140 
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-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
         436            4          799          721          142         1151 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         642         1250          395         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-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         683          290          628          594          629           45 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 
          98         1970          202         1110          611          735 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
         432           46          443          391          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         225          484          175          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 
        1207          654         1660         1422         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7063 
         129         1253         1000         1057         1959         1750 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          877         1353         1960         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         998          391          303         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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 
         362          311          345          354          234          479 
TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7383 
        1440          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-CR-7404 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
        1472          584          546         2327         1958          519 
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-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
        1960         1948         1957         1937         1973         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y 
        1984         1958         1981          851         1945         1960 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT 
        1954         1722         1977         1970         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
         110          646          714          606         1950          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-D6-A6EK TCGA-D6-A6EM 
         106          128          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7590 
         435          424          389         1778         1081          775 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
         622          369          340          490          658           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
         585            3           14           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
          58          133          414          206            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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         588          351          224          378          168           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-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IF 
        1559         1120          578         1917          553          245 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A7JJ 
         225          567          198          168         1326          214 

  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                            5                             2 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                         5480                          3835 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          721                           685 
[1] "5.0 - 5480.0 (721.0)" "2.0 - 3835.0 (685.0)"
[1] "hr=" "1.3"
D44V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 15(5Q12.1) MUTATED         9       33        30       106         4
  DEL PEAK 15(5Q12.1) WILD-TYPE      17       42        44       129         8
                               vv
clus                            STAGE IVC
  DEL PEAK 15(5Q12.1) MUTATED           0
  DEL PEAK 15(5Q12.1) WILD-TYPE         1
D44V3, multiclass
           clus
vv          DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  STAGE I                             9                            17
  STAGE II                           33                            42
  STAGE III                          30                            44
  STAGE IVA                         106                           129
  STAGE IVB                           4                             8
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 15(5Q12.1) MUTATED      14 56 35 79
  DEL PEAK 15(5Q12.1) WILD-TYPE    33 71 59 83
D44V4, multiclass
       clus
vv      DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  T0+T1                          14                            33
  T2                             56                            71
  T3                             35                            59
  T4                             79                            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 15(5Q12.1) MUTATED    62  30  72   3
  DEL PEAK 15(5Q12.1) WILD-TYPE 108  33  80   5
D44V5, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  N0                          62                           108
  N1                          30                            33
  N2                          72                            80
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 15(5Q12.1) MUTATED    66   0  23
  DEL PEAK 15(5Q12.1) WILD-TYPE 101   1  35
D44V6, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  M0                          66                           101
  M1                           0                             1
  MX                          23                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    44 160
  DEL PEAK 15(5Q12.1) WILD-TYPE  88 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     44  160
  DEL PEAK 15(5Q12.1) WILD-TYPE   88  196
        clus
vv       DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  FEMALE                          44                            88
  MALE                           160                           196
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(5Q12.1) MUTATED                                     199
  DEL PEAK 15(5Q12.1) WILD-TYPE                                   278
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 15(5Q12.1) MUTATED                                                             1
  DEL PEAK 15(5Q12.1) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 15(5Q12.1) MUTATED                                                     4
  DEL PEAK 15(5Q12.1) WILD-TYPE                                                   6
D44V8, multiclass
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               199
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 278
  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"
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    37 167
  DEL PEAK 15(5Q12.1) WILD-TYPE  42 242
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     37  167
  DEL PEAK 15(5Q12.1) WILD-TYPE   42  242
     clus
vv    DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  NO                           37                            42
  YES                         167                           242
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(5Q12.1) MUTATED                                  1     3
  DEL PEAK 15(5Q12.1) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q12.1) MUTATED                          28   164
  DEL PEAK 15(5Q12.1) WILD-TYPE                        16   251
D44V12, multiclass
                                  clus
vv                                 DEL PEAK 15(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    164
                                  clus
vv                                 DEL PEAK 15(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   16
  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"
D44V13, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    13 171
  DEL PEAK 15(5Q12.1) WILD-TYPE  11 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     13  171
  DEL PEAK 15(5Q12.1) WILD-TYPE   11  260
                        clus
vv                       DEL PEAK 15(5Q12.1) MUTATED
  HISPANIC OR LATINO                              13
  NOT HISPANIC OR LATINO                         171
                        clus
vv                       DEL PEAK 15(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           260
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 16(5Q15) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(5Q15) MUTATED   138  44
  DEL PEAK 16(5Q15) WILD-TYPE 163  69
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                        182                         232 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                         44                          69 
$`DEL PEAK 16(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-A4IG TCGA-BA-A4IH 
          63          384          113          236          855          622 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4217 
         850          351          216          182          142          187 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         278          133          423         1153          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
         624            5         1157         1230          392          817 
TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 
         993          395          625         1330         1988         1007 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1045         1081         1966          630          933          629 
TCGA-CN-6013 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         628          432         1970          224          318          394 
TCGA-CN-6997 TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 
         429          535          526          348          367          298 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
         317          341         1959         1179         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH 
         509         1274         1950          707          785          303 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 
         950          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         1952         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-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6K1 
        5480         1940         1946         1075          906          685 
TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4ZB 
         317          237          701          491          106          376 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         424          368          338         1778          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
         548         1965          575          299          368          324 
TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-A6C4 TCGA-H7-A6C5 
        1131           92          384           14          414          403 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O 
           5           37           33          360          412          360 
TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
         552           56          240         1726         1954         1968 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z7 
         400          357          218          228          387          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B 
         149          135          135          157         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1252         1278         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH 
        1497          665 

$`DEL PEAK 16(5Q15) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
        1762          725          623         1636         1747          644 
TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4223 
         895          918         1976          314          623         2878 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 
         140          558          310          536          687          638 
TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
         436            4          799          721          142         1151 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 
         642         1250         1960          811         1268          173 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1980         1977         1980         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6022 
         290          594          629           45           98          202 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
        1110          611          735          432           46          443 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
         391          904          645          225          484          175 
TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         223         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1393         1399          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
         985         1959         1750         1309          877         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 
        1960         1963          893          998          391         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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1050         1125         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         354          234          479          889           30          972 
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-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-CV-5434 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 
        1077          911         3295          584         2327         1958 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         519          406          701          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-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1969         1966         1959         1936         1959         1945 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 
        1979         1444         1960         1974         1948         1957 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1937         1973         1937         1984         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
         851         1945         1960         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        1970         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         606         1950          321          828          773          292 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK 
          77          154          568          128          539          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 
         232          435          389         1081          775          622 
TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
         369          340          490          658           15          585 
TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
           3           13            6          407           58          133 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
         206            2           25           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 
          25           11           49           10          111         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L 
         485          122          441          588          440          351 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         224          378          168           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         1559         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 
         578         1917          553          245          225          567 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A7JJ TCGA-UF-A7JS 
         168         1326          214          413 

  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                          5                           2 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                       5480                        3835 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                      647.5                       721.5 
[1] "5.0 - 5480.0 (647.5)" "2.0 - 3835.0 (721.5)"
[1] "hr=" "1.2"
D45V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 16(5Q15) MUTATED         9       34        33       111         4
  DEL PEAK 16(5Q15) WILD-TYPE      17       41        41       124         8
                             vv
clus                          STAGE IVC
  DEL PEAK 16(5Q15) MUTATED           0
  DEL PEAK 16(5Q15) WILD-TYPE         1
D45V3, multiclass
           clus
vv          DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  STAGE I                           9                          17
  STAGE II                         34                          41
  STAGE III                        33                          41
  STAGE IVA                       111                         124
  STAGE IVB                         4                           8
  STAGE IVC                         0                           1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 16(5Q15) MUTATED      14 58 38 83
  DEL PEAK 16(5Q15) WILD-TYPE    33 69 56 79
D45V4, multiclass
       clus
vv      DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  T0+T1                        14                          33
  T2                           58                          69
  T3                           38                          56
  T4                           83                          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 16(5Q15) MUTATED    69  30  72   3
  DEL PEAK 16(5Q15) WILD-TYPE 101  33  80   5
D45V5, multiclass
    clus
vv   DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  N0                        69                         101
  N1                        30                          33
  N2                        72                          80
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 MX
  DEL PEAK 16(5Q15) MUTATED   74  0 24
  DEL PEAK 16(5Q15) WILD-TYPE 93  1 34
D45V6, multiclass
    clus
vv   DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  M0                        74                          93
  M1                         0                           1
  MX                        24                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(5Q15) MUTATED    48 167
  DEL PEAK 16(5Q15) WILD-TYPE  84 189
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     48  167
  DEL PEAK 16(5Q15) WILD-TYPE   84  189
        clus
vv       DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  FEMALE                        48                          84
  MALE                         167                         189
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q15) MUTATED                                     209
  DEL PEAK 16(5Q15) WILD-TYPE                                   268
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 16(5Q15) MUTATED                                                             1
  DEL PEAK 16(5Q15) WILD-TYPE                                                           0
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 16(5Q15) MUTATED                                                     5
  DEL PEAK 16(5Q15) WILD-TYPE                                                   5
D45V8, multiclass
                                                             clus
vv                                                            DEL PEAK 16(5Q15) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             209
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 5
                                                             clus
vv                                                            DEL PEAK 16(5Q15) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               268
  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"
D45V9, binary
                             cls
clus                            0   1
  DEL PEAK 16(5Q15) MUTATED    38 177
  DEL PEAK 16(5Q15) WILD-TYPE  41 232
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     38  177
  DEL PEAK 16(5Q15) WILD-TYPE   41  232
     clus
vv    DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  NO                         38                          41
  YES                       177                         232
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(5Q15) MUTATED                                  1     5
  DEL PEAK 16(5Q15) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(5Q15) MUTATED                          28   173
  DEL PEAK 16(5Q15) WILD-TYPE                        16   242
D45V12, multiclass
                                  clus
vv                                 DEL PEAK 16(5Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               28
  WHITE                                                  173
                                  clus
vv                                 DEL PEAK 16(5Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    242
[1] 4 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(5Q15) MUTATED    13 182
  DEL PEAK 16(5Q15) WILD-TYPE  11 249
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     13  182
  DEL PEAK 16(5Q15) WILD-TYPE   11  249
                        clus
vv                       DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  HISPANIC OR LATINO                            13                          11
  NOT HISPANIC OR LATINO                       182                         249
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 17(5Q35.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(5Q35.3) MUTATED   124  41
  DEL PEAK 17(5Q35.3) WILD-TYPE 177  72
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                          165                           249 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                           41                            72 
$`DEL PEAK 17(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-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
         113          236          855          622          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7862 
         216          182          142          187          278          536 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 
         687         1153         1955          624            5         1157 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 
        1230          392          817          993          625         1330 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 
        1988         1007         1045         1081         1966          630 
TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         629          432         1970          224          318          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63W 
         735          432          429          535          526          348 
TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
         367          317         1959         1179         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH 
         509         1274         1950          707          785          303 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6493 
         950          358         1971          514          379         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1435         1191         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 
         759           30         1036          907          156          181 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5440 
        1472          522         1950         3295         1438         1978 
TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
        2886         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 
        1665         1970         1959         1957         1969         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 
        1959         1970         1939         1987         1095          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-7435 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CV-A6JU TCGA-CX-7082 
        1959         5480         1940         1075          110          317 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A6EO TCGA-D6-A6EP 
         237          701          154          106          435          424 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         368          338          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         1131           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          552           56          254 
TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH 
         240         1726         1954          357          218          228 
TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B 
         387          198          149          157         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1252         1278         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1497          665          214 

$`DEL PEAK 17(5Q35.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          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-A4IF TCGA-BA-A4II TCGA-BA-A6DG TCGA-BA-A6DJ 
         644           63          895          918         1976          314 
TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
         623         2878          140          133          558          310 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 
         423          638          428          436            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         721          142         1151          642         1250          395 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
        1960          811         1268          173         1980         1977 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1980         1966         1975          683          290          933 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6022 
         628          594          629           45           98          202 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
        1110          611           46          443          391          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 
         645          225          484          175          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
         985         1959         1750         1309          877         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 
        1960         1963          893          998          391         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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1050         1125         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 
         354          234          350          479         1440          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-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 
         930          216         1077          911         1955          584 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         701          641         1899         1948         1969         1952 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7097 
        3835         1948         1969         1966         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1936         1959         1945         1979         1952         1444 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 
        1960         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-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1945         1960         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        1970          906         1959          670          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 
         606          685         1950          321          828          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 
         292           77          491          568          128          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
         376          483          232          389         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-A6C5 TCGA-H7-A76A TCGA-HD-7229 
         407           58          133          403          206            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-KU-A6H7 TCGA-KU-A6H8 
         588          440          351          224          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 
          14           34          392          111          112          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1559         1120          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         553          245          225          567          135          135 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A7JS 
         168         1326          413 

  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                            5                             2 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                         5480                          3835 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                          665                           721 
[1] "5.0 - 5480.0 (665.0)" "2.0 - 3835.0 (721.0)"
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 17(5Q35.3) MUTATED         8       28        34        96         4
  DEL PEAK 17(5Q35.3) WILD-TYPE      18       47        40       139         8
                               vv
clus                            STAGE IVC
  DEL PEAK 17(5Q35.3) MUTATED           0
  DEL PEAK 17(5Q35.3) WILD-TYPE         1
D46V3, multiclass
           clus
vv          DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  STAGE I                             8                            18
  STAGE II                           28                            47
  STAGE III                          34                            40
  STAGE IVA                          96                           139
  STAGE IVB                           4                             8
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1 T2 T3 T4
  DEL PEAK 17(5Q35.3) MUTATED      11 52 40 68
  DEL PEAK 17(5Q35.3) WILD-TYPE    36 75 54 94
D46V4, multiclass
       clus
vv      DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  T0+T1                          11                            36
  T2                             52                            75
  T3                             40                            54
  T4                             68                            94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 17(5Q35.3) MUTATED    62  28  65   2
  DEL PEAK 17(5Q35.3) WILD-TYPE 108  35  87   6
D46V5, multiclass
    clus
vv   DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  N0                          62                           108
  N1                          28                            35
  N2                          65                            87
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK 17(5Q35.3) MUTATED   68  0 19
  DEL PEAK 17(5Q35.3) WILD-TYPE 99  1 39
D46V6, multiclass
    clus
vv   DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  M0                          68                            99
  M1                           0                             1
  MX                          19                            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q35.3) MUTATED    44 147
  DEL PEAK 17(5Q35.3) WILD-TYPE  88 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q35.3) MUTATED     44  147
  DEL PEAK 17(5Q35.3) WILD-TYPE   88  209
        clus
vv       DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  FEMALE                          44                            88
  MALE                           147                           209
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(5Q35.3) MUTATED                                     185
  DEL PEAK 17(5Q35.3) WILD-TYPE                                   292
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 17(5Q35.3) MUTATED                                                             1
  DEL PEAK 17(5Q35.3) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 17(5Q35.3) MUTATED                                                     5
  DEL PEAK 17(5Q35.3) WILD-TYPE                                                   5
D46V8, multiclass
                                                             clus
vv                                                            DEL PEAK 17(5Q35.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               185
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
                                                             clus
vv                                                            DEL PEAK 17(5Q35.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 292
  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"
D46V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q35.3) MUTATED    34 157
  DEL PEAK 17(5Q35.3) WILD-TYPE  45 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q35.3) MUTATED     34  157
  DEL PEAK 17(5Q35.3) WILD-TYPE   45  252
     clus
vv    DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  NO                           34                            45
  YES                         157                           252
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(5Q35.3) MUTATED                                  1     4
  DEL PEAK 17(5Q35.3) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(5Q35.3) MUTATED                          23   154
  DEL PEAK 17(5Q35.3) WILD-TYPE                        21   261
D46V12, multiclass
                                  clus
vv                                 DEL PEAK 17(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 23
  WHITE                                                    154
                                  clus
vv                                 DEL PEAK 17(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      261
[1] 4 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(5Q35.3) MUTATED    11 162
  DEL PEAK 17(5Q35.3) WILD-TYPE  13 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q35.3) MUTATED     11  162
  DEL PEAK 17(5Q35.3) WILD-TYPE   13  269
                        clus
vv                       DEL PEAK 17(5Q35.3) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         162
                        clus
vv                       DEL PEAK 17(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           269
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 18(6P25.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(6P25.3) MUTATED    54  25
  DEL PEAK 18(6P25.3) WILD-TYPE 247  88
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           79                           335 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           25                            88 
$`DEL PEAK 18(6P25.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-5152 TCGA-BA-5559 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7862 
         102         1288         1747          140          133          536 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5359 
         721         1157         1151         1250          811         1980 
TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 
        1975          630          594          202          224          611 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A641 
         735          429          443          391          225          367 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI 
         317         1000         1057          707          998          950 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7371 
        1125         1969          379         1956         1191         1979 
TCGA-CR-7373 TCGA-CR-7388 TCGA-CR-7399 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         889         1951          181         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6934 
         584         1978         1958         2437          215         1948 
TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7248 TCGA-CV-7254 
        1969         1969         1970         1939         1967         1976 
TCGA-CV-7418 TCGA-CV-7430 TCGA-CV-A6JT TCGA-CV-A6JY TCGA-D6-6823 TCGA-D6-6826 
        1955         1972          670          646          701          154 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-F7-A50I 
         368          338         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-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T8 TCGA-QK-A8ZA TCGA-UF-A71E 
         240         1726          578          400          135         1278 
TCGA-UF-A7JJ 
         214 

$`DEL PEAK 18(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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 
         142          187         2878          278          558          310 
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-4726 
        1955          624            5            4          799          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        1230          392          817          993          642          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         625         1960         1330         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1045          173         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1966          683          290          933          629          628 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
         629           45          432           98         1970         1110 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B 
         318          394          432           46          535          904 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V1 
         645          526          484          348          175          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 
        1393         1399          341          129         1253          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1960         1963          893          785          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         1952         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-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU 
        1977         1970         1075          906         1959          110 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          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-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 
         232          435          424          389         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 
        1030          548         1965          775          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          15          585            3          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         360          224          552          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          34          392           56          111          254          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z 
        1559         1120         1954         1917         1968          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         567          198          149          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA 
        1326         1663         1319         1252         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         484          735         1497          665          413 

  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                            5                             2 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                         3295                          5480 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                          707                           687 
[1] "5.0 - 3295.0 (707.0)" "2.0 - 5480.0 (687.0)"
[1] "hr=" "1"  
D47V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 18(6P25.3) MUTATED         2       10        13        55         2
  DEL PEAK 18(6P25.3) WILD-TYPE      24       65        61       180        10
                               vv
clus                            STAGE IVC
  DEL PEAK 18(6P25.3) MUTATED           0
  DEL PEAK 18(6P25.3) WILD-TYPE         1
D47V3, multiclass
           clus
vv          DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  STAGE I                             2                            24
  STAGE II                           10                            65
  STAGE III                          13                            61
  STAGE IVA                          55                           180
  STAGE IVB                           2                            10
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 18(6P25.3) MUTATED       5  18  21  39
  DEL PEAK 18(6P25.3) WILD-TYPE    42 109  73 123
D47V4, multiclass
       clus
vv      DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  T0+T1                           5                            42
  T2                             18                           109
  T3                             21                            73
  T4                             39                           123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 18(6P25.3) MUTATED    29  11  34   1
  DEL PEAK 18(6P25.3) WILD-TYPE 141  52 118   7
D47V5, multiclass
    clus
vv   DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  N0                          29                           141
  N1                          11                            52
  N2                          34                           118
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 18(6P25.3) MUTATED    26   0  14
  DEL PEAK 18(6P25.3) WILD-TYPE 141   1  44
D47V6, multiclass
    clus
vv   DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  M0                          26                           141
  M1                           0                             1
  MX                          14                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED    19  72
  DEL PEAK 18(6P25.3) WILD-TYPE 113 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED     19   72
  DEL PEAK 18(6P25.3) WILD-TYPE  113  284
        clus
vv       DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  FEMALE                          19                           113
  MALE                            72                           284
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6P25.3) MUTATED                                      89
  DEL PEAK 18(6P25.3) WILD-TYPE                                   388
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 18(6P25.3) MUTATED                                                             0
  DEL PEAK 18(6P25.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 18(6P25.3) MUTATED                                                     2
  DEL PEAK 18(6P25.3) WILD-TYPE                                                   8
D47V8, multiclass
                                                             clus
vv                                                            DEL PEAK 18(6P25.3) 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                                   2
                                                             clus
vv                                                            DEL PEAK 18(6P25.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 388
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
[1] 3 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(6P25.3) MUTATED    17  74
  DEL PEAK 18(6P25.3) WILD-TYPE  62 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED     17   74
  DEL PEAK 18(6P25.3) WILD-TYPE   62  335
     clus
vv    DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  NO                           17                            62
  YES                          74                           335
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(6P25.3) MUTATED                                  0     0
  DEL PEAK 18(6P25.3) WILD-TYPE                                2    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(6P25.3) MUTATED                          14    72
  DEL PEAK 18(6P25.3) WILD-TYPE                        30   343
D47V12, multiclass
                                  clus
vv                                 DEL PEAK 18(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                     72
                                  clus
vv                                 DEL PEAK 18(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   30
  WHITE                                                      343
[1] 4 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(6P25.3) MUTATED     4  78
  DEL PEAK 18(6P25.3) WILD-TYPE  20 353
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED      4   78
  DEL PEAK 18(6P25.3) WILD-TYPE   20  353
                        clus
vv                       DEL PEAK 18(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          78
                        clus
vv                       DEL PEAK 18(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           353
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 19(7Q31.1) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(7Q31.1) MUTATED    44  21
  DEL PEAK 19(7Q31.1) WILD-TYPE 257  92
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           65                           349 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           21                            92 
$`DEL PEAK 19(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-A4IH TCGA-BA-A6DE TCGA-BB-7861 TCGA-BB-7872 TCGA-C9-A47Z 
         384          622          182          310          436            5 
TCGA-C9-A480 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-5359 
           4          817          993         1250          625         1980 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6998 TCGA-CN-A49B 
         290          933           45          318           46          904 
TCGA-CN-A6V3 TCGA-CQ-6218 TCGA-CQ-A4CA TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-7365 
         298         1253         1963          358         1971         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5444 
        1440         1245           30          156          181         2437 
TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
        2641         1665         1957         1969         1959         1959 
TCGA-CV-7180 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JE TCGA-CX-7082 
        1987         1984         1959         1981         1075          317 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EM TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A623 
         701          154          232          658           15            6 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-KU-A66T TCGA-KU-A6H7 TCGA-P3-A5QE 
         441          360          412          552          378         1559 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A8Z9 TCGA-QK-A8ZB 
        1954         1968          553          149          135 

$`DEL PEAK 19(7Q31.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 
         102          283         1983          276          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-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II 
          63          113          236          895          855          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         850          351          216         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
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-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         428         1955          624          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4736 
         142         1230         1151          392          642          395 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1045          173         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 
        1966         1975          683          630          629          628 
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-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
        1110          224          611          394          735          432 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
         429          443          535          391          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         526          484          348          175          367          223 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          317          341          129         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1007          509         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1353         1960          707          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         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         1952         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-A45R TCGA-CV-A45Y 
        1937         1958          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         606          685         1950          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
         773          292           77          491          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
         128          539          376          483          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         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-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         490           92          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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         206            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-A61E 
         111           33         1057          485          122          588 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
         440          351          360          224          168           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-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         240          910         1726         1120          578         1917 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         400          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K 
         387          567          198          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1326         1663         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS 
         413 

  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                            4                             2 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                         2641                          5480 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                          622                           721 
[1] "4.0 - 2641.0 (622.0)" "2.0 - 5480.0 (721.0)"
[1] "hr=" "1"  
D48V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 19(7Q31.1) MUTATED         3       10        12        40         0
  DEL PEAK 19(7Q31.1) WILD-TYPE      23       65        62       195        12
                               vv
clus                            STAGE IVC
  DEL PEAK 19(7Q31.1) MUTATED           0
  DEL PEAK 19(7Q31.1) WILD-TYPE         1
D48V3, multiclass
           clus
vv          DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  STAGE I                             3                            23
  STAGE II                           10                            65
  STAGE III                          12                            62
  STAGE IVA                          40                           195
  STAGE IVB                           0                            12
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 19(7Q31.1) MUTATED       5  22  14  24
  DEL PEAK 19(7Q31.1) WILD-TYPE    42 105  80 138
D48V4, multiclass
       clus
vv      DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  T0+T1                           5                            42
  T2                             22                           105
  T3                             14                            80
  T4                             24                           138
[1] 4 2
[1] TRUE
[1] "dimension 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(7Q31.1) MUTATED    18  16  26   0
  DEL PEAK 19(7Q31.1) WILD-TYPE 152  47 126   8
D48V5, multiclass
    clus
vv   DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  N0                          18                           152
  N1                          16                            47
  N2                          26                           126
  N3                           0                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 19(7Q31.1) MUTATED    24   0   8
  DEL PEAK 19(7Q31.1) WILD-TYPE 143   1  50
D48V6, multiclass
    clus
vv   DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  M0                          24                           143
  M1                           0                             1
  MX                           8                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(7Q31.1) MUTATED    20  53
  DEL PEAK 19(7Q31.1) WILD-TYPE 112 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q31.1) MUTATED     20   53
  DEL PEAK 19(7Q31.1) WILD-TYPE  112  303
        clus
vv       DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  FEMALE                          20                           112
  MALE                            53                           303
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(7Q31.1) MUTATED                                      71
  DEL PEAK 19(7Q31.1) WILD-TYPE                                   406
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 19(7Q31.1) MUTATED                                                             0
  DEL PEAK 19(7Q31.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 19(7Q31.1) MUTATED                                                     2
  DEL PEAK 19(7Q31.1) WILD-TYPE                                                   8
D48V8, multiclass
                                                             clus
vv                                                            DEL PEAK 19(7Q31.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                71
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
                                                             clus
vv                                                            DEL PEAK 19(7Q31.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 406
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
[1] 3 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(7Q31.1) MUTATED    15  58
  DEL PEAK 19(7Q31.1) WILD-TYPE  64 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q31.1) MUTATED     15   58
  DEL PEAK 19(7Q31.1) WILD-TYPE   64  351
     clus
vv    DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  NO                           15                            64
  YES                          58                           351
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(7Q31.1) MUTATED                                  0     3
  DEL PEAK 19(7Q31.1) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(7Q31.1) MUTATED                           7    62
  DEL PEAK 19(7Q31.1) WILD-TYPE                        37   353
D48V12, multiclass
                                  clus
vv                                 DEL PEAK 19(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     62
                                  clus
vv                                 DEL PEAK 19(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      353
[1] 4 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(7Q31.1) MUTATED     3  67
  DEL PEAK 19(7Q31.1) WILD-TYPE  21 364
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q31.1) MUTATED      3   67
  DEL PEAK 19(7Q31.1) WILD-TYPE   21  364
                        clus
vv                       DEL PEAK 19(7Q31.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       DEL PEAK 19(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           364
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 20(7Q36.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(7Q36.1) MUTATED    73  33
  DEL PEAK 20(7Q36.1) WILD-TYPE 228  80
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                          106                           308 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                           33                            80 
$`DEL PEAK 20(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-A4IG TCGA-BA-A4IH TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-7863 
         236          855          622          182          142          423 
TCGA-BB-7872 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 
         436          392          817          993         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
         625         1960         1007          173         1980         1977 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
         290          933          629          628          594           45 
TCGA-CN-6988 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63U 
         318          429           46          535          904          526 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5331 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-7067 
         348          175         1399         1000         1959          509 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6478 
        1960         1963          893          358         1971         1969 
TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7374 TCGA-CR-7385 
         350         1191         1245         1960           30          997 
TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 
         156          522         2437         1665         1970         1969 
TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7180 
        1959         1957         1969         1959         1959         1987 
TCGA-CV-7254 TCGA-CV-7424 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A6JE TCGA-CV-A6JU 
        1976         1947         1984         1959         1075          110 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EM 
         685          317          828          701          154          232 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-7588 TCGA-DQ-7594 TCGA-F7-8489 TCGA-F7-A50G 
         435          368         1965          368          658           15 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7632 
          14            6          133          111         1057          441 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67A 
         412          440          552          378           14          392 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
        1559         1954         1968          400          149          135 
TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JS 
         157         1326         1894          413 

$`DEL PEAK 20(7Q36.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         102          283         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-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 
         451          384          113          895          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
         351          216         1976          314          623          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-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         536          687          638         1153          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4739 TCGA-CN-4740 
         142         1230         1151          642         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 
        1268         1988         1045         1081         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 
        1966         1975          683          630          629          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 
          98         1970          202         1110          224          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C 
         394          735          432          443          391          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         225          484          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 
        1207          654         1660         1422         1393          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         341          129         1253         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1179         1750         1560         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
         877         1950         1353          707          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         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-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-7367 TCGA-CR-7370 
         379          479         1956         1435         1440          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-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         796         1954         1430         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-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-5440 TCGA-CV-5441 
        3295         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840          215         1315          641         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1948         1952         3835         1948         1969         1966 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        3837         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1945         1979         1952         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-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1937         1973         1972         1937 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1958         1981          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          670          646          714          606 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
        1950          321          237          773          292           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         483          424          389          338         1778         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-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         299          369          324          340         1131          490 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 
          92          585            3          384           13          407 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
          58          414          403          206            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-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
          11           49           10           33          485          122 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 
         588          360          351          360          224          168 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
          34           56          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z 
         910         1726         1120          578         1917          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71B 
         567          198          135          168         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1252         1278         1043          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ 
         665          214 

  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                            6                             2 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                         2437                          5480 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                        623.5                         730.0 
[1] "6.0 - 2437.0 (623.5)" "2.0 - 5480.0 (730.0)"
[1] "hr=" "1.1"
D49V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 20(7Q36.1) MUTATED         7       14        18        61         5
  DEL PEAK 20(7Q36.1) WILD-TYPE      19       61        56       174         7
                               vv
clus                            STAGE IVC
  DEL PEAK 20(7Q36.1) MUTATED           0
  DEL PEAK 20(7Q36.1) WILD-TYPE         1
D49V3, multiclass
           clus
vv          DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  STAGE I                             7                            19
  STAGE II                           14                            61
  STAGE III                          18                            56
  STAGE IVA                          61                           174
  STAGE IVB                           5                             7
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 20(7Q36.1) MUTATED      13  32  20  45
  DEL PEAK 20(7Q36.1) WILD-TYPE    34  95  74 117
D49V4, multiclass
       clus
vv      DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  T0+T1                          13                            34
  T2                             32                            95
  T3                             20                            74
  T4                             45                           117
[1] 4 2
[1] TRUE
[1] "dimension 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(7Q36.1) MUTATED    36  20  40   4
  DEL PEAK 20(7Q36.1) WILD-TYPE 134  43 112   4
D49V5, multiclass
    clus
vv   DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  N0                          36                           134
  N1                          20                            43
  N2                          40                           112
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 20(7Q36.1) MUTATED    39   0  15
  DEL PEAK 20(7Q36.1) WILD-TYPE 128   1  43
D49V6, multiclass
    clus
vv   DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  M0                          39                           128
  M1                           0                             1
  MX                          15                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q36.1) MUTATED    29  95
  DEL PEAK 20(7Q36.1) WILD-TYPE 103 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.1) MUTATED     29   95
  DEL PEAK 20(7Q36.1) WILD-TYPE  103  261
        clus
vv       DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  FEMALE                          29                           103
  MALE                            95                           261
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q36.1) MUTATED                                     121
  DEL PEAK 20(7Q36.1) WILD-TYPE                                   356
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 20(7Q36.1) MUTATED                                                             0
  DEL PEAK 20(7Q36.1) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 20(7Q36.1) MUTATED                                                     3
  DEL PEAK 20(7Q36.1) WILD-TYPE                                                   7
D49V8, multiclass
                                                             clus
vv                                                            DEL PEAK 20(7Q36.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               121
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
                                                             clus
vv                                                            DEL PEAK 20(7Q36.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 356
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
[1] 3 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(7Q36.1) MUTATED    21 103
  DEL PEAK 20(7Q36.1) WILD-TYPE  58 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.1) MUTATED     21  103
  DEL PEAK 20(7Q36.1) WILD-TYPE   58  306
     clus
vv    DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  NO                           21                            58
  YES                         103                           306
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(7Q36.1) MUTATED                                  0     3
  DEL PEAK 20(7Q36.1) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(7Q36.1) MUTATED                          15   104
  DEL PEAK 20(7Q36.1) WILD-TYPE                        29   311
D49V12, multiclass
                                  clus
vv                                 DEL PEAK 20(7Q36.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    104
                                  clus
vv                                 DEL PEAK 20(7Q36.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      311
[1] 4 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(7Q36.1) MUTATED     5 111
  DEL PEAK 20(7Q36.1) WILD-TYPE  19 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.1) MUTATED      5  111
  DEL PEAK 20(7Q36.1) WILD-TYPE   19  320
                        clus
vv                       DEL PEAK 20(7Q36.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         111
                        clus
vv                       DEL PEAK 20(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           320
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 21(8P23.2) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(8P23.2) MUTATED   159  74
  DEL PEAK 21(8P23.2) WILD-TYPE 142  39
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          233                           181 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                           74                            39 
$`DEL PEAK 21(8P23.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 
         102          462         1983          248          722          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
         623         1636          190          451          384          113 
TCGA-BA-7269 TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DJ 
         236          918          850          216          182          314 
TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 
         142          278          133          536          423         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
         428          436            5            4          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         142         1230          392         1250          395         1960 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         811         1988         1045         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1966         1966         1975          683          290          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6024 
         629          628          594           45           98          224 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A 
         611          394          432          429          443          391 
TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
         904          348          367          654         1422         1393 
TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         317          129         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
        1274          877         1950         1353         1960          893 
TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6471 TCGA-CR-6474 
         998          950         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         1952         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-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JD 
        1945         5480         1940         1946         1722         1970 
TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        1075         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 
         606          317          828          292          701          491 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         154          106          539          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         368          389         1778         1081         1030          548 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         575          299         1131          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-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 
          58          133          414            2            5           55 
TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E 
          25           49           33         1057          485          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X 
         360          412          440          351          552           34 
TCGA-MT-A67D TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
          56          254          240         1726         1954         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
         400          553          357          218          228          387 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71B 
         149          135          135          157          168         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JJ 
        1252         1278         1043         1894          214 

$`DEL PEAK 21(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-A4IG TCGA-BA-A4IH 
        1747          644           63          895          855          622 
TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
         351         1976          623          187         2878          140 
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-CN-4722 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4737 
         799         1151          817          993          642          625 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-6010 
        1330         1268         1007          173         1980          630 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
         629          432         1970          202         1110          318 
TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         735           46          535          645          225          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         484          175          223          298         1466         1207 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-A4C9 
        1660         1399          341         1253         1000          707 
TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
        1963          785          391          303         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
         799         1777         1521         1050         1125          514 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
         362          311          345          234          350          479 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7379 
        1956         1191         1245          105         1979         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         796          997          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5439 
         898          216          156          911         1472          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 
        1978         2327         1958          406          701          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6945 
        1315         1665          641         1948         1959         1969 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7242 
        1959         1959         1939         1987         1979         1095 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7432 TCGA-CV-7435 
        1960         1974         1948         1955         1937         1959 
TCGA-CV-A45O TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JN TCGA-CV-A6K1 
         851         1960         1954         1977          906          685 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6827 
        1950          321          237          773           77          568 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 
         128          376          483          338          516         1965 
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-A61V TCGA-H7-7774 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 
         384          407          403          206           25           37 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7631 
          44           24           11           10          111          122 
TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         441          360          224          378          168           14 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         392          111          112          910         1559         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 
         578         1917          245          225          567          198 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1326         1663          484          735         1497          665 
TCGA-UF-A7JS 
         413 

  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                            2                            10 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                         5480                          2878 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          759                           644 
[1] "2.0 - 5480.0 (759.0)"  "10.0 - 2878.0 (644.0)"
[1] "hr=" "1.1"
D50V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 21(8P23.2) MUTATED        16       43        48       144         9
  DEL PEAK 21(8P23.2) WILD-TYPE      10       32        26        91         3
                               vv
clus                            STAGE IVC
  DEL PEAK 21(8P23.2) MUTATED           1
  DEL PEAK 21(8P23.2) WILD-TYPE         0
D50V3, multiclass
           clus
vv          DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  STAGE I                            16                            10
  STAGE II                           43                            32
  STAGE III                          48                            26
  STAGE IVA                         144                            91
  STAGE IVB                           9                             3
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 21(8P23.2) MUTATED      27  72  59 104
  DEL PEAK 21(8P23.2) WILD-TYPE    20  55  35  58
D50V4, multiclass
       clus
vv      DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  T0+T1                          27                            20
  T2                             72                            55
  T3                             59                            35
  T4                            104                            58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2 N3
  DEL PEAK 21(8P23.2) MUTATED   98 43 93  5
  DEL PEAK 21(8P23.2) WILD-TYPE 72 20 59  3
D50V5, multiclass
    clus
vv   DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  N0                          98                            72
  N1                          43                            20
  N2                          93                            59
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 21(8P23.2) MUTATED   106   1  30
  DEL PEAK 21(8P23.2) WILD-TYPE  61   0  28
D50V6, multiclass
    clus
vv   DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  M0                         106                            61
  M1                           1                             0
  MX                          30                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED    82 201
  DEL PEAK 21(8P23.2) WILD-TYPE  50 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED     82  201
  DEL PEAK 21(8P23.2) WILD-TYPE   50  155
        clus
vv       DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  FEMALE                          82                            50
  MALE                           201                           155
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(8P23.2) MUTATED                                     280
  DEL PEAK 21(8P23.2) WILD-TYPE                                   197
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 21(8P23.2) MUTATED                                                             0
  DEL PEAK 21(8P23.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 21(8P23.2) MUTATED                                                     3
  DEL PEAK 21(8P23.2) WILD-TYPE                                                   7
D50V8, multiclass
                                                             clus
vv                                                            DEL PEAK 21(8P23.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               280
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
                                                             clus
vv                                                            DEL PEAK 21(8P23.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 197
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
[1] 3 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(8P23.2) MUTATED    47 236
  DEL PEAK 21(8P23.2) WILD-TYPE  32 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED     47  236
  DEL PEAK 21(8P23.2) WILD-TYPE   32  173
     clus
vv    DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  NO                           47                            32
  YES                         236                           173
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(8P23.2) MUTATED                                  1     9
  DEL PEAK 21(8P23.2) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8P23.2) MUTATED                          25   238
  DEL PEAK 21(8P23.2) WILD-TYPE                        19   177
D50V12, multiclass
                                  clus
vv                                 DEL PEAK 21(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    238
                                  clus
vv                                 DEL PEAK 21(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED    18 247
  DEL PEAK 21(8P23.2) WILD-TYPE   6 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED     18  247
  DEL PEAK 21(8P23.2) WILD-TYPE    6  184
                        clus
vv                       DEL PEAK 21(8P23.2) MUTATED
  HISPANIC OR LATINO                              18
  NOT HISPANIC OR LATINO                         247
                        clus
vv                       DEL PEAK 21(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           184
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 22(9P23) MUTATION ANALYSIS
D51V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 22(9P23) MUTATED   140  55
  DEL PEAK 22(9P23) WILD-TYPE 161  58
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        195                         219 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         55                          58 
$`DEL PEAK 22(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-A4II TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP 
         895          918          850          182          623          142 
TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         278          536          423         1153          428          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
        1955          624          721          142         1230          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 
         817          993         1250          625          811         1988 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6020 
        1045         1081         1980         1966          629           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-A49A TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 
         429          391          526          484          348          367 
TCGA-CQ-5327 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1660          317         1000          985         1959         1959 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
        1750         1560         1007          509         1274         1950 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 
        1963          893          950          358         1050         1971 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 
         514          354          379          350         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 
        1440         1245          759          889           30         1954 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
        1951          392          907          216          156         1077 
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-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        2641         1478         1315         1970         1948         1969 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        3835         1969         1969         3837         1959         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1939         1945         1987         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7430 
         954          797         1099         1955         1957         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45Y 
        1937         1984         1959         1981         1945         1960 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1946         1954         1722          670          110          646 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
        1950          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          539          376 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 
         435          424          368          389          338          516 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I 
         548         1965          575          324         1131           92 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          14            6           58          403            2            5 
TCGA-HD-7754 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G 
          25           25           49          111          485          360 
TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5QA 
         440          552           34           56          240         1726 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
        1954         1968          400          553          228          387 
TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         198          135          157         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
        1252         1278         1043         1894          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

$`DEL PEAK 22(9P23) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
         102         1983          722         1288         1762          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH 
         623         1636         1747          113          855          622 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
         351          216         1976          314          187         2878 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 
         140          133          558          310          687          638 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 
           5            4          799         1157         1151          642 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 
         395         1960         1330         1268         1007          173 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1977         1966         1975          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          933          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
         432         1110          735          432           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63Y TCGA-CN-A6V1 
         535          904          645          225          175          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
         298         1466         1207          654         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6229 
        1399          341          129         1253         1057         1179 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CD 
        1309          877         1353         1960          707          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         785          391          303         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6478 
         799         1777         1521         1966         1125         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 
         362          311          345          234          479         1956 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1960          105         1979          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         796          997         1430          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         898          930          181          911         1472          522 
TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
        3295         1978         2886         2327         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
         406          701         1840          215         1665          641 
TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1899         1952         1959         1948         1966         1957 
TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7248 
        1959         1970         1936         1959         1979         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 
        1960         1976         1974         1948         1947         1937 
TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A468 
        1973         1958          851         5480         1940         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CV-A6K0 
        1970         1075          906         1959          714          606 
TCGA-CV-A6K1 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK 
         685          321           77          491          568          483 
TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         232         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-H7-A76A TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         133          414          206           37           55           44 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          24           11           10           33         1057          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         441          588          412          351          360          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
         378          168           14          392          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         254          910         1559         1120          578         1917 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z9 
         357          245          218          225          567          149 
TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A7JC 
         135          168          484 

  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                          2                           3 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                       3837                        5480 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        670                         707 
[1] "2.0 - 3837.0 (670.0)" "3.0 - 5480.0 (707.0)"
[1] "hr=" "1.1"
D51V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 22(9P23) MUTATED        11       33        31       117         6
  DEL PEAK 22(9P23) WILD-TYPE      15       42        43       118         6
                             vv
clus                          STAGE IVC
  DEL PEAK 22(9P23) MUTATED           1
  DEL PEAK 22(9P23) WILD-TYPE         0
D51V3, multiclass
           clus
vv          DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  STAGE I                          11                          15
  STAGE II                         33                          42
  STAGE III                        31                          43
  STAGE IVA                       117                         118
  STAGE IVB                         6                           6
  STAGE IVC                         1                           0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1 T2 T3 T4
  DEL PEAK 22(9P23) MUTATED      18 55 44 84
  DEL PEAK 22(9P23) WILD-TYPE    29 72 50 78
D51V4, multiclass
       clus
vv      DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  T0+T1                        18                          29
  T2                           55                          72
  T3                           44                          50
  T4                           84                          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 22(9P23) MUTATED   84 28 71  3
  DEL PEAK 22(9P23) WILD-TYPE 86 35 81  5
D51V5, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  N0                        84                          86
  N1                        28                          35
  N2                        71                          81
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 MX
  DEL PEAK 22(9P23) MUTATED   78  1 22
  DEL PEAK 22(9P23) WILD-TYPE 89  0 36
D51V6, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  M0                        78                          89
  M1                         1                           0
  MX                        22                          36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                             cls
clus                            0   1
  DEL PEAK 22(9P23) MUTATED    52 172
  DEL PEAK 22(9P23) WILD-TYPE  80 184
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     52  172
  DEL PEAK 22(9P23) WILD-TYPE   80  184
        clus
vv       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  FEMALE                        52                          80
  MALE                         172                         184
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(9P23) MUTATED                                     220
  DEL PEAK 22(9P23) WILD-TYPE                                   257
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 22(9P23) MUTATED                                                             0
  DEL PEAK 22(9P23) WILD-TYPE                                                           1
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 22(9P23) MUTATED                                                     4
  DEL PEAK 22(9P23) WILD-TYPE                                                   6
D51V8, multiclass
                                                             clus
vv                                                            DEL PEAK 22(9P23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                             220
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                         0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 4
                                                             clus
vv                                                            DEL PEAK 22(9P23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               257
  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(9P23) MUTATED    34 190
  DEL PEAK 22(9P23) WILD-TYPE  45 219
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     34  190
  DEL PEAK 22(9P23) WILD-TYPE   45  219
     clus
vv    DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  NO                         34                          45
  YES                       190                         219
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(9P23) MUTATED                                  1     5
  DEL PEAK 22(9P23) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P23) MUTATED                          26   183
  DEL PEAK 22(9P23) WILD-TYPE                        18   232
D51V12, multiclass
                                  clus
vv                                 DEL PEAK 22(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               26
  WHITE                                                  183
                                  clus
vv                                 DEL PEAK 22(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    232
[1] 4 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(9P23) MUTATED    12 189
  DEL PEAK 22(9P23) WILD-TYPE  12 242
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     12  189
  DEL PEAK 22(9P23) WILD-TYPE   12  242
                        clus
vv                       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  HISPANIC OR LATINO                            12                          12
  NOT HISPANIC OR LATINO                       189                         242
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 23(9P21.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 23(9P21.3) MUTATED   168  72
  DEL PEAK 23(9P21.3) WILD-TYPE 133  41
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          240                           174 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                           72                            41 
$`DEL PEAK 23(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-A4II TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 
         918          850          182          623          142          278 
TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         133          536         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         624            4          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 
        1151          392          817          993         1250          625 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 
        1330          811         1988         1007         1045         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6012 
        1977         1980         1966          683          933          629 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
         594           45           98         1970          202          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A49A 
         318          611          394          429           46          391 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 
         526          348          367          298         1207          654 
TCGA-CQ-5327 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        1660          317         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1274          877         1950          707         1963          893 
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         1952         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-A45Y 
        1984         1958         1959         1981         1945         1960 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1946         1954         1722          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         714          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
         828          292          701          154          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         539          376          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
         338         1081          516          548         1965          575 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
         324         1131          490           15           92          384 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 
          14            6          407          133          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-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
          11           49          111           33          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-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A6SX 
         552          168           34           56          240         1954 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A8Z7 
         578         1968          400          553          228          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1663         1319         1252         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          665          214          413 

$`DEL PEAK 23(9P21.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         102          283         1983          722         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A4IG 
         725          623         1636         1747          113          855 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
         622          351          216         1976          314          187 
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-C9-A47Z TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 
         638            5          799          642          395         1960 
TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5374 
        1268          173         1980         1966         1975          290 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6994 
         630          628          629          432         1110          735 
TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         432          443          535          904          645          225 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-5330 
         484          175          223         1466         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-A4C6 
        1399          341          129         1179         1750         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1960          998          785          391          303          950 
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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1966         1125          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
         234          479         1956         1440         1960          105 
TCGA-CR-7371 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
        1979         1968         1036          997         1430          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7402 
         913          946          908          898          930          911 
TCGA-CR-7404 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
        1472         1978         2886         2327         1958          701 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6942 TCGA-CV-6943 
        1840          215         1665          641         3835         1948 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7100 
        1966         1957         1959         3837         1970         1959 
TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 
        1979         1967         1960         1976         1974         1948 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A468 
        1947         1973          851         5480         1940         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6K0 TCGA-D6-6516 
        1970         1075          906         1959          606          773 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-DQ-5624 
          77          491          568          483          232         1778 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1030          775          622          299          369          368 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-H7-8501 
         340          658          585            3           13           58 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-8314 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61H 
         414          206           44           10         1057          412 
TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
         351          378           14          392          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T2 
         254          910         1726         1559         1120         1917 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         357          245          218          225          387          567 

  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                            2                             3 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                         3295                          5480 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          645                           792 
[1] "2.0 - 3295.0 (645.0)" "3.0 - 5480.0 (792.0)"
[1] "hr=" "1.8"
D52V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 23(9P21.3) MUTATED        14       41        40       155         7
  DEL PEAK 23(9P21.3) WILD-TYPE      12       34        34        80         5
                               vv
clus                            STAGE IVC
  DEL PEAK 23(9P21.3) MUTATED           1
  DEL PEAK 23(9P21.3) WILD-TYPE         0
D52V3, multiclass
           clus
vv          DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  STAGE I                            14                            12
  STAGE II                           41                            34
  STAGE III                          40                            34
  STAGE IVA                         155                            80
  STAGE IVB                           7                             5
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 23(9P21.3) MUTATED      22  70  60 108
  DEL PEAK 23(9P21.3) WILD-TYPE    25  57  34  54
D52V4, multiclass
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  T0+T1                          22                            25
  T2                             70                            57
  T3                             60                            34
  T4                            108                            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 23(9P21.3) MUTATED   107  35  97   4
  DEL PEAK 23(9P21.3) WILD-TYPE  63  28  55   4
D52V5, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  N0                         107                            63
  N1                          35                            28
  N2                          97                            55
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK 23(9P21.3) MUTATED   97  1 31
  DEL PEAK 23(9P21.3) WILD-TYPE 70  0 27
D52V6, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  M0                          97                            70
  M1                           1                             0
  MX                          31                            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    77 207
  DEL PEAK 23(9P21.3) WILD-TYPE  55 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     77  207
  DEL PEAK 23(9P21.3) WILD-TYPE   55  149
        clus
vv       DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  FEMALE                          77                            55
  MALE                           207                           149
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P21.3) MUTATED                                     279
  DEL PEAK 23(9P21.3) WILD-TYPE                                   198
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 23(9P21.3) MUTATED                                                             1
  DEL PEAK 23(9P21.3) WILD-TYPE                                                           0
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 23(9P21.3) MUTATED                                                     4
  DEL PEAK 23(9P21.3) WILD-TYPE                                                   6
D52V8, multiclass
                                                             clus
vv                                                            DEL PEAK 23(9P21.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               279
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
                                                             clus
vv                                                            DEL PEAK 23(9P21.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 198
  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"
D52V9, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    43 241
  DEL PEAK 23(9P21.3) WILD-TYPE  36 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     43  241
  DEL PEAK 23(9P21.3) WILD-TYPE   36  168
     clus
vv    DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  NO                           43                            36
  YES                         241                           168
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(9P21.3) MUTATED                                  1     5
  DEL PEAK 23(9P21.3) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P21.3) MUTATED                          31   239
  DEL PEAK 23(9P21.3) WILD-TYPE                        13   176
D52V12, multiclass
                                  clus
vv                                 DEL PEAK 23(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 31
  WHITE                                                    239
                                  clus
vv                                 DEL PEAK 23(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      176
[1] 4 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(9P21.3) MUTATED    14 245
  DEL PEAK 23(9P21.3) WILD-TYPE  10 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     14  245
  DEL PEAK 23(9P21.3) WILD-TYPE   10  186
                        clus
vv                       DEL PEAK 23(9P21.3) MUTATED
  HISPANIC OR LATINO                              14
  NOT HISPANIC OR LATINO                         245
                        clus
vv                       DEL PEAK 23(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           186
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 24(9Q21.11) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(9Q21.11) MUTATED    57  28
  DEL PEAK 24(9Q21.11) WILD-TYPE 244  85
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                            85                            329 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                            28                             85 
$`DEL PEAK 24(9Q21.11) MUTATED`
TCGA-BA-4074 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4II 
         462          451           63          384          236          918 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7870 TCGA-CN-4730 TCGA-CN-4740 TCGA-CN-5356 
         623          142         1153          817          811         1045 
TCGA-CN-5367 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CQ-5332 
        1966           45           98          318          611          317 
TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CR-5247 
        1959          509         1274         1950          893          358 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7369 
        1050         1971          350         1435         1191         1960 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5441 
         759           30          972         1955         1438         2886 
TCGA-CV-5973 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7102 
        2641         1959         1969         1959         1970         1945 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7254 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 
        1952          954         1976         1937         1959         1981 
TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A6JU TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 
        1960         1722          110          237          701          154 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5629 
         128          539          435          424          389          516 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 
         548          575         1131           92           14            6 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ 
         414          403            5           55           25          111 
TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IJ 
         552           56          240         1954         1968          387 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JD 
         149          135          135         1326         1663          735 
TCGA-UF-A7JJ 
         214 

$`DEL PEAK 24(9Q21.11) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          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-6873 TCGA-BA-A4IF 
        1636         1747          190          644          113          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          850          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
        1976          314          187         2878          278          140 
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-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         638          428          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         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
        1151          392          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         625         1960         1330         1268         1988         1007 
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-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
         628          594          629          432         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
        1110          224          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
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-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1393         1399          341          129         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
        1000         1057          985         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1560         1007         1309          877         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
         707         1963          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1521         1966         1125          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 
         311          345          354          234          379          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
        1956         1440         1245          105         1979          889 
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-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
         911         1472          522         1950         3295          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-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-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          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-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         3837         1970         1936         1959         1939 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 
        1987         1979         1444         1095          797         1967 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1960         1099         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
        1947         1937         1973         1972         1984         1958 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
         851         1945         5480         1940         1946         1954 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         646          714          606          685         1950          317 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         321          828          773          292           77          491 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ 
         568          106          376          483          232          368 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7590 
         338         1778         1081         1030         1965          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-A50J TCGA-F7-A61S TCGA-F7-A61V 
         490          658           15          585            3          384 
TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
          13          407           58          133          206            2 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
          25           37           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-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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         224          378          168           14           34          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1726         1559 
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-A6V9 TCGA-QK-A8Z7 
         245          218          228          225          567          198 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         157          168         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
        1894          484         1497          665          413 

  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                             5                              2 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                          2886                           5480 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                           611                            714 
[1] "5.0 - 2886.0 (611.0)" "2.0 - 5480.0 (714.0)"
[1] "hr=" "1.3"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 24(9Q21.11) MUTATED         4       16        17        47         2
  DEL PEAK 24(9Q21.11) WILD-TYPE      22       59        57       188        10
                                vv
clus                             STAGE IVC
  DEL PEAK 24(9Q21.11) MUTATED           1
  DEL PEAK 24(9Q21.11) WILD-TYPE         0
D53V3, multiclass
           clus
vv          DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  STAGE I                              4                             22
  STAGE II                            16                             59
  STAGE III                           17                             57
  STAGE IVA                           47                            188
  STAGE IVB                            2                             10
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 24(9Q21.11) MUTATED       9  30  15  34
  DEL PEAK 24(9Q21.11) WILD-TYPE    38  97  79 128
D53V4, multiclass
       clus
vv      DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  T0+T1                            9                             38
  T2                              30                             97
  T3                              15                             79
  T4                              34                            128
[1] 4 2
[1] TRUE
[1] "dimension 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(9Q21.11) MUTATED    37  15  30   1
  DEL PEAK 24(9Q21.11) WILD-TYPE 133  48 122   7
D53V5, multiclass
    clus
vv   DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  N0                           37                            133
  N1                           15                             48
  N2                           30                            122
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 24(9Q21.11) MUTATED    41   1   9
  DEL PEAK 24(9Q21.11) WILD-TYPE 126   0  49
D53V6, multiclass
    clus
vv   DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  M0                           41                            126
  M1                            1                              0
  MX                            9                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(9Q21.11) MUTATED    23  75
  DEL PEAK 24(9Q21.11) WILD-TYPE 109 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(9Q21.11) MUTATED     23   75
  DEL PEAK 24(9Q21.11) WILD-TYPE  109  281
        clus
vv       DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  FEMALE                           23                            109
  MALE                             75                            281
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9Q21.11) MUTATED                                      98
  DEL PEAK 24(9Q21.11) WILD-TYPE                                   379
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 24(9Q21.11) MUTATED                                                             0
  DEL PEAK 24(9Q21.11) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 24(9Q21.11) MUTATED                                                     0
  DEL PEAK 24(9Q21.11) WILD-TYPE                                                  10
D53V8, multiclass
                                                             clus
vv                                                            DEL PEAK 24(9Q21.11) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 98
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 24(9Q21.11) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  379
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     10
[1] 3 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(9Q21.11) MUTATED    17  81
  DEL PEAK 24(9Q21.11) WILD-TYPE  62 328
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(9Q21.11) MUTATED     17   81
  DEL PEAK 24(9Q21.11) WILD-TYPE   62  328
     clus
vv    DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  NO                            17                             62
  YES                           81                            328
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(9Q21.11) MUTATED                                  1     1
  DEL PEAK 24(9Q21.11) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(9Q21.11) MUTATED                          12    79
  DEL PEAK 24(9Q21.11) WILD-TYPE                        32   336
D53V12, multiclass
                                  clus
vv                                 DEL PEAK 24(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      79
                                  clus
vv                                 DEL PEAK 24(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    32
  WHITE                                                       336
[1] 4 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(9Q21.11) MUTATED     4  84
  DEL PEAK 24(9Q21.11) WILD-TYPE  20 347
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(9Q21.11) MUTATED      4   84
  DEL PEAK 24(9Q21.11) WILD-TYPE   20  347
                        clus
vv                       DEL PEAK 24(9Q21.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 24(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            347
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 25(9Q34.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 25(9Q34.3) MUTATED    42  21
  DEL PEAK 25(9Q34.3) WILD-TYPE 259  92
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           63                           351 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           21                            92 
$`DEL PEAK 25(9Q34.3) MUTATED`
TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7864 
          63          236          314          278          133          687 
TCGA-BB-7870 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-A63U 
        1153         1250          811           45           98          526 
TCGA-CN-A63Y TCGA-CQ-5327 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 
         175         1660         1959         1959          509         1274 
TCGA-CQ-7072 TCGA-CQ-A4CA TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 
        1950         1963          391          358         1050         1971 
TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7399 TCGA-CV-5430 
        1435          759           30          392          181         1955 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6941 
        3295         1438         2886         2641         1970         1959 
TCGA-CV-6945 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7243 
        1969         3837         1959         1970         1970          954 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JU 
        1959         1981         1945         1946         1722          110 
TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8635 
         548         1131           92          403            5           25 
TCGA-IQ-7630 TCGA-KU-A66T TCGA-P3-A5QA TCGA-QK-A6IJ TCGA-QK-A8ZA TCGA-QK-A8ZB 
         485          552         1726          387          135          135 
TCGA-UF-A719 TCGA-UF-A7JD TCGA-UF-A7JJ 
        1663          735          214 

$`DEL PEAK 25(9Q34.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         384          113          895          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DL 
         850          351          216          182         1976          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
         142          187         2878          140          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         536          423          638          428          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         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
         642          395          625         1960         1330         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          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          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         629          432         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         225          484          348          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207          654         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
         985         1179         1750         1560         1007         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877         1353         1960          707          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         785          303          950         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         1952         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-A45R 
        1972         1937         1984         1958          851         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1960         1940         1954         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          670          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          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-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         232          435          424          368          389          338 
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-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         133          414          206            2           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          55           44           24           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
         111           33         1057          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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         111          112          254          240          910         1559 
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-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         567          198          149          157          168         1326 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1319         1252         1278         1043         1894          484 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
        1497          665          413 

  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                            5                             2 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                         3837                          5480 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                          954                           670 
[1] "5.0 - 3837.0 (954.0)" "2.0 - 5480.0 (670.0)"
[1] "hr=" "1.2"
D54V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 25(9Q34.3) MUTATED         5       15        11        32         2
  DEL PEAK 25(9Q34.3) WILD-TYPE      21       60        63       203        10
                               vv
clus                            STAGE IVC
  DEL PEAK 25(9Q34.3) MUTATED           1
  DEL PEAK 25(9Q34.3) WILD-TYPE         0
D54V3, multiclass
           clus
vv          DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  STAGE I                             5                            21
  STAGE II                           15                            60
  STAGE III                          11                            63
  STAGE IVA                          32                           203
  STAGE IVB                           2                            10
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 25(9Q34.3) MUTATED       8  23  14  21
  DEL PEAK 25(9Q34.3) WILD-TYPE    39 104  80 141
D54V4, multiclass
       clus
vv      DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  T0+T1                           8                            39
  T2                             23                           104
  T3                             14                            80
  T4                             21                           141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 25(9Q34.3) MUTATED    28   8  23   1
  DEL PEAK 25(9Q34.3) WILD-TYPE 142  55 129   7
D54V5, multiclass
    clus
vv   DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  N0                          28                           142
  N1                           8                            55
  N2                          23                           129
  N3                           1                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 25(9Q34.3) MUTATED    22   1   7
  DEL PEAK 25(9Q34.3) WILD-TYPE 145   0  51
D54V6, multiclass
    clus
vv   DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  M0                          22                           145
  M1                           1                             0
  MX                           7                            51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 25(9Q34.3) MUTATED    22  52
  DEL PEAK 25(9Q34.3) WILD-TYPE 110 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9Q34.3) MUTATED     22   52
  DEL PEAK 25(9Q34.3) WILD-TYPE  110  304
        clus
vv       DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  FEMALE                          22                           110
  MALE                            52                           304
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9Q34.3) MUTATED                                      74
  DEL PEAK 25(9Q34.3) WILD-TYPE                                   403
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 25(9Q34.3) MUTATED                                                             0
  DEL PEAK 25(9Q34.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 25(9Q34.3) MUTATED                                                     0
  DEL PEAK 25(9Q34.3) WILD-TYPE                                                  10
D54V8, multiclass
                                                             clus
vv                                                            DEL PEAK 25(9Q34.3) 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 25(9Q34.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 403
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    10
[1] 3 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(9Q34.3) MUTATED    12  62
  DEL PEAK 25(9Q34.3) WILD-TYPE  67 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9Q34.3) MUTATED     12   62
  DEL PEAK 25(9Q34.3) WILD-TYPE   67  347
     clus
vv    DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  NO                           12                            67
  YES                          62                           347
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(9Q34.3) MUTATED                                  0     2
  DEL PEAK 25(9Q34.3) WILD-TYPE                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(9Q34.3) MUTATED                           9    57
  DEL PEAK 25(9Q34.3) WILD-TYPE                        35   358
D54V12, multiclass
                                  clus
vv                                 DEL PEAK 25(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     57
                                  clus
vv                                 DEL PEAK 25(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   35
  WHITE                                                      358
[1] 4 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(9Q34.3) MUTATED     5  61
  DEL PEAK 25(9Q34.3) WILD-TYPE  19 370
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9Q34.3) MUTATED      5   61
  DEL PEAK 25(9Q34.3) WILD-TYPE   19  370
                        clus
vv                       DEL PEAK 25(9Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK 25(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           370
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 26(10P15.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(10P15.3) MUTATED    84  47
  DEL PEAK 26(10P15.3) WILD-TYPE 217  66
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           131                            283 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                            47                             66 
$`DEL PEAK 26(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         1157          142 
TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 
         625         1007         1980         1081         1977          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
         933          629           45          432           98          318 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6223 
         611          432           46          348         1466         1057 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
         985         1959         1560          509         1274         1950 
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-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 
        1036          796         1954         1430          392          156 
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         1952 
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-CV-A6JT TCGA-CV-A6JY 
        1973         1937         1958         1970          670          646 
TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-A6EP TCGA-DQ-5629 
         685          828          292          154          424          516 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         548         1965          775          658           15           92 
TCGA-F7-A61V TCGA-F7-A620 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-IQ-A61G 
         384           13           25           11           49          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X TCGA-P3-A6SX 
         412          440          552          378           34         1954 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH 
        1917         1968          400          553          245          228 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 
         567          149          135          135          168         1326 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ 
        1319         1252          484          735          214 

$`DEL PEAK 26(10P15.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          462         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6871 
        1762          520          725          623         1636           63 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          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-7872 TCGA-BB-8596 
         536          423          687          638          436         1955 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
           4          799         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
         993          642         1250          395         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5365 
         811         1268         1988         1045          173         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 
        1966         1966         1975          683          630          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         594          629         1970          202         1110          224 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         394          735          429          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         904          645          225          526          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223          298         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
        1253         1000         1959         1179         1750         1007 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          877         1353          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         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-6477 TCGA-CR-6478 TCGA-CR-6480 
        1966         1050         1125          514         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-6493 TCGA-CR-7364 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7385 TCGA-CR-7388 
        1956         1435           30          972          997         1951 
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-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         216          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
         522         1950         3295          584          546         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2327         1958          406          701         2641         1478 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 
         215         1665          641         1899         1970         1969 
TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 
        1959         1948         1969         1969         1959         1970 
TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 
        1936         1987         1979         1444         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 
        1099         1974         1948         1957         1937         1972 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1984         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1960         1940         1946         1954         1722         1977 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
        1075          906         1959          110          714          606 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 
        1950          317          321          237          773          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
          77          491          568          106          128          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          232          435          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 
         338         1778         1081         1030          575          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 
         490          585            3           14            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            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-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-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 
         441          588          351          360          224          168 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          14          392           56          111          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         240          910         1726         1559         1120          578 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-AA3J 
         357          218          225          387          198          157 
TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH 
        1663         1278         1043         1894         1497          665 
TCGA-UF-A7JS 
         413 

  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                             5                              2 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                          3837                           5480 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           759                            683 
[1] "5.0 - 3837.0 (759.0)" "2.0 - 5480.0 (683.0)"
[1] "hr=" "1.5"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 26(10P15.3) MUTATED         5       22        22        89         3
  DEL PEAK 26(10P15.3) WILD-TYPE      21       53        52       146         9
                                vv
clus                             STAGE IVC
  DEL PEAK 26(10P15.3) MUTATED           0
  DEL PEAK 26(10P15.3) WILD-TYPE         1
D55V3, multiclass
           clus
vv          DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  STAGE I                              5                             21
  STAGE II                            22                             53
  STAGE III                           22                             52
  STAGE IVA                           89                            146
  STAGE IVB                            3                              9
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 26(10P15.3) MUTATED       8 40 30 63
  DEL PEAK 26(10P15.3) WILD-TYPE    39 87 64 99
D55V4, multiclass
       clus
vv      DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  T0+T1                            8                             39
  T2                              40                             87
  T3                              30                             64
  T4                              63                             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 26(10P15.3) MUTATED    46  22  60   1
  DEL PEAK 26(10P15.3) WILD-TYPE 124  41  92   7
D55V5, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  N0                           46                            124
  N1                           22                             41
  N2                           60                             92
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 26(10P15.3) MUTATED    53   0  18
  DEL PEAK 26(10P15.3) WILD-TYPE 114   1  40
D55V6, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  M0                           53                            114
  M1                            0                              1
  MX                           18                             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED    40 117
  DEL PEAK 26(10P15.3) WILD-TYPE  92 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     40  117
  DEL PEAK 26(10P15.3) WILD-TYPE   92  239
        clus
vv       DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  FEMALE                           40                             92
  MALE                            117                            239
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(10P15.3) MUTATED                                     157
  DEL PEAK 26(10P15.3) WILD-TYPE                                   320
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 26(10P15.3) MUTATED                                                             0
  DEL PEAK 26(10P15.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 26(10P15.3) MUTATED                                                     0
  DEL PEAK 26(10P15.3) WILD-TYPE                                                  10
D55V8, multiclass
                                                             clus
vv                                                            DEL PEAK 26(10P15.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                157
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 26(10P15.3) 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                                     10
[1] 3 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(10P15.3) MUTATED    32 125
  DEL PEAK 26(10P15.3) WILD-TYPE  47 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     32  125
  DEL PEAK 26(10P15.3) WILD-TYPE   47  284
     clus
vv    DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  NO                            32                             47
  YES                          125                            284
[1] 2 2
[1] FALSE
D55V10, continuous
D55V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(10P15.3) MUTATED                                  0     3
  DEL PEAK 26(10P15.3) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(10P15.3) MUTATED                          21   129
  DEL PEAK 26(10P15.3) WILD-TYPE                        23   286
D55V12, multiclass
                                  clus
vv                                 DEL PEAK 26(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     129
                                  clus
vv                                 DEL PEAK 26(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    23
  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"
D55V13, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED     7 139
  DEL PEAK 26(10P15.3) WILD-TYPE  17 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED      7  139
  DEL PEAK 26(10P15.3) WILD-TYPE   17  292
                        clus
vv                       DEL PEAK 26(10P15.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          139
                        clus
vv                       DEL PEAK 26(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 27(10P11.21) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(10P11.21) MUTATED    86  44
  DEL PEAK 27(10P11.21) WILD-TYPE 215  69
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                            130                             284 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                             44                              69 
$`DEL PEAK 27(10P11.21) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
         462          283          276         1747          190          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-7870 
         384          113          236          850          142         1153 
TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4737 TCGA-CN-5355 
         436          624            5          721          625         1007 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
        1081         1977          290          933          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A 
         432           98          318          432           46          391 
TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
         348         1466          317         1253         1057          985 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
        1959         1560          509         1274         1950         1960 
TCGA-CQ-A4CI TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 
         950         1971         1969          354         1191         1440 
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-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7398 
         796         1954         1430          392          907          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-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7219 
        1937         1958         1970          646          685          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ 
         292          701          154          376          424          368 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-F7-A50G 
         516          548         1965          775          369           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-HD-7753 TCGA-HD-A633 TCGA-IQ-A61G 
          92          384           14            5           49          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X 
         412          440          360          552          378           34 
TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
         240         1726         1917         1968          400          553 
TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K 
         228          567          149          135          135          168 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD 
        1326         1319          484          735 

$`DEL PEAK 27(10P11.21) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
          63          895          855          622          918          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
         216          182         1976          314          623          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-4727 TCGA-CN-4728 
           4          799         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
         173         1980         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 
         683          630          628          594          629         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         202         1110          224          611          394          735 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         429          443          535          904          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         526          484          175          367          223          298 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
         341          129         1000         1959         1179         1750 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1007         1309          877         1353          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
         893          998          785          391          303         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-6477 TCGA-CR-6480 TCGA-CR-6481 
        1966         1050         1125          514          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7385 
        1435         1979          972         1968         1036          997 
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-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         216          181         1077          911         1472         1955 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 
        2327         1958          406          701         1478          215 
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-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 
        1948         1969         1966         1969         1959         1970 
TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 
        1936         1987         1979         1952         1444         1960 
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-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1972         1984         1959         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1977         1075          906         1959          670          110 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         714          606         1950          317          321          237 
TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         773           77          491          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q 
         539          483          232          435          389          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
        1778         1081         1030          575          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
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-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
         133          414          403          206            2           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-KU-A6H8 TCGA-MT-A51W 
         441          588          351          224          168           14 
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-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-QK-A652 TCGA-QK-A6IF 
        1559         1120         1954          578          357          245 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-UF-A719 
         218          225          387          198          157         1663 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH 
        1252         1278         1043         1894         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                              5                               2 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                           3837                            5480 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                            693                             704 
[1] "5.0 - 3837.0 (693.0)" "2.0 - 5480.0 (704.0)"
[1] "hr=" "1.5"
D56V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 27(10P11.21) MUTATED         8       18        22        84
  DEL PEAK 27(10P11.21) WILD-TYPE      18       57        52       151
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 27(10P11.21) MUTATED           5         0
  DEL PEAK 27(10P11.21) WILD-TYPE         7         1
D56V3, multiclass
           clus
vv          DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  STAGE I                               8                              18
  STAGE II                             18                              57
  STAGE III                            22                              52
  STAGE IVA                            84                             151
  STAGE IVB                             5                               7
  STAGE IVC                             0                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 27(10P11.21) MUTATED      10  38  29  60
  DEL PEAK 27(10P11.21) WILD-TYPE    37  89  65 102
D56V4, multiclass
       clus
vv      DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  T0+T1                            10                              37
  T2                               38                              89
  T3                               29                              65
  T4                               60                             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"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 27(10P11.21) MUTATED    47  21  55   2
  DEL PEAK 27(10P11.21) WILD-TYPE 123  42  97   6
D56V5, multiclass
    clus
vv   DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  N0                            47                             123
  N1                            21                              42
  N2                            55                              97
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 27(10P11.21) MUTATED    52   0  17
  DEL PEAK 27(10P11.21) WILD-TYPE 115   1  41
D56V6, multiclass
    clus
vv   DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  M0                            52                             115
  M1                             0                               1
  MX                            17                              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(10P11.21) MUTATED    35 118
  DEL PEAK 27(10P11.21) WILD-TYPE  97 238
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10P11.21) MUTATED     35  118
  DEL PEAK 27(10P11.21) WILD-TYPE   97  238
        clus
vv       DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  FEMALE                            35                              97
  MALE                             118                             238
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P11.21) MUTATED                                     151
  DEL PEAK 27(10P11.21) WILD-TYPE                                   326
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 27(10P11.21) MUTATED                                                             1
  DEL PEAK 27(10P11.21) WILD-TYPE                                                           0
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 27(10P11.21) MUTATED                                                     1
  DEL PEAK 27(10P11.21) WILD-TYPE                                                   9
D56V8, multiclass
                                                             clus
vv                                                            DEL PEAK 27(10P11.21) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 151
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
                                                             clus
vv                                                            DEL PEAK 27(10P11.21) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   326
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       9
[1] 3 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(10P11.21) MUTATED    32 121
  DEL PEAK 27(10P11.21) WILD-TYPE  47 288
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10P11.21) MUTATED     32  121
  DEL PEAK 27(10P11.21) WILD-TYPE   47  288
     clus
vv    DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  NO                             32                              47
  YES                           121                             288
[1] 2 2
[1] FALSE
D56V10, continuous
D56V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(10P11.21) MUTATED                                  0     5
  DEL PEAK 27(10P11.21) WILD-TYPE                                2     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10P11.21) MUTATED                          23   121
  DEL PEAK 27(10P11.21) WILD-TYPE                        21   294
D56V12, multiclass
                                  clus
vv                                 DEL PEAK 27(10P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      121
                                  clus
vv                                 DEL PEAK 27(10P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     21
  WHITE                                                        294
[1] 4 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(10P11.21) MUTATED     9 132
  DEL PEAK 27(10P11.21) WILD-TYPE  15 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10P11.21) MUTATED      9  132
  DEL PEAK 27(10P11.21) WILD-TYPE   15  299
                        clus
vv                       DEL PEAK 27(10P11.21) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           132
                        clus
vv                       DEL PEAK 27(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  15
  NOT HISPANIC OR LATINO                             299
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 28(10Q23.31) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10Q23.31) MUTATED    73  38
  DEL PEAK 28(10Q23.31) WILD-TYPE 228  75
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            111                             303 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             38                              75 
$`DEL PEAK 28(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-A4IG TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-7861 TCGA-BB-7870 
         644          855          850          142          310         1153 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-5355 TCGA-CN-5359 
         624            5         1157         1230         1007         1980 
TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
        1081          290          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A63U 
        1970          224           46          535          391          526 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CR-6470 
         317         1000         1959         1560         1950         1521 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7368 
        1971          514          362          354         1191         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 
        1960          105          759          889           30         1954 
TCGA-CR-7386 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1430          156          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6935 TCGA-CV-6941 
         584         2641          215         1315         1969         1959 
TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 
        1969         1969         1959         3837         1970         1939 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 
        1095          954          797         1967         1974         1955 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-A460 TCGA-CV-A6JY TCGA-D6-6823 TCGA-D6-A4ZB 
        1947         1937         1946          646          701          376 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7588 
         424          368          389          338          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-H7-A76A TCGA-HD-A6HZ 
         575          775          369          340          206          111 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X 
         360          412          440          552          378           34 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-QK-A6IH 
         254          240         1559         1954          578          228 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         567          149          135          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JC 
        1319         1043          484 

$`DEL PEAK 28(10Q23.31) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         102          415         1983          248          722         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         725          623         1636          190          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II 
         384          113          236          895          622          918 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
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         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1045          173         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        1975          683          630          933          628          594 
TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         629          202         1110          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C 
         735          432          429          443          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         225          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
        1393         1399          341          129         1253         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
         985         1959         1179         1750         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309         1274          877         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6481 
        1777         1966         1050         1125         1969          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1435         1440         1979          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         796          997         1951          392          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-5439 TCGA-CV-5440 
        1077          911         1472         1955          546         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-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
         701         1478         1840         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-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1957         1959         1970         1936         1959         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 
        1987         1979         1952         1444         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1099         1948         1957         1937         1973         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-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        5480         1960         1940         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK 
         154          568          106          128          539          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         232          435         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         1131          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-KU-A6H8 TCGA-MT-A51W 
         588          351          360          224          168           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA 
         392           56          111          112          910         1726 
TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1120         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZB 
         245          218          225          387          198          135 
TCGA-QK-AA3J TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
         157         1252         1278         1894          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                              5                               2 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                           3837                            5480 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            646                             707 
[1] "5.0 - 3837.0 (646.0)" "2.0 - 5480.0 (707.0)"
[1] "hr=" "1.4"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 28(10Q23.31) MUTATED         3       20        22        59
  DEL PEAK 28(10Q23.31) WILD-TYPE      23       55        52       176
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 28(10Q23.31) MUTATED           4         0
  DEL PEAK 28(10Q23.31) WILD-TYPE         8         1
D57V3, multiclass
           clus
vv          DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  STAGE I                               3                              23
  STAGE II                             20                              55
  STAGE III                            22                              52
  STAGE IVA                            59                             176
  STAGE IVB                             4                               8
  STAGE IVC                             0                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 28(10Q23.31) MUTATED       8  35  27  40
  DEL PEAK 28(10Q23.31) WILD-TYPE    39  92  67 122
D57V4, multiclass
       clus
vv      DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T0+T1                             8                              39
  T2                               35                              92
  T3                               27                              67
  T4                               40                             122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 28(10Q23.31) MUTATED    43  15  41   2
  DEL PEAK 28(10Q23.31) WILD-TYPE 127  48 111   6
D57V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                            43                             127
  N1                            15                              48
  N2                            41                             111
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 28(10Q23.31) MUTATED    44   0  17
  DEL PEAK 28(10Q23.31) WILD-TYPE 123   1  41
D57V6, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  M0                            44                             123
  M1                             0                               1
  MX                            17                              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    26 101
  DEL PEAK 28(10Q23.31) WILD-TYPE 106 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     26  101
  DEL PEAK 28(10Q23.31) WILD-TYPE  106  255
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            26                             106
  MALE                             101                             255
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10Q23.31) MUTATED                                     126
  DEL PEAK 28(10Q23.31) WILD-TYPE                                   351
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 28(10Q23.31) MUTATED                                                             0
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 28(10Q23.31) MUTATED                                                     1
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                   9
D57V8, multiclass
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) 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                                     1
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) 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                                       9
[1] 3 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(10Q23.31) MUTATED    22 105
  DEL PEAK 28(10Q23.31) WILD-TYPE  57 304
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     22  105
  DEL PEAK 28(10Q23.31) WILD-TYPE   57  304
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                             22                              57
  YES                           105                             304
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(10Q23.31) MUTATED                                  0     3
  DEL PEAK 28(10Q23.31) WILD-TYPE                                2     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(10Q23.31) MUTATED                          17   105
  DEL PEAK 28(10Q23.31) WILD-TYPE                        27   310
D57V12, multiclass
                                  clus
vv                                 DEL PEAK 28(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      105
                                  clus
vv                                 DEL PEAK 28(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     27
  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"
D57V13, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     8 110
  DEL PEAK 28(10Q23.31) WILD-TYPE  16 321
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      8  110
  DEL PEAK 28(10Q23.31) WILD-TYPE   16  321
                        clus
vv                       DEL PEAK 28(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           110
                        clus
vv                       DEL PEAK 28(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             321
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 29(11P15.5) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(11P15.5) MUTATED    94  39
  DEL PEAK 29(11P15.5) WILD-TYPE 207  74
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           133                            281 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            39                             74 
$`DEL PEAK 29(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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         236          855          622          918          850          351 
TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-8596 TCGA-CN-4725 
         182          142          133         1153         1955         1157 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 
        1151          392         1250          395         1330          811 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5374 
        1045         1980         1977         1980         1966          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6988 
         933          629          432           98         1970          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A49C TCGA-CN-A63U 
         611          394          429           46          645          526 
TCGA-CN-A63Y TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
         175          317         1000         1959          707          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 
        2562          358         1663          514         1969          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 
         345          354           30         1954          997         1951 
TCGA-CR-7389 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5439 
         392          181         1472         1955         1950          546 
TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-7091 
         215         1970         1952         3835         1969         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 
        1970         1970         1959         1939         1945         1952 
TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Y 
         797         1099         1972         1959         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JU TCGA-CX-7082 TCGA-D6-8568 TCGA-D6-A4ZB 
        1940         1946          110          317          106          376 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7589 
         424          389          338         1778          516          575 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
         368          340         1131          490           15           92 
TCGA-F7-A623 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           6          414            5           37           55           44 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A67G 
          25          111          441          360          552          112 
TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IF 
         254         1120          578         1968          400          245 
TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K 
         228          198          149          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA 
        1326         1663         1319         1252         1278         1894 
TCGA-UF-A7JH 
         665 

$`DEL PEAK 29(11P15.5) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 
         102          462          283          415         1983          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DG 
        1747          644          113          895          216         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         314          623          187         2878          278          140 
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-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         428          436          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         721          142         1230          817          993          642 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
         625         1960         1268         1988         1007          173 
TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 
        1081         1966         1975          683          630          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         594          629           45          202         1110          224 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         735          432          443          535          391          904 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         225          484          348          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
        1399          341          129         1253         1057          985 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
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-6480 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
        1125         1971          362          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-7376 
        1960          105         1979          759          889          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 
        1968         1036          796         1430          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-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1077          911          522         3295         1438          584 
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-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
         406          701         2641         1478         1840         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 
        1665          641         1899         1948         1969         1959 
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-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1936         1987         1979         1444         1095          954 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1960         1976         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 
        1957         1947         1937         1973         1937         1984 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A464 
        1958         1981          851         1945         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
         646          714          606          685         1950          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-D6-A6EK 
         491          154          568          128          539          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         232          435          368         1081         1030          548 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 
        1965          775          622          299          369          324 
TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658          585            3          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
         407           58          133          403          206            2 
TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          25           24           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
        1057          485          122          588          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         351          360          224          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 
          34          392           56          111          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 
        1726         1559         1954         1917          553          357 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8ZB TCGA-UF-A7J9 
         218          225          387          567          135         1043 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          214          413 

  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                             5                              2 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                          5480                           3837 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           552                            759 
[1] "5.0 - 5480.0 (552.0)" "2.0 - 3837.0 (759.0)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 29(11P15.5) MUTATED         5       19        20        75         8
  DEL PEAK 29(11P15.5) WILD-TYPE      21       56        54       160         4
                                vv
clus                             STAGE IVC
  DEL PEAK 29(11P15.5) MUTATED           0
  DEL PEAK 29(11P15.5) WILD-TYPE         1
D58V3, multiclass
           clus
vv          DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  STAGE I                              5                             21
  STAGE II                            19                             56
  STAGE III                           20                             54
  STAGE IVA                           75                            160
  STAGE IVB                            8                              4
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 29(11P15.5) MUTATED      14  35  26  56
  DEL PEAK 29(11P15.5) WILD-TYPE    33  92  68 106
D58V4, multiclass
       clus
vv      DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T0+T1                           14                             33
  T2                              35                             92
  T3                              26                             68
  T4                              56                            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
  DEL PEAK 29(11P15.5) MUTATED    45  18  46   6
  DEL PEAK 29(11P15.5) WILD-TYPE 125  45 106   2
D58V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                           45                            125
  N1                           18                             45
  N2                           46                            106
  N3                            6                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 29(11P15.5) MUTATED    50   0  19
  DEL PEAK 29(11P15.5) WILD-TYPE 117   1  39
D58V6, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  M0                           50                            117
  M1                            0                              1
  MX                           19                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    38 119
  DEL PEAK 29(11P15.5) WILD-TYPE  94 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     38  119
  DEL PEAK 29(11P15.5) WILD-TYPE   94  237
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           38                             94
  MALE                            119                            237
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(11P15.5) MUTATED                                     150
  DEL PEAK 29(11P15.5) WILD-TYPE                                   327
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 29(11P15.5) MUTATED                                                             0
  DEL PEAK 29(11P15.5) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 29(11P15.5) MUTATED                                                     7
  DEL PEAK 29(11P15.5) WILD-TYPE                                                   3
D58V8, multiclass
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                150
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    7
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  327
  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"
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    25 132
  DEL PEAK 29(11P15.5) WILD-TYPE  54 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     25  132
  DEL PEAK 29(11P15.5) WILD-TYPE   54  277
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                            25                             54
  YES                          132                            277
[1] 2 2
[1] FALSE
D58V10, continuous
D58V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(11P15.5) MUTATED                                  1     1
  DEL PEAK 29(11P15.5) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(11P15.5) MUTATED                          21   129
  DEL PEAK 29(11P15.5) WILD-TYPE                        23   286
D58V12, multiclass
                                  clus
vv                                 DEL PEAK 29(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     129
                                  clus
vv                                 DEL PEAK 29(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    23
  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"
D58V13, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    11 131
  DEL PEAK 29(11P15.5) WILD-TYPE  13 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     11  131
  DEL PEAK 29(11P15.5) WILD-TYPE   13  300
                        clus
vv                       DEL PEAK 29(11P15.5) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          131
                        clus
vv                       DEL PEAK 29(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            300
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 30(11Q23.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(11Q23.1) MUTATED   144  60
  DEL PEAK 30(11Q23.1) WILD-TYPE 157  53
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                           204                            210 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                            60                             53 
$`DEL PEAK 30(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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
         113          236          855          622          918          351 
TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 
        1976          623          187         2878          133          558 
TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-4727 
         310          638         1153          428         1955         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5359 
        1151          392         1250         1330         1268         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-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6021 
         290          933          629          628           98         1970 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 
         224          611          394          735           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63Y 
         535          391          904          645          225          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 
         367         1466          317         1000          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1959         1179          509         1960         1963          893 
TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         998         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1777         1521         1050         1125         1971          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-6493 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
         379          350         1956         1960          105         1979 
TCGA-CR-7377 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7404 
        1968         1954          997         1951          181         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1955          522         1950          546         1978         2886 
TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
        1958          406         2641         1478         1840         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
        1665          641         1970         1969         1952         3835 
TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7406 TCGA-CV-7418 
        1959         1939         1945         1952         1974         1955 
TCGA-CV-7422 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R 
        1957         1973         1937         1984         1959         5480 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 
        1960         1946         1075          906          317          237 
TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-D6-A6ES 
         828          701          491          539          424          389 
TCGA-D6-A74Q TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
         338         1965          575          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
         368          340         1131          490           15           92 
TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 
           6          133          414          403          206            5 
TCGA-HD-8314 TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
          44         1057          360          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
         360          552          378           14           34           56 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 
         112          240         1726         1120         1954         1968 
TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z7 
         400          245          218          228          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71B 
         149          135          157          168         1663         1319 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS 
        1278         1894          484          735          665          413 

$`DEL PEAK 30(11Q23.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5557 
         102          283          722         1288          725          623 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
        1636          644          895          850          216          182 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7863 
         314          142          278          140          536          423 
TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         687          436          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         721         1157          142          817          993          642 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 
         395          625         1960          811         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 
        1045          173          683          630          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6996 
          45          432          202         1110          318          432 
TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A6V1 TCGA-CN-A6V3 
         429          526          484          348          223          298 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7064 
         341          129         1253         1057         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1007         1309         1274          877         1950         1353 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-6471 
         707          785          391          303          950         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-A45Z TCGA-CV-A461 TCGA-CV-A464 
        1981          851         1945         1940         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1977         1970         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6516 
         714          606          685         1950          321          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         292           77          154          568          106          128 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5624 
         376          483          232          435          368         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7595 
        1081          516         1030          548          299          324 
TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658          585            3          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         407           58            2           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-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-KU-A66S 
          33          485          122          441          588          224 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         168          392          111          254          910         1559 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ 
         578         1917          553          357          225          387 
TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JJ 
         135         1326         1252         1043         1497          214 

  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                             5                              2 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                          5480                           3295 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                           735                            686 
[1] "5.0 - 5480.0 (735.0)" "2.0 - 3295.0 (686.0)"
[1] "hr=" "1.4"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 30(11Q23.1) MUTATED        11       32        31       107         6
  DEL PEAK 30(11Q23.1) WILD-TYPE      15       43        43       128         6
                                vv
clus                             STAGE IVC
  DEL PEAK 30(11Q23.1) MUTATED           0
  DEL PEAK 30(11Q23.1) WILD-TYPE         1
D59V3, multiclass
           clus
vv          DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  STAGE I                             11                             15
  STAGE II                            32                             43
  STAGE III                           31                             43
  STAGE IVA                          107                            128
  STAGE IVB                            6                              6
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 30(11Q23.1) MUTATED      22 59 42 69
  DEL PEAK 30(11Q23.1) WILD-TYPE    25 68 52 93
D59V4, multiclass
       clus
vv      DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  T0+T1                           22                             25
  T2                              59                             68
  T3                              42                             52
  T4                              69                             93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 30(11Q23.1) MUTATED    63  26  84   3
  DEL PEAK 30(11Q23.1) WILD-TYPE 107  37  68   5
D59V5, multiclass
    clus
vv   DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  N0                           63                            107
  N1                           26                             37
  N2                           84                             68
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 30(11Q23.1) MUTATED   70  0 30
  DEL PEAK 30(11Q23.1) WILD-TYPE 97  1 28
D59V6, multiclass
    clus
vv   DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  M0                           70                             97
  M1                            0                              1
  MX                           30                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.1) MUTATED    42 188
  DEL PEAK 30(11Q23.1) WILD-TYPE  90 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.1) MUTATED     42  188
  DEL PEAK 30(11Q23.1) WILD-TYPE   90  168
        clus
vv       DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  FEMALE                           42                             90
  MALE                            188                            168
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11Q23.1) MUTATED                                     223
  DEL PEAK 30(11Q23.1) WILD-TYPE                                   254
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 30(11Q23.1) MUTATED                                                             1
  DEL PEAK 30(11Q23.1) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 30(11Q23.1) MUTATED                                                     6
  DEL PEAK 30(11Q23.1) WILD-TYPE                                                   4
D59V8, multiclass
                                                             clus
vv                                                            DEL PEAK 30(11Q23.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                223
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
                                                             clus
vv                                                            DEL PEAK 30(11Q23.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  254
  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"
D59V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.1) MUTATED    43 187
  DEL PEAK 30(11Q23.1) WILD-TYPE  36 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.1) MUTATED     43  187
  DEL PEAK 30(11Q23.1) WILD-TYPE   36  222
     clus
vv    DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  NO                            43                             36
  YES                          187                            222
[1] 2 2
[1] FALSE
D59V10, continuous
D59V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(11Q23.1) MUTATED                                  1     1
  DEL PEAK 30(11Q23.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(11Q23.1) MUTATED                          23   197
  DEL PEAK 30(11Q23.1) WILD-TYPE                        21   218
D59V12, multiclass
                                  clus
vv                                 DEL PEAK 30(11Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     197
                                  clus
vv                                 DEL PEAK 30(11Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       218
[1] 4 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(11Q23.1) MUTATED    14 198
  DEL PEAK 30(11Q23.1) WILD-TYPE  10 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.1) MUTATED     14  198
  DEL PEAK 30(11Q23.1) WILD-TYPE   10  233
                        clus
vv                       DEL PEAK 30(11Q23.1) MUTATED
  HISPANIC OR LATINO                               14
  NOT HISPANIC OR LATINO                          198
                        clus
vv                       DEL PEAK 30(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            233
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 31(12Q24.33) MUTATION ANALYSIS
D60V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 31(12Q24.33) MUTATED    34  18
  DEL PEAK 31(12Q24.33) WILD-TYPE 267  95
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             52                             362 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             18                              95 
$`DEL PEAK 31(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-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-8596 TCGA-CN-4726 
         622          850          182          142         1955          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5374 
        1230         1151         1330         1007         1980          290 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A49B TCGA-CQ-5332 TCGA-CR-6493 
         224          318          735          904          317         1956 
TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5966 TCGA-CV-5976 
         105         1954          907         1955          519         1478 
TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7102 
        1665         1969         3837         1959         1939         1945 
TCGA-CV-7254 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A6JY TCGA-CX-7219 TCGA-D6-A4Z9 
        1976         1937         1959          646          828          539 
TCGA-D6-A6EP TCGA-DQ-5629 TCGA-F7-7848 TCGA-H7-A6C5 TCGA-IQ-A61G TCGA-KU-A66T 
         424          516         1131          403          360          552 
TCGA-P3-A5QA TCGA-QK-A8Z7 TCGA-UF-A719 TCGA-UF-A7JF 
        1726          198         1663         1497 

$`DEL PEAK 31(12Q24.33) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          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-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-A4IG 
        1636         1747          644           63          384          855 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         918          351          216         1976          314          623 
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         1157          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
        1250          395          625         1960          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1988         1045          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          683          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          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         1110          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         645          225          526          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422         1393         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         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         1952         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-A45R 
        1984         1958         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1960         1940         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
         154          568          106          128          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         232          435          368          389          338         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-F7-8298 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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          206            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-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-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         360          224          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         392           56          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1559         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 TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         228          225          387          567          149          135 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D 
         135          157          168         1326         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        1278         1043         1894          484          735          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                            105                               2 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                           3837                            5480 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                          872.5                           684.0 
[1] "105.0 - 3837.0 (872.5)" "2.0 - 5480.0 (684.0)"  
[1] "hr=" "1.4"
D60V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 31(12Q24.33) MUTATED         3        8         6        33
  DEL PEAK 31(12Q24.33) WILD-TYPE      23       67        68       202
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 31(12Q24.33) MUTATED           2         0
  DEL PEAK 31(12Q24.33) WILD-TYPE        10         1
D60V3, multiclass
           clus
vv          DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  STAGE I                               3                              23
  STAGE II                              8                              67
  STAGE III                             6                              68
  STAGE IVA                            33                             202
  STAGE IVB                             2                              10
  STAGE IVC                             0                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 31(12Q24.33) MUTATED       3  13  10  26
  DEL PEAK 31(12Q24.33) WILD-TYPE    44 114  84 136
D60V4, multiclass
       clus
vv      DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  T0+T1                             3                              44
  T2                               13                             114
  T3                               10                              84
  T4                               26                             136
[1] 4 2
[1] TRUE
[1] "dimension 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(12Q24.33) MUTATED    18   6  20   2
  DEL PEAK 31(12Q24.33) WILD-TYPE 152  57 132   6
D60V5, multiclass
    clus
vv   DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  N0                            18                             152
  N1                             6                              57
  N2                            20                             132
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 31(12Q24.33) MUTATED    19   0   8
  DEL PEAK 31(12Q24.33) WILD-TYPE 148   1  50
D60V6, multiclass
    clus
vv   DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  M0                            19                             148
  M1                             0                               1
  MX                             8                              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                                 cls
clus                                0   1
  DEL PEAK 31(12Q24.33) MUTATED    14  44
  DEL PEAK 31(12Q24.33) WILD-TYPE 118 312
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED     14   44
  DEL PEAK 31(12Q24.33) WILD-TYPE  118  312
        clus
vv       DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  FEMALE                            14                             118
  MALE                              44                             312
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                                      56
  DEL PEAK 31(12Q24.33) WILD-TYPE                                   421
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 31(12Q24.33) MUTATED                                                             0
  DEL PEAK 31(12Q24.33) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 31(12Q24.33) MUTATED                                                     2
  DEL PEAK 31(12Q24.33) WILD-TYPE                                                   8
D60V8, multiclass
                                                             clus
vv                                                            DEL PEAK 31(12Q24.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  56
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     2
                                                             clus
vv                                                            DEL PEAK 31(12Q24.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   421
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       8
[1] 3 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(12Q24.33) MUTATED    10  48
  DEL PEAK 31(12Q24.33) WILD-TYPE  69 361
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED     10   48
  DEL PEAK 31(12Q24.33) WILD-TYPE   69  361
     clus
vv    DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  NO                             10                              69
  YES                            48                             361
[1] 2 2
[1] FALSE
D60V10, continuous
D60V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(12Q24.33) MUTATED                                  0     0
  DEL PEAK 31(12Q24.33) WILD-TYPE                                2    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(12Q24.33) MUTATED                          10    45
  DEL PEAK 31(12Q24.33) WILD-TYPE                        34   370
D60V12, multiclass
                                  clus
vv                                 DEL PEAK 31(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       45
                                  clus
vv                                 DEL PEAK 31(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                     34
  WHITE                                                        370
[1] 4 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(12Q24.33) MUTATED     4  49
  DEL PEAK 31(12Q24.33) WILD-TYPE  20 382
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED      4   49
  DEL PEAK 31(12Q24.33) WILD-TYPE   20  382
                        clus
vv                       DEL PEAK 31(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            49
                        clus
vv                       DEL PEAK 31(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             382
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 32(13Q12.11) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(13Q12.11) MUTATED   137  53
  DEL PEAK 32(13Q12.11) WILD-TYPE 164  60
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            190                             224 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                             53                              60 
$`DEL PEAK 32(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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DL 
         855          622          918          351          182          623 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
         278          133          536          687         1153          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 
        1955          624            5          721         1157          392 
TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 
         817          625         1330          811         1045         1081 
TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1977         1966          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
         629           45           98         1970          202          224 
TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         318          735          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5330 
         391          645          225          526          348         1393 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 
        1000         1959         1560         1007          509         1950 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CI 
        1960          707         1963          893          785          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6487 
        2562          358         1050         1969          311          234 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7371 
         379         1956         1435         1191         1440         1979 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 
         759           30         1036          997         1430          907 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
         216          181          911         1955         1950         3295 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 
        1978         2886          519          406         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 
         215         1315         1970         1948         1969         1959 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 
        3835         1969         1957         1969         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 
        1970         1936         1959         1945         1987         1952 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 
        1095          797         1967         1974         1955         1957 
TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JE 
        1959         5480         1960         1954         1722         1075 
TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6825 
         906          110          237          828          701          491 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         154          106          539          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
         368          389          338          516         1030         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G 
         575          299          324          340         1131           15 
TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          92           14            6          403            2            5 
TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61G 
          55           25           49          111          441          360 
TCGA-IQ-A61O TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
         360          112          254         1726         1954         1968 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         218          228          567          198          149          135 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E 
         135          168         1326         1663         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JS 
        1043          484          665          413 

$`DEL PEAK 32(13Q12.11) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5153 
         102          283          415         1983          722         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
         725          623         1636          451          895          850 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
         216         1976          314          142          187         2878 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 
         140          558          310          423          638          436 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4731 
           4          799          142         1230         1151          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
         642         1250          395         1960         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 
        1007          173         1980         1980         1966         1975 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6989 
         628          594          629          432         1110          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         394          432          904          484          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         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         1253 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
        1057          985         1959         1179         1750         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1274          877         1353          998          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-6936 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 
         641         1899         1952         1948         1966         1959 
TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 
        3837         1939         1979         1444          954         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1976         1099         1948         1947         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-A45Z TCGA-CV-A460 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO 
        1945         1940         1946         1977         1970         1959 
TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         670          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6827 
         317          321          773          292           77          568 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 
         128          376          483         1778         1081          548 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 
         775          622          369          368          490          658 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 
         585            3          384           13          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 
         133          414          206           25           37           44 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          24           11           10           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S 
         122          588          412          440          351          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         552          378          168           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
          56          111          240          910         1559         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 TCGA-QK-AA3J TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD 
         225          387          157         1319         1894          735 
TCGA-UF-A7JF TCGA-UF-A7JJ 
        1497          214 

  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                              2                               3 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                           5480                            3837 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            685                             718 
[1] "2.0 - 5480.0 (685.0)" "3.0 - 3837.0 (718.0)"
[1] "hr=" "1"  
D61V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 32(13Q12.11) MUTATED         8       26        33       113
  DEL PEAK 32(13Q12.11) WILD-TYPE      18       49        41       122
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 32(13Q12.11) MUTATED           6         1
  DEL PEAK 32(13Q12.11) WILD-TYPE         6         0
D61V3, multiclass
           clus
vv          DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  STAGE I                               8                              18
  STAGE II                             26                              49
  STAGE III                            33                              41
  STAGE IVA                           113                             122
  STAGE IVB                             6                               6
  STAGE IVC                             1                               0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1 T2 T3 T4
  DEL PEAK 32(13Q12.11) MUTATED      15 53 43 80
  DEL PEAK 32(13Q12.11) WILD-TYPE    32 74 51 82
D61V4, multiclass
       clus
vv      DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  T0+T1                            15                              32
  T2                               53                              74
  T3                               43                              51
  T4                               80                              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 32(13Q12.11) MUTATED    67  31  75   3
  DEL PEAK 32(13Q12.11) WILD-TYPE 103  32  77   5
D61V5, multiclass
    clus
vv   DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  N0                            67                             103
  N1                            31                              32
  N2                            75                              77
  N3                             3                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 MX
  DEL PEAK 32(13Q12.11) MUTATED   75  1 23
  DEL PEAK 32(13Q12.11) WILD-TYPE 92  0 35
D61V6, multiclass
    clus
vv   DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  M0                            75                              92
  M1                             1                               0
  MX                            23                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED    50 169
  DEL PEAK 32(13Q12.11) WILD-TYPE  82 187
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED     50  169
  DEL PEAK 32(13Q12.11) WILD-TYPE   82  187
        clus
vv       DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  FEMALE                            50                              82
  MALE                             169                             187
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                                     214
  DEL PEAK 32(13Q12.11) WILD-TYPE                                   263
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 32(13Q12.11) MUTATED                                                             1
  DEL PEAK 32(13Q12.11) WILD-TYPE                                                           0
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 32(13Q12.11) MUTATED                                                     4
  DEL PEAK 32(13Q12.11) WILD-TYPE                                                   6
D61V8, multiclass
                                                             clus
vv                                                            DEL PEAK 32(13Q12.11) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 214
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
                                                             clus
vv                                                            DEL PEAK 32(13Q12.11) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   263
  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"
D61V9, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED    35 184
  DEL PEAK 32(13Q12.11) WILD-TYPE  44 225
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED     35  184
  DEL PEAK 32(13Q12.11) WILD-TYPE   44  225
     clus
vv    DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  NO                             35                              44
  YES                           184                             225
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(13Q12.11) MUTATED                                  2     3
  DEL PEAK 32(13Q12.11) WILD-TYPE                                0     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(13Q12.11) MUTATED                          26   179
  DEL PEAK 32(13Q12.11) WILD-TYPE                        18   236
D61V12, multiclass
                                  clus
vv                                 DEL PEAK 32(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      179
                                  clus
vv                                 DEL PEAK 32(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     18
  WHITE                                                        236
[1] 4 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(13Q12.11) MUTATED    14 182
  DEL PEAK 32(13Q12.11) WILD-TYPE  10 249
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED     14  182
  DEL PEAK 32(13Q12.11) WILD-TYPE   10  249
                        clus
vv                       DEL PEAK 32(13Q12.11) MUTATED
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           182
                        clus
vv                       DEL PEAK 32(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             249
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 33(13Q14.2) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(13Q14.2) MUTATED   132  43
  DEL PEAK 33(13Q14.2) WILD-TYPE 169  70
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                           175                            239 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                            43                             70 
$`DEL PEAK 33(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-A4IG 
        1747          644           63          113          236          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DL 
         622          918          850          351          216          623 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          278          133          558          310          536 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         687         1153          428         1955          624            5 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 
         721         1157          817         1330          811         1045 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1081         1977         1980         1966          683          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         933          629           45           98         1970          202 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         224          318          735           46          443          535 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5330 
         391          645          225          348         1466         1393 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4CA 
         985         1959         1560         1007          509         1963 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         998          785          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6477 TCGA-CR-6478 
        1152         1777         1521         1050          514         1969 
TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 
         311          234         1435         1191          759           30 
TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 
        1036          997         1430          216          181          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5977 
        1472         1955         1950         3295         2886         1840 
TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-6960 
         215         1970         1959         3835         1957         1969 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7235 
        1959         1970         1936         1959         1987         1952 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 
        1095          797         1967         1974         1955         1957 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 
        1959         1981         5480         1960         1954         1722 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6825 
        1075          906          317          237          828          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-DQ-5630 
         154          568          106          539          424         1030 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 
        1965          575          775          299          324          340 
TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A76A 
        1131           15           92           14            6          206 
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-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 
         111          360          552          378          112          254 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IH 
        1726         1559         1954         1968          218          228 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K 
         567          198          149          135          135          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
        1326         1663         1252         1278         1043          484 
TCGA-UF-A7JS 
         413 

$`DEL PEAK 33(13Q14.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5556 
         102          283          415         1983          722          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF 
         623         1636          190          451          384          895 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4225 
         182         1976          314          142          187          140 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 
         423          638          436            4          799          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1230         1151          392          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         395          625         1960         1268         1988         1007 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6013 
         173         1980         1966         1975          630          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 
         594          629          432         1110          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         432          429          904          526          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223          298         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         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
        1000         1057         1959         1179         1750         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 
         893          391          303          799         1966         1125 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
        1971          362          345          354          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
         479         1956         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 
        1979          889          972         1968          796         1954 
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-7398 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5435 
         898          930          156         1077          522         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         584          546         1978         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
         519          406          701         2641         1478         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1665          641         1899         1948         1969         1952 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1948         1969         1966         1959         3837         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 
        1939         1945         1979         1444          954         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1976         1099         1948         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        1972         1937         1984         1958          851         1945 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT 
        1940         1946         1977         1970         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
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-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          232          435          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7591 
         338         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-KU-A6H8 
         360          412          440          351          224          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A7D7 
          14           34          392           56          111          240 
TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
         910         1120          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-AA3J TCGA-UF-A71B 
         357          245          225          387          157         1319 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          735         1497          665          214 

  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                             5                              2 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                          5480                           3837 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                           775                            665 
[1] "5.0 - 5480.0 (775.0)" "2.0 - 3837.0 (665.0)"
[1] "hr=" "1.3"
D62V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 33(13Q14.2) MUTATED        11       23        33        95         6
  DEL PEAK 33(13Q14.2) WILD-TYPE      15       52        41       140         6
                                vv
clus                             STAGE IVC
  DEL PEAK 33(13Q14.2) MUTATED           1
  DEL PEAK 33(13Q14.2) WILD-TYPE         0
D62V3, multiclass
           clus
vv          DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  STAGE I                             11                             15
  STAGE II                            23                             52
  STAGE III                           33                             41
  STAGE IVA                           95                            140
  STAGE IVB                            6                              6
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 33(13Q14.2) MUTATED      21 53 35 64
  DEL PEAK 33(13Q14.2) WILD-TYPE    26 74 59 98
D62V4, multiclass
       clus
vv      DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  T0+T1                           21                             26
  T2                              53                             74
  T3                              35                             59
  T4                              64                             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
  DEL PEAK 33(13Q14.2) MUTATED    61  26  67   4
  DEL PEAK 33(13Q14.2) WILD-TYPE 109  37  85   4
D62V5, multiclass
    clus
vv   DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  N0                           61                            109
  N1                           26                             37
  N2                           67                             85
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 33(13Q14.2) MUTATED    66   1  25
  DEL PEAK 33(13Q14.2) WILD-TYPE 101   0  33
D62V6, multiclass
    clus
vv   DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  M0                           66                            101
  M1                            1                              0
  MX                           25                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q14.2) MUTATED    47 155
  DEL PEAK 33(13Q14.2) WILD-TYPE  85 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q14.2) MUTATED     47  155
  DEL PEAK 33(13Q14.2) WILD-TYPE   85  201
        clus
vv       DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  FEMALE                           47                             85
  MALE                            155                            201
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q14.2) MUTATED                                     195
  DEL PEAK 33(13Q14.2) WILD-TYPE                                   282
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 33(13Q14.2) MUTATED                                                             1
  DEL PEAK 33(13Q14.2) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 33(13Q14.2) MUTATED                                                     6
  DEL PEAK 33(13Q14.2) WILD-TYPE                                                   4
D62V8, multiclass
                                                             clus
vv                                                            DEL PEAK 33(13Q14.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                195
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
                                                             clus
vv                                                            DEL PEAK 33(13Q14.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  282
  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"
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q14.2) MUTATED    34 168
  DEL PEAK 33(13Q14.2) WILD-TYPE  45 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q14.2) MUTATED     34  168
  DEL PEAK 33(13Q14.2) WILD-TYPE   45  241
     clus
vv    DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  NO                            34                             45
  YES                          168                            241
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(13Q14.2) MUTATED                                  2     3
  DEL PEAK 33(13Q14.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q14.2) MUTATED                          25   165
  DEL PEAK 33(13Q14.2) WILD-TYPE                        19   250
D62V12, multiclass
                                  clus
vv                                 DEL PEAK 33(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     165
                                  clus
vv                                 DEL PEAK 33(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       250
[1] 4 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(13Q14.2) MUTATED    12 170
  DEL PEAK 33(13Q14.2) WILD-TYPE  12 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q14.2) MUTATED     12  170
  DEL PEAK 33(13Q14.2) WILD-TYPE   12  261
                        clus
vv                       DEL PEAK 33(13Q14.2) MUTATED
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          170
                        clus
vv                       DEL PEAK 33(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            261
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 34(14Q11.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(14Q11.2) MUTATED    43  19
  DEL PEAK 34(14Q11.2) WILD-TYPE 258  94
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            62                            352 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            19                             94 
$`DEL PEAK 34(14Q11.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-6871 
         102          283          276         1288          644           63 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BB-7862 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 
         622          850          536         1157          392         1250 
TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-A49A TCGA-CN-A63U TCGA-CQ-5332 
         933          432           98          391          526          317 
TCGA-CQ-6221 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6491 
        1000         1950          358         1050          354          350 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7388 TCGA-CR-7398 
        1956         1191         1440          105         1951          156 
TCGA-CR-7399 TCGA-CV-5435 TCGA-CV-5966 TCGA-CV-6935 TCGA-CV-6945 TCGA-CV-7180 
         181         1438          519         1969         1969         1987 
TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6K1 
        1937         1959         1940         1946          646          685 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-5629 
         154          128          539          232          424          516 
TCGA-F7-7848 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-8224 TCGA-HD-A633 
        1131          403          206            2           55           49 
TCGA-P3-A6T0 TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         578          198          157         1663         1319         1252 
TCGA-UF-A7JA TCGA-UF-A7JF 
        1894         1497 

$`DEL PEAK 34(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-A4IG 
         451          384          113          236          895          855 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         918          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         623          142          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         1230         1151 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         817          993          642          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
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          683          290          630          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 
         628          594          629           45         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1110          224          318          611          394          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
         432          429           46          443          535          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         645          225          484          348          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1393         1399          341          129         1253 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1560         1007          509         1309         1274          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1353         1960          707         1963          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         785          391          303          950         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-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-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         234          379          479         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-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
        1036          796         1954          997         1430          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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         216         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958         2437          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        1478         1840          215         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1899         1970         1948         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-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-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1945         1979         1952         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-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1972         1984         1958         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        5480         1960         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
        1075          906         1959          670          110          714 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         606         1950          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-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         106          376          483          435          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         338         1778         1081         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-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         324          340          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-7753 TCGA-HD-7754 
         407           58          133          414            5           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-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-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         588          360          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         224          552          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         392           56          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
         910         1726         1559         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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         228          225          387          567          149          135 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
         135          168         1326         1278         1043          484 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735          665          214          413 

  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                             2                              3 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                          1987                           5480 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                         558.5                          723.5 
[1] "2.0 - 1987.0 (558.5)" "3.0 - 5480.0 (723.5)"
[1] "hr=" "2"  
D63V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 34(14Q11.2) MUTATED         1       15         8        36         1
  DEL PEAK 34(14Q11.2) WILD-TYPE      25       60        66       199        11
                                vv
clus                             STAGE IVC
  DEL PEAK 34(14Q11.2) MUTATED           0
  DEL PEAK 34(14Q11.2) WILD-TYPE         1
D63V3, multiclass
           clus
vv          DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  STAGE I                              1                             25
  STAGE II                            15                             60
  STAGE III                            8                             66
  STAGE IVA                           36                            199
  STAGE IVB                            1                             11
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 34(14Q11.2) MUTATED       3  20  13  26
  DEL PEAK 34(14Q11.2) WILD-TYPE    44 107  81 136
D63V4, multiclass
       clus
vv      DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  T0+T1                            3                             44
  T2                              20                            107
  T3                              13                             81
  T4                              26                            136
[1] 4 2
[1] TRUE
[1] "dimension 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(14Q11.2) MUTATED    27  10  21   0
  DEL PEAK 34(14Q11.2) WILD-TYPE 143  53 131   8
D63V5, multiclass
    clus
vv   DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  N0                           27                            143
  N1                           10                             53
  N2                           21                            131
  N3                            0                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 34(14Q11.2) MUTATED    27   0   6
  DEL PEAK 34(14Q11.2) WILD-TYPE 140   1  52
D63V6, multiclass
    clus
vv   DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  M0                           27                            140
  M1                            0                              1
  MX                            6                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q11.2) MUTATED    15  55
  DEL PEAK 34(14Q11.2) WILD-TYPE 117 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q11.2) MUTATED     15   55
  DEL PEAK 34(14Q11.2) WILD-TYPE  117  301
        clus
vv       DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  FEMALE                           15                            117
  MALE                             55                            301
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(14Q11.2) MUTATED                                      67
  DEL PEAK 34(14Q11.2) WILD-TYPE                                   410
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 34(14Q11.2) MUTATED                                                             0
  DEL PEAK 34(14Q11.2) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 34(14Q11.2) MUTATED                                                     3
  DEL PEAK 34(14Q11.2) WILD-TYPE                                                   7
D63V8, multiclass
                                                             clus
vv                                                            DEL PEAK 34(14Q11.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 67
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            DEL PEAK 34(14Q11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  410
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      7
[1] 3 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(14Q11.2) MUTATED    11  59
  DEL PEAK 34(14Q11.2) WILD-TYPE  68 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q11.2) MUTATED     11   59
  DEL PEAK 34(14Q11.2) WILD-TYPE   68  350
     clus
vv    DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  NO                            11                             68
  YES                           59                            350
[1] 2 2
[1] FALSE
D63V10, continuous
D63V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(14Q11.2) MUTATED                                  0     1
  DEL PEAK 34(14Q11.2) WILD-TYPE                                2    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(14Q11.2) MUTATED                          10    58
  DEL PEAK 34(14Q11.2) WILD-TYPE                        34   357
D63V12, multiclass
                                  clus
vv                                 DEL PEAK 34(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      58
                                  clus
vv                                 DEL PEAK 34(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       357
[1] 4 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(14Q11.2) MUTATED     0  61
  DEL PEAK 34(14Q11.2) WILD-TYPE  24 370
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q11.2) MUTATED      0   61
  DEL PEAK 34(14Q11.2) WILD-TYPE   24  370
                        clus
vv                       DEL PEAK 34(14Q11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 34(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 24
  NOT HISPANIC OR LATINO                            370
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 35(14Q32.32) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(14Q32.32) MUTATED    43  18
  DEL PEAK 35(14Q32.32) WILD-TYPE 258  95
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             61                             353 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             18                              95 
$`DEL PEAK 35(14Q32.32) MUTATED`
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-6869 
         102          276         1288         1762         1747          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 
         451           63          622          142         2878          140 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7866 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-6019 
         558          536          638         1151         1250          432 
TCGA-CN-6020 TCGA-CN-6992 TCGA-CN-A63U TCGA-CN-A63Y TCGA-CQ-6221 TCGA-CR-5247 
          98          394          526          175         1000          358 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-7398 
         799         1777         1521         1050          362          156 
TCGA-CR-7399 TCGA-CV-5434 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5978 
         181         3295         2327         1958          519          215 
TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7435 
         641         1969         1967         1974         1957         1959 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-D6-8569 TCGA-D6-A6EM 
        1940         1946          646          685          128          232 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-H7-A6C5 TCGA-H7-A76A 
         548          775          369          340          403          206 
TCGA-HD-8224 TCGA-HD-A6HZ TCGA-MZ-A6I9 TCGA-P3-A6T0 TCGA-UF-A71D TCGA-UF-A71E 
          55          111          254          578         1252         1278 
TCGA-UF-A7J9 
        1043 

$`DEL PEAK 35(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-A4IG TCGA-BA-A4II TCGA-BA-A6D8 
         113          236          895          855          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
         187          278          133          310          423          687 
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-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
         392          817          993          642          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1045          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         735          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
         391          904          645          225          484          348 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         129         1253         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6471 TCGA-CR-6473 
         950         2562         1663         1152         1966         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971          514         1969          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-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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         216         1077          911         1472         1955          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-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2437          406          701         2641         1478         1840 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        1315         1665         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-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
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-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 
        1952         1444         1095          954          797         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 
        1976         1099         1948         1955         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-A45R TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 
         851         1945         5480         1960         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         110          714          606         1950          317          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-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          154          568          106          539          376 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         483          435          424          368          389          338 
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-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 
         622          299          368          324         1131          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-8314 
         414            2            5           25           37           44 
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-KU-A66T 
         412          440          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          240          910         1726         1559 
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          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         567          198          149          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC 
         168         1326         1663         1319         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             55                               2 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                           3295                            5480 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                            622                             725 
[1] "55.0 - 3295.0 (622.0)" "2.0 - 5480.0 (725.0)" 
[1] "hr=" "1.2"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 35(14Q32.32) MUTATED         0       12         7        28
  DEL PEAK 35(14Q32.32) WILD-TYPE      26       63        67       207
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 35(14Q32.32) MUTATED           2         0
  DEL PEAK 35(14Q32.32) WILD-TYPE        10         1
D64V3, multiclass
           clus
vv          DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  STAGE I                               0                              26
  STAGE II                             12                              63
  STAGE III                             7                              67
  STAGE IVA                            28                             207
  STAGE IVB                             2                              10
  STAGE IVC                             0                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 35(14Q32.32) MUTATED       2  18  13  18
  DEL PEAK 35(14Q32.32) WILD-TYPE    45 109  81 144
D64V4, multiclass
       clus
vv      DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  T0+T1                             2                              45
  T2                               18                             109
  T3                               13                              81
  T4                               18                             144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 35(14Q32.32) MUTATED    20   7  17   2
  DEL PEAK 35(14Q32.32) WILD-TYPE 150  56 135   6
D64V5, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  N0                            20                             150
  N1                             7                              56
  N2                            17                             135
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 35(14Q32.32) MUTATED    17   0   6
  DEL PEAK 35(14Q32.32) WILD-TYPE 150   1  52
D64V6, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  M0                            17                             150
  M1                             0                               1
  MX                             6                              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED    13  55
  DEL PEAK 35(14Q32.32) WILD-TYPE 119 301
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     13   55
  DEL PEAK 35(14Q32.32) WILD-TYPE  119  301
        clus
vv       DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  FEMALE                            13                             119
  MALE                              55                             301
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q32.32) MUTATED                                      66
  DEL PEAK 35(14Q32.32) WILD-TYPE                                   411
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 35(14Q32.32) MUTATED                                                             0
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 35(14Q32.32) MUTATED                                                     2
  DEL PEAK 35(14Q32.32) WILD-TYPE                                                   8
D64V8, multiclass
                                                             clus
vv                                                            DEL PEAK 35(14Q32.32) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  66
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     2
                                                             clus
vv                                                            DEL PEAK 35(14Q32.32) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   411
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       8
[1] 3 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(14Q32.32) MUTATED    15  53
  DEL PEAK 35(14Q32.32) WILD-TYPE  64 356
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     15   53
  DEL PEAK 35(14Q32.32) WILD-TYPE   64  356
     clus
vv    DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  NO                             15                              64
  YES                            53                             356
[1] 2 2
[1] FALSE
D64V10, continuous
D64V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(14Q32.32) MUTATED                                  0     0
  DEL PEAK 35(14Q32.32) WILD-TYPE                                2    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(14Q32.32) MUTATED                          10    58
  DEL PEAK 35(14Q32.32) WILD-TYPE                        34   357
D64V12, multiclass
                                  clus
vv                                 DEL PEAK 35(14Q32.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       58
                                  clus
vv                                 DEL PEAK 35(14Q32.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                     34
  WHITE                                                        357
[1] 4 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(14Q32.32) MUTATED     2  59
  DEL PEAK 35(14Q32.32) WILD-TYPE  22 372
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED      2   59
  DEL PEAK 35(14Q32.32) WILD-TYPE   22  372
                        clus
vv                       DEL PEAK 35(14Q32.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            59
                        clus
vv                       DEL PEAK 35(14Q32.32) WILD-TYPE
  HISPANIC OR LATINO                                  22
  NOT HISPANIC OR LATINO                             372
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 36(15Q15.1) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(15Q15.1) MUTATED    67  30
  DEL PEAK 36(15Q15.1) WILD-TYPE 234  83
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                            97                            317 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                            30                             83 
$`DEL PEAK 36(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-A4IG TCGA-BA-A4II TCGA-BA-A6DE TCGA-BA-A8YP 
         236          895          855          918          182          142 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4725 
        2878          140          638         1153          428         1157 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6012 
        1151          817         1980         1977         1975          629 
TCGA-CN-6016 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         594         1970          224          432          429           46 
TCGA-CN-A499 TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6224 
         535          348          367         1393          317          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1959         1179          509         1950         1353         1960 
TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-7373 
         785         2562         1971         1969          362          889 
TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 
         911         1438         2886          519          406         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1840         1315         1970         1957         1969         1959 
TCGA-CV-7095 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7254 TCGA-CV-7261 
        1970         1952         1095          954         1976         1099 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A460 TCGA-CV-A6JZ 
        1947         1937         1959         5480         1946          714 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EO TCGA-D6-A74Q 
         828          292          701          154          435          338 
TCGA-DQ-5624 TCGA-DQ-5631 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-A76A 
        1778          548           92            3            6          206 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-P3-A5QA TCGA-P3-A6T4 
         588          412          360          552         1726         1968 
TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JA 
         218          149          135         1326         1663         1894 
TCGA-UF-A7JD 
         735 

$`DEL PEAK 36(15Q15.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 
         248          722          725          623         1636          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
          63          384          113          622          850          351 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 
         216         1976          314          623          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-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         436         1955          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
         721          142         1230          392          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
        1268         1988         1007         1045          173         1081 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1980         1966         1966          683          290          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         933          628          629           45          432           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         202         1110          318          611          394          735 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         484          175          223          298         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-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 
        1253         1000         1057         1959         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1007         1309         1274          877          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
         893          998          391          303          950          358 
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-6481 TCGA-CR-6482 TCGA-CR-6484 
        1050         1125          514          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-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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         759           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         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-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         156          181         1077         1472         1955          522 
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-5443 TCGA-CV-5444 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6003 
        1958         2437          701         2641          215         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
         641         1899         1948         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7091 
        3835         1948         1969         1966         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-7238 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 
        1979         1444          797         1967         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1957         1937         1973         1972 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y 
        1984         1958         1981          851         1945         1960 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1940         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 
         906         1959          670          110          646          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
         685         1950          317          321          237          773 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
          77          491          568          106          128          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          232          424          368          389 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
        1081          516         1030         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-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V 
        1131          490          658           15          585          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13          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-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-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
         360          440          351          224          378          168 
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-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          240          910         1559         1120         1954 
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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB 
         228          225          387          567          198          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         157          168         1319         1252         1278         1043 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484         1497          665          214          413 

  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                             3                              2 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                          5480                           3837 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                           911                            645 
[1] "3.0 - 5480.0 (911.0)" "2.0 - 3837.0 (645.0)"
[1] "hr=" "1.1"
D65V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 36(15Q15.1) MUTATED         3       23        16        52         3
  DEL PEAK 36(15Q15.1) WILD-TYPE      23       52        58       183         9
                                vv
clus                             STAGE IVC
  DEL PEAK 36(15Q15.1) MUTATED           0
  DEL PEAK 36(15Q15.1) WILD-TYPE         1
D65V3, multiclass
           clus
vv          DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  STAGE I                              3                             23
  STAGE II                            23                             52
  STAGE III                           16                             58
  STAGE IVA                           52                            183
  STAGE IVB                            3                              9
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 36(15Q15.1) MUTATED       6  35  23  35
  DEL PEAK 36(15Q15.1) WILD-TYPE    41  92  71 127
D65V4, multiclass
       clus
vv      DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  T0+T1                            6                             41
  T2                              35                             92
  T3                              23                             71
  T4                              35                            127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 36(15Q15.1) MUTATED    36  13  37   3
  DEL PEAK 36(15Q15.1) WILD-TYPE 134  50 115   5
D65V5, multiclass
    clus
vv   DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  N0                           36                            134
  N1                           13                             50
  N2                           37                            115
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 36(15Q15.1) MUTATED    31   0  15
  DEL PEAK 36(15Q15.1) WILD-TYPE 136   1  43
D65V6, multiclass
    clus
vv   DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  M0                           31                            136
  M1                            0                              1
  MX                           15                             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q15.1) MUTATED    26  89
  DEL PEAK 36(15Q15.1) WILD-TYPE 106 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q15.1) MUTATED     26   89
  DEL PEAK 36(15Q15.1) WILD-TYPE  106  267
        clus
vv       DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  FEMALE                           26                            106
  MALE                             89                            267
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(15Q15.1) MUTATED                                     114
  DEL PEAK 36(15Q15.1) WILD-TYPE                                   363
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 36(15Q15.1) MUTATED                                                             1
  DEL PEAK 36(15Q15.1) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 36(15Q15.1) MUTATED                                                     0
  DEL PEAK 36(15Q15.1) WILD-TYPE                                                  10
D65V8, multiclass
                                                             clus
vv                                                            DEL PEAK 36(15Q15.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                114
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
                                                             clus
vv                                                            DEL PEAK 36(15Q15.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  363
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     10
[1] 3 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(15Q15.1) MUTATED    22  93
  DEL PEAK 36(15Q15.1) WILD-TYPE  57 316
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q15.1) MUTATED     22   93
  DEL PEAK 36(15Q15.1) WILD-TYPE   57  316
     clus
vv    DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  NO                            22                             57
  YES                           93                            316
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(15Q15.1) MUTATED                                  0     2
  DEL PEAK 36(15Q15.1) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(15Q15.1) MUTATED                          10    98
  DEL PEAK 36(15Q15.1) WILD-TYPE                        34   317
D65V12, multiclass
                                  clus
vv                                 DEL PEAK 36(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      98
                                  clus
vv                                 DEL PEAK 36(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  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"
D65V13, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q15.1) MUTATED     9  97
  DEL PEAK 36(15Q15.1) WILD-TYPE  15 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q15.1) MUTATED      9   97
  DEL PEAK 36(15Q15.1) WILD-TYPE   15  334
                        clus
vv                       DEL PEAK 36(15Q15.1) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                           97
                        clus
vv                       DEL PEAK 36(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            334
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 37(16Q23.1) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16Q23.1) MUTATED    56  20
  DEL PEAK 37(16Q23.1) WILD-TYPE 245  93
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            76                            338 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            20                             93 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-A4IH TCGA-BB-4225 
         415          276         1762         1747          622          140 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 
         133          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         1045         1081         1977          290 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49A 
         629           98         1970          432          535          391 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CR-5243 TCGA-CR-6467 
         225          526          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-7374 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
          30          156          911         2886         1958         2437 
TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7261 
         519          215         1959         1952         1960         1099 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-A460 TCGA-CV-A6JN 
        1955         1947         1973         1937         1946          906 
TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-7588 
         317          237          568          539          232         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50I TCGA-HD-8224 
         575          775          622          299           92           55 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-KU-A6H7 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A6IF 
         588          412          378         1559         1120          245 
TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 
         135         1663         1278         1043 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          462          283         1983          248          722 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
        1288          520          725          623         1636          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-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          855          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 
        2878          278          558          423          687          428 
TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         436            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142         1230         1151          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 
        1268         1988         1007          173         1980         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          683          630          933 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 
         628          594          629           45          432          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1110          224          318          611          394          735 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V 
         429           46          443          904          645          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         707         1963          893          998          785          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          950          358         1663         1152          799 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1521         1966         1971          514         1969          362 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        1435         1191         1440         1960         1979          759 
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-7399 
         946          908          898          930          216          181 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5970 
        1438          584          546         1978         2327          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
         701         2641         1478         1840         1315         1665 
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-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-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-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-7254 TCGA-CV-7406 
        1095          954          797         1967         1976         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
        1948         1957         1937         1972         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1959         1981          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1940         1954         1722         1977         1970         1075 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         685         1950          321          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
         701           77          491          154          106          128 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         338         1778         1081          516         1030          548 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          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-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          407           58          133          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         403          206            2            5           25           37 
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-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         360          440          351          360          224          552 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SX 
         112          254          240          910         1726         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         578         1917         1968          400          553          357 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         218          228          225          387          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B 
         149          135          157          168         1326         1319 
TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1252         1894          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            30                              2 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          2886                           5480 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                         626.5                          710.5 
[1] "30.0 - 2886.0 (626.5)" "2.0 - 5480.0 (710.5)" 
[1] "hr=" "1"  
D66V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 37(16Q23.1) MUTATED         2       10        14        37         4
  DEL PEAK 37(16Q23.1) WILD-TYPE      24       65        60       198         8
                                vv
clus                             STAGE IVC
  DEL PEAK 37(16Q23.1) MUTATED           0
  DEL PEAK 37(16Q23.1) WILD-TYPE         1
D66V3, multiclass
           clus
vv          DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  STAGE I                              2                             24
  STAGE II                            10                             65
  STAGE III                           14                             60
  STAGE IVA                           37                            198
  STAGE IVB                            4                              8
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 37(16Q23.1) MUTATED       5  22  17  24
  DEL PEAK 37(16Q23.1) WILD-TYPE    42 105  77 138
D66V4, multiclass
       clus
vv      DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  T0+T1                            5                             42
  T2                              22                            105
  T3                              17                             77
  T4                              24                            138
[1] 4 2
[1] TRUE
[1] "dimension 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(16Q23.1) MUTATED    21  14  24   3
  DEL PEAK 37(16Q23.1) WILD-TYPE 149  49 128   5
D66V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  N0                           21                            149
  N1                           14                             49
  N2                           24                            128
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 37(16Q23.1) MUTATED    21   0  11
  DEL PEAK 37(16Q23.1) WILD-TYPE 146   1  47
D66V6, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  M0                           21                            146
  M1                            0                              1
  MX                           11                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    19  70
  DEL PEAK 37(16Q23.1) WILD-TYPE 113 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     19   70
  DEL PEAK 37(16Q23.1) WILD-TYPE  113  286
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  FEMALE                           19                            113
  MALE                             70                            286
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                                      85
  DEL PEAK 37(16Q23.1) WILD-TYPE                                   392
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 37(16Q23.1) MUTATED                                                             0
  DEL PEAK 37(16Q23.1) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 37(16Q23.1) MUTATED                                                     4
  DEL PEAK 37(16Q23.1) WILD-TYPE                                                   6
D66V8, multiclass
                                                             clus
vv                                                            DEL PEAK 37(16Q23.1) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 85
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            DEL PEAK 37(16Q23.1) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  392
  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"
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    13  76
  DEL PEAK 37(16Q23.1) WILD-TYPE  66 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     13   76
  DEL PEAK 37(16Q23.1) WILD-TYPE   66  333
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  NO                            13                             66
  YES                           76                            333
[1] 2 2
[1] FALSE
D66V10, continuous
D66V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(16Q23.1) MUTATED                                  1     2
  DEL PEAK 37(16Q23.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16Q23.1) MUTATED                          10    75
  DEL PEAK 37(16Q23.1) WILD-TYPE                        34   340
D66V12, multiclass
                                  clus
vv                                 DEL PEAK 37(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      75
                                  clus
vv                                 DEL PEAK 37(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       340
[1] 4 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(16Q23.1) MUTATED     3  81
  DEL PEAK 37(16Q23.1) WILD-TYPE  21 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      3   81
  DEL PEAK 37(16Q23.1) WILD-TYPE   21  350
                        clus
vv                       DEL PEAK 37(16Q23.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK 37(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            350
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 38(16Q23.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16Q23.3) MUTATED    63  20
  DEL PEAK 38(16Q23.3) WILD-TYPE 238  93
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                            83                            331 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                            20                             93 
$`DEL PEAK 38(16Q23.3) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-A4IH 
         415          276          722         1762         1747          622 
TCGA-BA-A6DA TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 
         351          140          310          536          638         1153 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4729 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 
        1955          624          392         1045         1081         1977 
TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49A 
         290          629         1970          432          535          391 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-6218 TCGA-CQ-6224 
         225          526         1207         1660         1253          985 
TCGA-CQ-A4C7 TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6481 
        1960         2562         1777         1050         1125          311 
TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5430 
         354         1245          105          156          911         1955 
TCGA-CV-5432 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5978 
        1950         2886         1958         2437          519          215 
TCGA-CV-6941 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7235 TCGA-CV-7261 TCGA-CV-7418 
        1959         1970         1970         1952         1099         1955 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-A460 TCGA-CX-7082 TCGA-CX-7086 
        1947         1973         1937         1946          317          237 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         568          539          232         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50I TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61H 
         622          299           92           55          588          412 
TCGA-KU-A6H7 TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T8 TCGA-QK-A6IF 
         378          240         1559         1120          400          245 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 
         149          135         1663         1278         1043 

$`DEL PEAK 38(16Q23.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5152 
         102          462          283         1983          248         1288 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
         520          725          623         1636          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         451           63          384          113          236          895 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         855          918          850          216          182         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         314          623          142          187         2878          278 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 
         133          558          423          687          428          436 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1230         1151          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 
        1988         1007          173         1980         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1966         1975          683          630          933          628 
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-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1110          224          318          611          394          735 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V 
         429           46          443          904          645          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         654         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         129         1000         1057         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1750         1560         1007          509         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877         1950         1353          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
         998          785          391          303          950          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6474 
        1663         1152          799         1521         1966         1971 
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-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-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-7399 TCGA-CR-7401 TCGA-CR-7404 
         898          930          216          181         1077         1472 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
         522         3295         1438          584          546         1978 
TCGA-CV-5442 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2327          406          701         2641         1478         1840 
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-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1969         1952         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-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-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 
        1974         1948         1957         1937         1972         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1958         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1940         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 
         714          606          685         1950          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-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
         106          128          376          483          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         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 
        1131          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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            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-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         122          441          360          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         224          552          168           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         1726 
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-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         218          228          225          387          567          198 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D 
         135          157          168         1326         1319         1252 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS 
         413 

  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                            55                              2 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                          2886                           5480 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                           722                            701 
[1] "55.0 - 2886.0 (722.0)" "2.0 - 5480.0 (701.0)" 
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 38(16Q23.3) MUTATED         2       12        15        43         4
  DEL PEAK 38(16Q23.3) WILD-TYPE      24       63        59       192         8
                                vv
clus                             STAGE IVC
  DEL PEAK 38(16Q23.3) MUTATED           0
  DEL PEAK 38(16Q23.3) WILD-TYPE         1
D67V3, multiclass
           clus
vv          DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  STAGE I                              2                             24
  STAGE II                            12                             63
  STAGE III                           15                             59
  STAGE IVA                           43                            192
  STAGE IVB                            4                              8
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 38(16Q23.3) MUTATED       5  23  22  27
  DEL PEAK 38(16Q23.3) WILD-TYPE    42 104  72 135
D67V4, multiclass
       clus
vv      DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  T0+T1                            5                             42
  T2                              23                            104
  T3                              22                             72
  T4                              27                            135
[1] 4 2
[1] TRUE
[1] "dimension 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(16Q23.3) MUTATED    23  13  30   3
  DEL PEAK 38(16Q23.3) WILD-TYPE 147  50 122   5
D67V5, multiclass
    clus
vv   DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  N0                           23                            147
  N1                           13                             50
  N2                           30                            122
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 38(16Q23.3) MUTATED    24   0  13
  DEL PEAK 38(16Q23.3) WILD-TYPE 143   1  45
D67V6, multiclass
    clus
vv   DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  M0                           24                            143
  M1                            0                              1
  MX                           13                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.3) MUTATED    23  73
  DEL PEAK 38(16Q23.3) WILD-TYPE 109 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.3) MUTATED     23   73
  DEL PEAK 38(16Q23.3) WILD-TYPE  109  283
        clus
vv       DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  FEMALE                           23                            109
  MALE                             73                            283
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16Q23.3) MUTATED                                      92
  DEL PEAK 38(16Q23.3) WILD-TYPE                                   385
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 38(16Q23.3) MUTATED                                                             0
  DEL PEAK 38(16Q23.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 38(16Q23.3) MUTATED                                                     4
  DEL PEAK 38(16Q23.3) WILD-TYPE                                                   6
D67V8, multiclass
                                                             clus
vv                                                            DEL PEAK 38(16Q23.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 92
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            DEL PEAK 38(16Q23.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  385
  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(16Q23.3) MUTATED    16  80
  DEL PEAK 38(16Q23.3) WILD-TYPE  63 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.3) MUTATED     16   80
  DEL PEAK 38(16Q23.3) WILD-TYPE   63  329
     clus
vv    DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  NO                            16                             63
  YES                           80                            329
[1] 2 2
[1] FALSE
D67V10, continuous
D67V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(16Q23.3) MUTATED                                  1     3
  DEL PEAK 38(16Q23.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16Q23.3) MUTATED                          10    80
  DEL PEAK 38(16Q23.3) WILD-TYPE                        34   335
D67V12, multiclass
                                  clus
vv                                 DEL PEAK 38(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      80
                                  clus
vv                                 DEL PEAK 38(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       335
[1] 4 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(16Q23.3) MUTATED     5  86
  DEL PEAK 38(16Q23.3) WILD-TYPE  19 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.3) MUTATED      5   86
  DEL PEAK 38(16Q23.3) WILD-TYPE   19  345
                        clus
vv                       DEL PEAK 38(16Q23.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK 38(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            345
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 39(17P11.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17P11.2) MUTATED    53  27
  DEL PEAK 39(17P11.2) WILD-TYPE 248  86
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            80                            334 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            27                             86 
$`DEL PEAK 39(17P11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
         283          248          623         1747          190          451 
TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP 
          63          622          918          850          182          142 
TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4725 
        2878          536          638          428          624         1157 
TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6988 TCGA-CN-A63W TCGA-CQ-6221 
         817         1330          290          318          348         1000 
TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6472 
        1959          509         1960          707          950         1050 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7390 
         354          379         1435         1960         1979          907 
TCGA-CR-7398 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-6441 
         156          546         2437          519          406         1970 
TCGA-CV-6961 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7406 
        1959         1945         1987          797         1976         1974 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-A460 TCGA-CV-A6JU TCGA-CX-7086 
        1947         1973         1959         1946          110          237 
TCGA-CX-7219 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-7588 TCGA-DQ-7591 
         828          154          128          232         1965          622 
TCGA-DQ-7595 TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8635 
         324           13            6          403            5           25 
TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5QA 
         485          360          412           56          112         1726 
TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
        1954          400          553          198          149          135 
TCGA-QK-A8ZB TCGA-UF-A7JH 
         135          665 

$`DEL PEAK 39(17P11.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
         102          462          415         1983          276          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 
        1288         1762          520          725         1636          644 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DA 
         384          113          236          895          855          351 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 
         216         1976          314          623          187          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
         140          133          558          310          423          687 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
        1153          436         1955            5            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
         721          142         1230         1151          392          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
         642         1250          395          625         1960          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988         1007         1045          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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         683          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         629           45          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
        1110          224          611          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         429           46          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         645          225          526          484          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
        1253         1057          985         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1560         1007         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1353         1963          893          998          785          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-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-6491 
        1969          362          311          345          234          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 
         479         1956         1191         1440         1245          105 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          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-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-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295         1438          584         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2327         1958          701         2641         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-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-7090 TCGA-CV-7091 TCGA-CV-7095 
        1966         1957         1969         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 
        1970         1936         1959         1939         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1444         1095          954         1967         1960         1099 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1948         1955         1957         1937         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1984         1958         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1940         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        1075          906         1959          670          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 
         606          685         1950          317          321          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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         539          376          483          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         389          338         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         548          575          775          299          369          368 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-7774 TCGA-H7-8501 
         585            3          384           14          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         133          414          206            2           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          55           44           24           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
         111           33         1057          122          441          588 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         440          351          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 
         168           14           34          392          111          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         240          910         1559         1120          578         1917 
TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
        1968          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         387          567          157          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1319         1252         1278         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          214          413 

  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                             5                              2 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                          2878                           5480 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                         549.5                          747.0 
[1] "5.0 - 2878.0 (549.5)" "2.0 - 5480.0 (747.0)"
[1] "hr=" "1.3"
D68V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 39(17P11.2) MUTATED         3       20        16        40         3
  DEL PEAK 39(17P11.2) WILD-TYPE      23       55        58       195         9
                                vv
clus                             STAGE IVC
  DEL PEAK 39(17P11.2) MUTATED           1
  DEL PEAK 39(17P11.2) WILD-TYPE         0
D68V3, multiclass
           clus
vv          DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  STAGE I                              3                             23
  STAGE II                            20                             55
  STAGE III                           16                             58
  STAGE IVA                           40                            195
  STAGE IVB                            3                              9
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 39(17P11.2) MUTATED       9  28  19  28
  DEL PEAK 39(17P11.2) WILD-TYPE    38  99  75 134
D68V4, multiclass
       clus
vv      DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  T0+T1                            9                             38
  T2                              28                             99
  T3                              19                             75
  T4                              28                            134
[1] 4 2
[1] TRUE
[1] "dimension 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(17P11.2) MUTATED    29  16  30   2
  DEL PEAK 39(17P11.2) WILD-TYPE 141  47 122   6
D68V5, multiclass
    clus
vv   DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  N0                           29                            141
  N1                           16                             47
  N2                           30                            122
  N3                            2                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 39(17P11.2) MUTATED    31   1  13
  DEL PEAK 39(17P11.2) WILD-TYPE 136   0  45
D68V6, multiclass
    clus
vv   DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  M0                           31                            136
  M1                            1                              0
  MX                           13                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P11.2) MUTATED    23  70
  DEL PEAK 39(17P11.2) WILD-TYPE 109 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED     23   70
  DEL PEAK 39(17P11.2) WILD-TYPE  109  286
        clus
vv       DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  FEMALE                           23                            109
  MALE                             70                            286
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(17P11.2) MUTATED                                      90
  DEL PEAK 39(17P11.2) WILD-TYPE                                   387
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 39(17P11.2) MUTATED                                                             0
  DEL PEAK 39(17P11.2) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 39(17P11.2) MUTATED                                                     3
  DEL PEAK 39(17P11.2) WILD-TYPE                                                   7
D68V8, multiclass
                                                             clus
vv                                                            DEL PEAK 39(17P11.2) 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                                    3
                                                             clus
vv                                                            DEL PEAK 39(17P11.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  387
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      7
[1] 3 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(17P11.2) MUTATED    10  83
  DEL PEAK 39(17P11.2) WILD-TYPE  69 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED     10   83
  DEL PEAK 39(17P11.2) WILD-TYPE   69  326
     clus
vv    DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  NO                            10                             69
  YES                           83                            326
[1] 2 2
[1] FALSE
D68V10, continuous
D68V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(17P11.2) MUTATED                                  0     2
  DEL PEAK 39(17P11.2) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17P11.2) MUTATED                          17    71
  DEL PEAK 39(17P11.2) WILD-TYPE                        27   344
D68V12, multiclass
                                  clus
vv                                 DEL PEAK 39(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      71
                                  clus
vv                                 DEL PEAK 39(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       344
[1] 4 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(17P11.2) MUTATED     8  79
  DEL PEAK 39(17P11.2) WILD-TYPE  16 352
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED      8   79
  DEL PEAK 39(17P11.2) WILD-TYPE   16  352
                        clus
vv                       DEL PEAK 39(17P11.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK 39(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            352
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 40(17Q25.3) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17Q25.3) MUTATED    43  18
  DEL PEAK 40(17Q25.3) WILD-TYPE 258  95
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            61                            353 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            18                             95 
$`DEL PEAK 40(17Q25.3) MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4II TCGA-BA-A8YP 
         283          190          451           63          918          142 
TCGA-BB-4223 TCGA-BB-4227 TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6011 
        2878          133          721         1330          290          933 
TCGA-CN-6992 TCGA-CN-A63Y TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-7067 
         394          175          317         1000          985          509 
TCGA-CQ-A4C9 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6481 
         707         1663         1152         1966         1971          311 
TCGA-CR-6484 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5966 
         354           30          997         1472         1955          519 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7248 TCGA-D6-6826 TCGA-D6-A74Q 
        1959         1970         1939         1967          154          338 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7594 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 
         548         1965          368           15           92            6 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H 
          25           55          111          485          360          412 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         360          552          378          112          254          240 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA 
        1726         1559         1954          387          149          135 
TCGA-UF-A719 
        1663 

$`DEL PEAK 40(17Q25.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          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-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1636         1747          644          384          113          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          855          622          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 
         182         1976          314          623          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         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         395          625         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1007         1045          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          683          630 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          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         1110          224          318 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         611          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          348          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
         341          129         1253         1057         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1179         1750         1560         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877         1950         1353         1960         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         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         1952 
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-A45R TCGA-CV-A45Y 
        1959         1981          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          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-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 
        1778         1081          516         1030          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         622          299          369          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         490          658          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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
         206            2            5           37           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-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S 
         122          441          588          440          351          224 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
         910         1120          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-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         567          198          135          157          168         1326 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1319         1252         1278         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                             6                              2 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                          2878                           5480 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                           412                            759 
[1] "6.0 - 2878.0 (412.0)" "2.0 - 5480.0 (759.0)"
[1] "hr=" "1.6"
D69V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 40(17Q25.3) MUTATED         3        8         8        31         3
  DEL PEAK 40(17Q25.3) WILD-TYPE      23       67        66       204         9
                                vv
clus                             STAGE IVC
  DEL PEAK 40(17Q25.3) MUTATED           0
  DEL PEAK 40(17Q25.3) WILD-TYPE         1
D69V3, multiclass
           clus
vv          DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  STAGE I                              3                             23
  STAGE II                             8                             67
  STAGE III                            8                             66
  STAGE IVA                           31                            204
  STAGE IVB                            3                              9
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 40(17Q25.3) MUTATED       6  23   6  20
  DEL PEAK 40(17Q25.3) WILD-TYPE    41 104  88 142
D69V4, multiclass
       clus
vv      DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  T0+T1                            6                             41
  T2                              23                            104
  T3                               6                             88
  T4                              20                            142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 40(17Q25.3) MUTATED    16   8  22   3
  DEL PEAK 40(17Q25.3) WILD-TYPE 154  55 130   5
D69V5, multiclass
    clus
vv   DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  N0                           16                            154
  N1                            8                             55
  N2                           22                            130
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 40(17Q25.3) MUTATED    21   0  13
  DEL PEAK 40(17Q25.3) WILD-TYPE 146   1  45
D69V6, multiclass
    clus
vv   DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  M0                           21                            146
  M1                            0                              1
  MX                           13                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q25.3) MUTATED    15  51
  DEL PEAK 40(17Q25.3) WILD-TYPE 117 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q25.3) MUTATED     15   51
  DEL PEAK 40(17Q25.3) WILD-TYPE  117  305
        clus
vv       DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  FEMALE                           15                            117
  MALE                             51                            305
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17Q25.3) MUTATED                                      64
  DEL PEAK 40(17Q25.3) WILD-TYPE                                   413
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 40(17Q25.3) MUTATED                                                             1
  DEL PEAK 40(17Q25.3) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 40(17Q25.3) MUTATED                                                     1
  DEL PEAK 40(17Q25.3) WILD-TYPE                                                   9
D69V8, multiclass
                                                             clus
vv                                                            DEL PEAK 40(17Q25.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 64
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
                                                             clus
vv                                                            DEL PEAK 40(17Q25.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  413
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      9
[1] 3 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(17Q25.3) MUTATED    14  52
  DEL PEAK 40(17Q25.3) WILD-TYPE  65 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q25.3) MUTATED     14   52
  DEL PEAK 40(17Q25.3) WILD-TYPE   65  357
     clus
vv    DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  NO                            14                             65
  YES                           52                            357
[1] 2 2
[1] FALSE
D69V10, continuous
D69V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(17Q25.3) MUTATED                                  0     1
  DEL PEAK 40(17Q25.3) WILD-TYPE                                2    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17Q25.3) MUTATED                           8    53
  DEL PEAK 40(17Q25.3) WILD-TYPE                        36   362
D69V12, multiclass
                                  clus
vv                                 DEL PEAK 40(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 40(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    36
  WHITE                                                       362
[1] 4 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(17Q25.3) MUTATED     7  54
  DEL PEAK 40(17Q25.3) WILD-TYPE  17 377
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q25.3) MUTATED      7   54
  DEL PEAK 40(17Q25.3) WILD-TYPE   17  377
                        clus
vv                       DEL PEAK 40(17Q25.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK 40(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            377
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 41(18Q21.2) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q21.2) MUTATED   152  63
  DEL PEAK 41(18Q21.2) WILD-TYPE 149  50
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           215                            199 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                            63                             50 
$`DEL PEAK 41(18Q21.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5557 
         102          462          283          415         1288          623 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
        1636          190          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          918          850          216          182 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 
         623          187          278          536         1153          428 
TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
         436          624            5            4          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 
         142         1230         1151          817         1250          625 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
        1330          811         1007         1977         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
        1975          683          630          933          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         432           98          202          224          318          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63U 
         735          432           46          535          225          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 
         348          367          654          317         1253         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
         985         1959         1959         1179         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CG 
         509         1950         1353         1960          893          391 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6488 
         950          358         1971          362          354          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 
         350          479         1956         1191          105          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 
         889           30         1968         1036         1954         1430 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
         181         1077          911         1950         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         1978         2886         2437          519          406 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        2641         1478         1840         1315         1665         1970 
TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1969         3835         1969         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 
        3837         1959         1970         1970         1939         1987 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1952         1095          954          797         1967         1960 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1955         1947         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A6JN TCGA-CV-A6JT 
        1959         1981         1960         1954          906          670 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         110          714          685          237          828          773 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EO 
         701          491          106          128          539          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         424          368          338         1778          516         1030 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 
        1965          575          299          324         1131          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
          15           92           14           13            6           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 
         133          414          403            2            5           37 
TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G 
          55           25          111          485          588          360 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         412          351          360          224          552           14 
TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 
          34           56         1726          578         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         553          357          228          149          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 
         157          168         1663         1319         1252         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JS 
        1894          484          735         1497          413 

$`DEL PEAK 41(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-A4IG TCGA-BA-A4IH TCGA-BA-A6DA 
         725         1747          644          855          622          351 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        1976          314          142         2878          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-8596 
         558          310          423          687          638         1955 
TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 
         799          392          993          642          395         1960 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1268         1988         1045          173         1980         1081 
TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 
        1980          290          628          594          629         1970 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
        1110          611          429          443          391          904 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         645          484          175          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        1207         1660         1422         1393         1399          341 
TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
         129         1000         1750         1309         1274          877 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-5243 
         707         1963          998          785          303         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-6478 TCGA-CR-6481 TCGA-CR-6482 
        1050         1125          514         1969          311          345 
TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
         234         1435         1440         1245         1960         1979 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         972          796          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-7398 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5442 
         156         1472         1955          522         3295         2327 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
        1958          701          215          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-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
        1945         1979         1444         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-A45O TCGA-CV-A45Q 
        1948         1957         1937         1973          851         1945 
TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        5480         1940         1946         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 
        1075         1959          646          606         1950          317 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB 
         321          292           77          154          568          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 
         483          232          389         1081          548          775 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50J 
         622          369          368          340          490          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 
           3          384          407          206           25           44 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
          24           11           49           10           33         1057 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61J TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A 
         122          441          440          378          168          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         111          112          254          240          910         1559 
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 TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-UF-A718 TCGA-UF-A71E TCGA-UF-A7JH 
         387          567          198         1326         1278          665 
TCGA-UF-A7JJ 
         214 

  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                             2                              3 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                          3837                           5480 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           630                            796 
[1] "2.0 - 3837.0 (630.0)" "3.0 - 5480.0 (796.0)"
[1] "hr=" "1.2"
D70V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 41(18Q21.2) MUTATED        16       39        38       130         5
  DEL PEAK 41(18Q21.2) WILD-TYPE      10       36        36       105         7
                                vv
clus                             STAGE IVC
  DEL PEAK 41(18Q21.2) MUTATED           1
  DEL PEAK 41(18Q21.2) WILD-TYPE         0
D70V3, multiclass
           clus
vv          DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  STAGE I                             16                             10
  STAGE II                            39                             36
  STAGE III                           38                             36
  STAGE IVA                          130                            105
  STAGE IVB                            5                              7
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 41(18Q21.2) MUTATED      25 64 50 91
  DEL PEAK 41(18Q21.2) WILD-TYPE    22 63 44 71
D70V4, multiclass
       clus
vv      DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  T0+T1                           25                             22
  T2                              64                             63
  T3                              50                             44
  T4                              91                             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 41(18Q21.2) MUTATED   89 36 87  3
  DEL PEAK 41(18Q21.2) WILD-TYPE 81 27 65  5
D70V5, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  N0                           89                             81
  N1                           36                             27
  N2                           87                             65
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 41(18Q21.2) MUTATED   84  1 30
  DEL PEAK 41(18Q21.2) WILD-TYPE 83  0 28
D70V6, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  M0                           84                             83
  M1                            1                              0
  MX                           30                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED    60 193
  DEL PEAK 41(18Q21.2) WILD-TYPE  72 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED     60  193
  DEL PEAK 41(18Q21.2) WILD-TYPE   72  163
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  FEMALE                           60                             72
  MALE                            193                            163
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                                     249
  DEL PEAK 41(18Q21.2) WILD-TYPE                                   228
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 41(18Q21.2) MUTATED                                                             1
  DEL PEAK 41(18Q21.2) WILD-TYPE                                                           0
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 41(18Q21.2) MUTATED                                                     3
  DEL PEAK 41(18Q21.2) WILD-TYPE                                                   7
D70V8, multiclass
                                                             clus
vv                                                            DEL PEAK 41(18Q21.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                249
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
                                                             clus
vv                                                            DEL PEAK 41(18Q21.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  228
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      7
[1] 3 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(18Q21.2) MUTATED    43 210
  DEL PEAK 41(18Q21.2) WILD-TYPE  36 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED     43  210
  DEL PEAK 41(18Q21.2) WILD-TYPE   36  199
     clus
vv    DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  NO                            43                             36
  YES                          210                            199
[1] 2 2
[1] FALSE
D70V10, continuous
D70V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(18Q21.2) MUTATED                                  2     8
  DEL PEAK 41(18Q21.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q21.2) MUTATED                          32   201
  DEL PEAK 41(18Q21.2) WILD-TYPE                        12   214
D70V12, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  32
  WHITE                                                     201
                                  clus
vv                                 DEL PEAK 41(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    12
  WHITE                                                       214
[1] 4 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(18Q21.2) MUTATED    17 218
  DEL PEAK 41(18Q21.2) WILD-TYPE   7 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED     17  218
  DEL PEAK 41(18Q21.2) WILD-TYPE    7  213
                        clus
vv                       DEL PEAK 41(18Q21.2) MUTATED
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          218
                        clus
vv                       DEL PEAK 41(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            213
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 42(18Q23) MUTATION ANALYSIS
D71V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 42(18Q23) MUTATED   164  67
  DEL PEAK 42(18Q23) WILD-TYPE 137  46
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         231                          183 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                          67                           46 
$`DEL PEAK 42(18Q23) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5152 
         102          462          283          415          248         1288 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         623         1636          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         384          113          895          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7862 
         216          182          623          142          278          536 
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-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
         392          817         1250          625         1330          811 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
        1988         1007         1980         1977         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
        1975          683          630          933          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         432           98          202          224          318          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         735          432           46          535          904          645 
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 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1179         1560         1007          509         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 
        1960          893          391          950          358         1971 
TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         362          354          379          350          479         1956 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 
        1191          105          759          889           30         1968 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
        1036         1954         1430          181         1077          911 
TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
        1472         1950         3295         1438          546         1978 
TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 
        2886         2437          519          406         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 
        1840          215         1315         1665         1970         1969 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        3835         1969         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1959         1970         1970         1939         1945         1987 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1952         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 
        1976         1099         1957         1947         1972         1937 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A461 
        1984         1959         1981         5480         1960         1954 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 
         670          110          714          685          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-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         539          376          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
         338         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         1131          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          552           14           34           56         1726 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
         578         1968          400          553          357          228 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A719 
         149          135          135          157          168         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1319         1252         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          214          413 

$`DEL PEAK 42(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-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DJ 
        1747          236          855          622         1976          314 
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-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-CN-4722 TCGA-CN-4731 TCGA-CN-4733 
         423          687          638          799          993          642 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
         395         1960         1268         1045          173         1081 
TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 
        1980          290          628          594          629         1970 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63V 
        1110          611          429          443          391          484 
TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 
         175          223          298         1466         1207         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 
        1422         1393         1399          341          129         1750 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD 
        1309         1274          877          707         1963          998 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         785          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-CV-5430 TCGA-CV-5431 
         898          930          216          156         1955          522 
TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 
         584         2327         1958          701          641         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-7099 
        1948         1952         1959         1948         1966         1936 
TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1959         1979         1444         1974         1948         1955 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Z 
        1937         1973         1958          851         1945         1940 
TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1946         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6516 
        1959          646          606         1950          321          773 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-DQ-5625 
          77          154          568          483          232         1081 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
         548          775          622          369          368          340 
TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-A76A 
         490          585            3          384          407          206 
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-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
         378          168          392          111          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
         240          910         1559         1120         1954         1917 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         245          218          225          387          567          198 
TCGA-UF-A718 TCGA-UF-A71E TCGA-UF-A7JH 
        1326         1278          665 

  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                           2                            3 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                        5480                         2878 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         645                          785 
[1] "2.0 - 5480.0 (645.0)" "3.0 - 2878.0 (785.0)"
[1] "hr=" "1"  
D71V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 42(18Q23) MUTATED        15       41        42       140         7
  DEL PEAK 42(18Q23) WILD-TYPE      11       34        32        95         5
                              vv
clus                           STAGE IVC
  DEL PEAK 42(18Q23) MUTATED           1
  DEL PEAK 42(18Q23) WILD-TYPE         0
D71V3, multiclass
           clus
vv          DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  STAGE I                           15                           11
  STAGE II                          41                           34
  STAGE III                         42                           32
  STAGE IVA                        140                           95
  STAGE IVB                          7                            5
  STAGE IVC                          1                            0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T0+T1  T2  T3  T4
  DEL PEAK 42(18Q23) MUTATED      23  68  55 102
  DEL PEAK 42(18Q23) WILD-TYPE    24  59  39  60
D71V4, multiclass
       clus
vv      DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  T0+T1                         23                           24
  T2                            68                           59
  T3                            55                           39
  T4                           102                           60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 42(18Q23) MUTATED   95 37 91  5
  DEL PEAK 42(18Q23) WILD-TYPE 75 26 61  3
D71V5, multiclass
    clus
vv   DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  N0                         95                           75
  N1                         37                           26
  N2                         91                           61
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  DEL PEAK 42(18Q23) MUTATED   93  1 33
  DEL PEAK 42(18Q23) WILD-TYPE 74  0 25
D71V6, multiclass
    clus
vv   DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  M0                         93                           74
  M1                          1                            0
  MX                         33                           25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED    67 205
  DEL PEAK 42(18Q23) WILD-TYPE  65 151
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     67  205
  DEL PEAK 42(18Q23) WILD-TYPE   65  151
        clus
vv       DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  FEMALE                         67                           65
  MALE                          205                          151
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(18Q23) MUTATED                                     269
  DEL PEAK 42(18Q23) WILD-TYPE                                   208
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 42(18Q23) MUTATED                                                             1
  DEL PEAK 42(18Q23) WILD-TYPE                                                           0
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 42(18Q23) MUTATED                                                     2
  DEL PEAK 42(18Q23) WILD-TYPE                                                   8
D71V8, multiclass
                                                             clus
vv                                                            DEL PEAK 42(18Q23) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                              269
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                          1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  2
                                                             clus
vv                                                            DEL PEAK 42(18Q23) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                208
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
[1] 3 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(18Q23) MUTATED    46 226
  DEL PEAK 42(18Q23) WILD-TYPE  33 183
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     46  226
  DEL PEAK 42(18Q23) WILD-TYPE   33  183
     clus
vv    DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  NO                          46                           33
  YES                        226                          183
[1] 2 2
[1] FALSE
D71V10, continuous
D71V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(18Q23) MUTATED                                  2     8
  DEL PEAK 42(18Q23) WILD-TYPE                                0     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q23) MUTATED                          33   219
  DEL PEAK 42(18Q23) WILD-TYPE                        11   196
D71V12, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     8
  BLACK OR AFRICAN AMERICAN                                33
  WHITE                                                   219
                                  clus
vv                                 DEL PEAK 42(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     196
[1] 4 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(18Q23) MUTATED    17 235
  DEL PEAK 42(18Q23) WILD-TYPE   7 196
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     17  235
  DEL PEAK 42(18Q23) WILD-TYPE    7  196
                        clus
vv                       DEL PEAK 42(18Q23) MUTATED
  HISPANIC OR LATINO                             17
  NOT HISPANIC OR LATINO                        235
                        clus
vv                       DEL PEAK 42(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          196
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 43(19P13.3) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(19P13.3) MUTATED    93  45
  DEL PEAK 43(19P13.3) WILD-TYPE 208  68
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           138                            276 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            45                             68 
$`DEL PEAK 43(19P13.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-6868 
         102          283          248         1288         1762          190 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DL 
          63          113          236          895          351          623 
TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4725 
         133          428          436         1955            5         1157 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         392          993         1250          395          625         1960 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 
        1268         1045         1980         1977         1980         1975 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
         290          933          629          628          594           45 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A63T 
          98          202          735          432          535          225 
TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-7064 
         367          298         1466         1393         1057         1560 
TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CR-6477 
        1274         1960          707         1963          998          514 
TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
         354         1435         1191         1979          889           30 
TCGA-CR-7377 TCGA-CR-7386 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5432 TCGA-CV-5434 
        1968         1430          156          181         1950         3295 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5979 TCGA-CV-6003 
        1438          546         1978          406         1315         1665 
TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7091 
        1970         1952         1969         1966         1959         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-7245 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7435 
         797         1976         1099         1973         1972         1959 
TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6516 TCGA-D6-6825 
        1981         1954          906          685          773          491 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
         154          128          232          368          389         1778 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 
        1965          575          622          299          324         1131 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A623 TCGA-HD-7753 
          15           92          585           14            6            5 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L 
          25          111         1057          588          360          351 
TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
         552           34          240         1954         1968          400 
TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         357          225          387          198          149          135 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JC TCGA-UF-A7JH 
         135          168         1326         1663          484          665 

$`DEL PEAK 43(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-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
         384          855          622          918          850          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
         182         1976          314          142          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         1230         1151          817          642 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
        1330          811         1988         1007          173         1081 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 
        1966         1966          683          630          629          432 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970         1110          224          318          611          394 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
         429           46          443          391          904          645 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5324 
         526          484          348          175          223         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         654         1660         1422         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         129         1253         1000          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
        1179         1750         1007          509         1309          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1950         1353          893          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         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-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-7367 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1956         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         105          759          972         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         997         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-5436 TCGA-CV-5441 TCGA-CV-5442 
        1472         1955          522          584         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958         2437          519          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 
        1840          215          641         1899         1948         1969 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 
        1959         3835         1948         1957         1969         3837 
TCGA-CV-7099 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1936         1979         1952         1444         1095          954 
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-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1947         1937         1937         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 
        1945         5480         1960         1940         1946         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1977         1970         1075         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         646          714          606         1950          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6827 
         237          828          292          701           77          568 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
         106          539          376          483          435          424 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
         338         1081          516         1030          548          775 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A61S 
         369          368          340          490          658            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-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         403          206            2           25           37           55 
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-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
         485          122          441          412          440          360 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         224          378          168           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         1726         1559 
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 TCGA-QK-A6V9 TCGA-QK-AA3J TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         228          567          157         1319         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1043         1894          735         1497          214          413 

  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                             5                              2 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                          3295                           5480 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                         647.0                          717.5 
[1] "5.0 - 3295.0 (647.0)" "2.0 - 5480.0 (717.5)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 43(19P13.3) MUTATED         6       20        31        85         3
  DEL PEAK 43(19P13.3) WILD-TYPE      20       55        43       150         9
                                vv
clus                             STAGE IVC
  DEL PEAK 43(19P13.3) MUTATED           1
  DEL PEAK 43(19P13.3) WILD-TYPE         0
D72V3, multiclass
           clus
vv          DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  STAGE I                              6                             20
  STAGE II                            20                             55
  STAGE III                           31                             43
  STAGE IVA                           85                            150
  STAGE IVB                            3                              9
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 43(19P13.3) MUTATED      13  40  36  60
  DEL PEAK 43(19P13.3) WILD-TYPE    34  87  58 102
D72V4, multiclass
       clus
vv      DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  T0+T1                           13                             34
  T2                              40                             87
  T3                              36                             58
  T4                              60                            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"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 43(19P13.3) MUTATED    49  28  58   3
  DEL PEAK 43(19P13.3) WILD-TYPE 121  35  94   5
D72V5, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  N0                           49                            121
  N1                           28                             35
  N2                           58                             94
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 43(19P13.3) MUTATED    54   1  19
  DEL PEAK 43(19P13.3) WILD-TYPE 113   0  39
D72V6, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  M0                           54                            113
  M1                            1                              0
  MX                           19                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    40 123
  DEL PEAK 43(19P13.3) WILD-TYPE  92 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     40  123
  DEL PEAK 43(19P13.3) WILD-TYPE   92  233
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  FEMALE                           40                             92
  MALE                            123                            233
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                     162
  DEL PEAK 43(19P13.3) WILD-TYPE                                   315
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 43(19P13.3) MUTATED                                                             0
  DEL PEAK 43(19P13.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 43(19P13.3) MUTATED                                                     1
  DEL PEAK 43(19P13.3) WILD-TYPE                                                   9
D72V8, multiclass
                                                             clus
vv                                                            DEL PEAK 43(19P13.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                162
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
                                                             clus
vv                                                            DEL PEAK 43(19P13.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  315
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      9
[1] 3 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(19P13.3) MUTATED    30 133
  DEL PEAK 43(19P13.3) WILD-TYPE  49 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     30  133
  DEL PEAK 43(19P13.3) WILD-TYPE   49  276
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  NO                            30                             49
  YES                          133                            276
[1] 2 2
[1] FALSE
D72V10, continuous
D72V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(19P13.3) MUTATED                                  1     4
  DEL PEAK 43(19P13.3) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(19P13.3) MUTATED                          16   136
  DEL PEAK 43(19P13.3) WILD-TYPE                        28   279
D72V12, multiclass
                                  clus
vv                                 DEL PEAK 43(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     136
                                  clus
vv                                 DEL PEAK 43(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    28
  WHITE                                                       279
[1] 4 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(19P13.3) MUTATED     9 144
  DEL PEAK 43(19P13.3) WILD-TYPE  15 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED      9  144
  DEL PEAK 43(19P13.3) WILD-TYPE   15  287
                        clus
vv                       DEL PEAK 43(19P13.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          144
                        clus
vv                       DEL PEAK 43(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            287
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 44(19Q13.43) MUTATION ANALYSIS
D73V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(19Q13.43) MUTATED    56  25
  DEL PEAK 44(19Q13.43) WILD-TYPE 245  88
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             81                             333 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             25                              88 
$`DEL PEAK 44(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         1157          142          625 
TCGA-CN-5356 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6989 
        1045          290          629           45         1970          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63U 
         394          735          432          429          391          526 
TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
         367          317         1560         1274         1960          707 
TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7374 
         950         1663          379         1191          889           30 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
         907          156          522         3295         1438          546 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6960 TCGA-CV-7097 TCGA-CV-7180 
        1315         1665         1959         1969         1970         1987 
TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7430 TCGA-CV-A6JN 
        1952          797         1976         1099         1972          906 
TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EO 
         685          292          154          128          232          435 
TCGA-D6-A6EP TCGA-DQ-7588 TCGA-F7-A61W TCGA-HD-7753 TCGA-IQ-A61L TCGA-MT-A51X 
         424         1965           14            5          351           34 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         357          228          387          198          149          135 
TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JC 
        1663         1252          484 

$`DEL PEAK 44(19Q13.43) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         102          462         1983          276          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-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         644           63          236          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         850          351          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         142          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-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
           4          799          721         1230         1151          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         817          993          642         1250          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
        1330          811         1268         1988         1007          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-6013 TCGA-CN-6016 
        1975          683          630          933          628          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         629          432           98          202         1110          224 
TCGA-CN-6988 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         318           46          443          535          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 
         225          484          348          175          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959         1179         1750         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CA 
         509         1309          877         1950         1353         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
         893          998          785          391          303         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-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-6491 TCGA-CR-6492 
         311          345          354          234          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1956         1435         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1979          759          972         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-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-5436 
        1077          911         1472         1955         1950          584 
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-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
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-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 
        3835         1948         1969         1966         1957         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        3837         1959         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 
        1945         1979         1444         1095          954         1967 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1960         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1937         1973         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
         701           77          491          568          106          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         376          483          368          389          338         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 
        1131          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-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
         133          414          403          206            2           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-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-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         360          224          552          378          168           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         392           56          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1726         1559         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG 
        1917         1968          400          553          245          218 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         225          567          135          157          168         1326 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
        1319         1278         1043         1894          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                              5                               2 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                           3295                            5480 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                            522                             775 
[1] "5.0 - 3295.0 (522.0)" "2.0 - 5480.0 (775.0)"
[1] "hr=" "1.5"
D73V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 44(19Q13.43) MUTATED         2       13        21        45
  DEL PEAK 44(19Q13.43) WILD-TYPE      24       62        53       190
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 44(19Q13.43) MUTATED           3         0
  DEL PEAK 44(19Q13.43) WILD-TYPE         9         1
D73V3, multiclass
           clus
vv          DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  STAGE I                               2                              24
  STAGE II                             13                              62
  STAGE III                            21                              53
  STAGE IVA                            45                             190
  STAGE IVB                             3                               9
  STAGE IVC                             0                               1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T0+T1  T2  T3  T4
  DEL PEAK 44(19Q13.43) MUTATED       5  24  27  28
  DEL PEAK 44(19Q13.43) WILD-TYPE    42 103  67 134
D73V4, multiclass
       clus
vv      DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  T0+T1                             5                              42
  T2                               24                             103
  T3                               27                              67
  T4                               28                             134
[1] 4 2
[1] TRUE
[1] "dimension 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(19Q13.43) MUTATED    29  14  33   1
  DEL PEAK 44(19Q13.43) WILD-TYPE 141  49 119   7
D73V5, multiclass
    clus
vv   DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  N0                            29                             141
  N1                            14                              49
  N2                            33                             119
  N3                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 44(19Q13.43) MUTATED    29   0   8
  DEL PEAK 44(19Q13.43) WILD-TYPE 138   1  50
D73V6, multiclass
    clus
vv   DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  M0                            29                             138
  M1                             0                               1
  MX                             8                              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED    24  69
  DEL PEAK 44(19Q13.43) WILD-TYPE 108 287
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     24   69
  DEL PEAK 44(19Q13.43) WILD-TYPE  108  287
        clus
vv       DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  FEMALE                            24                             108
  MALE                              69                             287
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19Q13.43) MUTATED                                      91
  DEL PEAK 44(19Q13.43) WILD-TYPE                                   386
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 44(19Q13.43) MUTATED                                                             0
  DEL PEAK 44(19Q13.43) WILD-TYPE                                                           1
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 44(19Q13.43) MUTATED                                                     2
  DEL PEAK 44(19Q13.43) WILD-TYPE                                                   8
D73V8, multiclass
                                                             clus
vv                                                            DEL PEAK 44(19Q13.43) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  91
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                             0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     2
                                                             clus
vv                                                            DEL PEAK 44(19Q13.43) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                   386
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       8
[1] 3 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(19Q13.43) MUTATED    17  76
  DEL PEAK 44(19Q13.43) WILD-TYPE  62 333
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     17   76
  DEL PEAK 44(19Q13.43) WILD-TYPE   62  333
     clus
vv    DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  NO                             17                              62
  YES                            76                             333
[1] 2 2
[1] FALSE
D73V10, continuous
D73V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(19Q13.43) MUTATED                                  0     2
  DEL PEAK 44(19Q13.43) WILD-TYPE                                2     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19Q13.43) MUTATED                          11    76
  DEL PEAK 44(19Q13.43) WILD-TYPE                        33   339
D73V12, multiclass
                                  clus
vv                                 DEL PEAK 44(19Q13.43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       76
                                  clus
vv                                 DEL PEAK 44(19Q13.43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     33
  WHITE                                                        339
[1] 4 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(19Q13.43) MUTATED     7  81
  DEL PEAK 44(19Q13.43) WILD-TYPE  17 350
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED      7   81
  DEL PEAK 44(19Q13.43) WILD-TYPE   17  350
                        clus
vv                       DEL PEAK 44(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            81
                        clus
vv                       DEL PEAK 44(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                             350
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 45(21Q22.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(21Q22.3) MUTATED   126  47
  DEL PEAK 45(21Q22.3) WILD-TYPE 175  66
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           173                            241 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                            47                             66 
$`DEL PEAK 45(21Q22.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
         102          283         1636         1747          190          451 
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7864 
          63          855          850          351          536          687 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 
         428         1955          624            5         1157          142 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
        1151          392          395          625         1960         1330 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1268         1988         1007         1081         1977         1980 
TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
        1975          290          630          629           45          432 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
        1970          202          318          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W 
         429           46          535          904          225          348 
TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 
        1466         1393          317         1057          985         1179 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1560         1007          509         1274         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1960          707         1963          785          303          950 
TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 
         358          514          354          379          350         1191 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
        1440         1960          105         1979          889           30 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 
        1951          392          181          522          546         1978 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
        2437          519         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6954 
        1315         1665         1970         1948         1959         1957 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7235 
        1959         3837         1959         1939         1987         1952 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
        1095          954          797         1967         1976         1099 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JN 
        1957         1947         1937         1959         1981          906 
TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1959          110          317          237          828          773 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM 
         701          491          154          539          376          232 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7592 
         368          338         1778          516         1965          299 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
         490           15           92          585          384           14 
TCGA-F7-A620 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          13           58          133          403            2            5 
TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
          24           49          111          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A5QA 
         440          351          552           34          240         1726 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IG 
        1954          578         1917         1968          400          218 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K 
         228          387          198          149          157          168 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        1278         1043          484          735          665 

$`DEL PEAK 45(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-A4IH TCGA-BA-A4II 
         384          113          236          895          622          918 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
         216          182         1976          314          623          142 
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         1230          817          993          642 
TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 
        1250          811         1045          173         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        1966          683          933          628          594          629 
TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A498 TCGA-CN-A49A 
          98         1110          224          611          443          391 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         645          526          484          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
         298         1207          654         1660         1422         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 
         341          129         1253         1000         1959         1959 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
        1750         1309          877          893          998          391 
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-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-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 
         584         2886         2327         1958          406          701 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
         641         1899         1969         1952         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1969         1966         1969         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7406 
        1959         1945         1979         1444         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 
        1948         1955         1937         1973         1972         1984 
TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1958          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         670          646          714          606          685         1950 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         321          292           77          568          106          128 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 
         483          435          424          389         1081         1030 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
         548          575          775          622          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A623 
         324          340         1131          658            3            6 
TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         407          414          206           25           37           55 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
          44           25           11           10           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
         485          122          441          360          224          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         168           14          392           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A64Z TCGA-QK-A652 
         254          910         1559         1120          553          357 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A718 
         245          225          567          135          135         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ 
        1663         1319         1252         1894         1497          214 
TCGA-UF-A7JS 
         413 

  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                             2                              3 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                          3837                           5480 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           625                            759 
[1] "2.0 - 3837.0 (625.0)" "3.0 - 5480.0 (759.0)"
[1] "hr=" "1"  
D74V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 45(21Q22.3) MUTATED        10       31        33        99         6
  DEL PEAK 45(21Q22.3) WILD-TYPE      16       44        41       136         6
                                vv
clus                             STAGE IVC
  DEL PEAK 45(21Q22.3) MUTATED           0
  DEL PEAK 45(21Q22.3) WILD-TYPE         1
D74V3, multiclass
           clus
vv          DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  STAGE I                             10                             16
  STAGE II                            31                             44
  STAGE III                           33                             41
  STAGE IVA                           99                            136
  STAGE IVB                            6                              6
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 45(21Q22.3) MUTATED      13 55 46 67
  DEL PEAK 45(21Q22.3) WILD-TYPE    34 72 48 95
D74V4, multiclass
       clus
vv      DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  T0+T1                           13                             34
  T2                              55                             72
  T3                              46                             48
  T4                              67                             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 45(21Q22.3) MUTATED    65  31  67   4
  DEL PEAK 45(21Q22.3) WILD-TYPE 105  32  85   4
D74V5, multiclass
    clus
vv   DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  N0                           65                            105
  N1                           31                             32
  N2                           67                             85
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 45(21Q22.3) MUTATED    63   0  29
  DEL PEAK 45(21Q22.3) WILD-TYPE 104   1  29
D74V6, multiclass
    clus
vv   DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  M0                           63                            104
  M1                            0                              1
  MX                           29                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED    50 148
  DEL PEAK 45(21Q22.3) WILD-TYPE  82 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     50  148
  DEL PEAK 45(21Q22.3) WILD-TYPE   82  208
        clus
vv       DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  FEMALE                           50                             82
  MALE                            148                            208
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(21Q22.3) MUTATED                                     194
  DEL PEAK 45(21Q22.3) WILD-TYPE                                   283
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 45(21Q22.3) MUTATED                                                             0
  DEL PEAK 45(21Q22.3) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 45(21Q22.3) MUTATED                                                     4
  DEL PEAK 45(21Q22.3) WILD-TYPE                                                   6
D74V8, multiclass
                                                             clus
vv                                                            DEL PEAK 45(21Q22.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                194
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            DEL PEAK 45(21Q22.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  283
  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"
D74V9, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED    30 168
  DEL PEAK 45(21Q22.3) WILD-TYPE  49 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     30  168
  DEL PEAK 45(21Q22.3) WILD-TYPE   49  241
     clus
vv    DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  NO                            30                             49
  YES                          168                            241
[1] 2 2
[1] FALSE
D74V10, continuous
D74V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 45(21Q22.3) MUTATED                                  1     7
  DEL PEAK 45(21Q22.3) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(21Q22.3) MUTATED                          25   159
  DEL PEAK 45(21Q22.3) WILD-TYPE                        19   256
D74V12, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     159
                                  clus
vv                                 DEL PEAK 45(21Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    19
  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"
D74V13, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED     9 174
  DEL PEAK 45(21Q22.3) WILD-TYPE  15 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED      9  174
  DEL PEAK 45(21Q22.3) WILD-TYPE   15  257
                        clus
vv                       DEL PEAK 45(21Q22.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          174
                        clus
vv                       DEL PEAK 45(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            257
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 46(XP22.2) MUTATION ANALYSIS
D75V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 46(XP22.2) MUTATED    78  39
  DEL PEAK 46(XP22.2) WILD-TYPE 223  74
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          117                           297 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           39                            74 
$`DEL PEAK 46(XP22.2) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-A4IG 
         415          276          248          190          384          855 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7862 
         622          850          182          623          142          536 
TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 
         428         1955         1157         1151          392         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 
         395          625         1980         1081          290          630 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
         629           45         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A49B TCGA-CQ-5330 
         394          432          429          391          904         1393 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7072 
         317         1253         1000         1959         1179         1950 
TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6477 
        1960          950          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         1952          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-A460 TCGA-CV-A6JN TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 
        1946          906          646          685          317          237 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EM 
         773          154          568          106          376          232 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 
         338         1081          516          548         1965          622 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A620 
         299         1131          658           15           14           13 
TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8635 TCGA-IQ-A61G TCGA-P3-A5QE TCGA-P3-A6T4 
         403           37           25          360         1559         1968 
TCGA-QK-A6IH TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JC 
         228          157         1663         1319         1278          484 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS 
         735          665          413 

$`DEL PEAK 46(XP22.2) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 
         102          462          283         1983          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-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451           63          113          236          895 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
         918          351          216         1976          314          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-7870 TCGA-BB-7872 TCGA-BB-8601 
         423          687          638         1153          436          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
           5            4          799          721          142         1230 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         817          993          642         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 
        1268         1988         1007         1045          173         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6011 
        1980         1966         1966         1975          683          933 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         628          594          629          432           98         1970 
TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C 
         202          735           46          443          535          645 
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-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 
        1422         1399          341          129         1057          985 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1274          877         1353          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 
         998          785          391          303         2562         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
         799         1777         1521         1966         1125         1971 
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-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         350          479         1435         1191         1440         1245 
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-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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 
        1077          911         1472          522         1950          584 
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-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
         701         2641          215         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1899         1948         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        1966         1957         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-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 
        1967         1960         1099         1974         1948         1957 
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-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1981          851         5480         1960         1940         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT 
        1722         1977         1970         1075         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 
         110          714          606         1950          321          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4Z9 
         292          701           77          491          128          539 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
         483          435          424          368          389         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-H7-A76A 
           6          407           58          133          414          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           2            5           25           55           44           24 
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-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-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
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-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX 
         254          240          910         1726         1120         1954 
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-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         218          225          387          567          198          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7J9 
         135          135          168         1326         1252         1043 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ 
        1894         1497          214 

  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           13                             2 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                         3295                          5480 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          646                           721 
[1] "13.0 - 3295.0 (646.0)" "2.0 - 5480.0 (721.0)" 
[1] "hr=" "1.8"
D75V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 46(XP22.2) MUTATED         6       19        21        67         6
  DEL PEAK 46(XP22.2) WILD-TYPE      20       56        53       168         6
                               vv
clus                            STAGE IVC
  DEL PEAK 46(XP22.2) MUTATED           1
  DEL PEAK 46(XP22.2) WILD-TYPE         0
D75V3, multiclass
           clus
vv          DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  STAGE I                             6                            20
  STAGE II                           19                            56
  STAGE III                          21                            53
  STAGE IVA                          67                           168
  STAGE IVB                           6                             6
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 46(XP22.2) MUTATED      11  30  39  44
  DEL PEAK 46(XP22.2) WILD-TYPE    36  97  55 118
D75V4, multiclass
       clus
vv      DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  T0+T1                          11                            36
  T2                             30                            97
  T3                             39                            55
  T4                             44                           118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 46(XP22.2) MUTATED    41  17  52   3
  DEL PEAK 46(XP22.2) WILD-TYPE 129  46 100   5
D75V5, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  N0                          41                           129
  N1                          17                            46
  N2                          52                           100
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 46(XP22.2) MUTATED    43   1  11
  DEL PEAK 46(XP22.2) WILD-TYPE 124   0  47
D75V6, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  M0                          43                           124
  M1                           1                             0
  MX                          11                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    32 109
  DEL PEAK 46(XP22.2) WILD-TYPE 100 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     32  109
  DEL PEAK 46(XP22.2) WILD-TYPE  100  247
        clus
vv       DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  FEMALE                          32                           100
  MALE                           109                           247
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                                     136
  DEL PEAK 46(XP22.2) WILD-TYPE                                   341
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 46(XP22.2) MUTATED                                                             0
  DEL PEAK 46(XP22.2) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 46(XP22.2) MUTATED                                                     5
  DEL PEAK 46(XP22.2) WILD-TYPE                                                   5
D75V8, multiclass
                                                             clus
vv                                                            DEL PEAK 46(XP22.2) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               136
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
                                                             clus
vv                                                            DEL PEAK 46(XP22.2) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 341
  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"
D75V9, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    29 112
  DEL PEAK 46(XP22.2) WILD-TYPE  50 297
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     29  112
  DEL PEAK 46(XP22.2) WILD-TYPE   50  297
     clus
vv    DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  NO                           29                            50
  YES                         112                           297
[1] 2 2
[1] FALSE
D75V10, continuous
D75V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 46(XP22.2) MUTATED                                  1     1
  DEL PEAK 46(XP22.2) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(XP22.2) MUTATED                          13   123
  DEL PEAK 46(XP22.2) WILD-TYPE                        31   292
D75V12, multiclass
                                  clus
vv                                 DEL PEAK 46(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    123
                                  clus
vv                                 DEL PEAK 46(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   31
  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"
D75V13, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED     7 125
  DEL PEAK 46(XP22.2) WILD-TYPE  17 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED      7  125
  DEL PEAK 46(XP22.2) WILD-TYPE   17  306
                        clus
vv                       DEL PEAK 46(XP22.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         125
                        clus
vv                       DEL PEAK 46(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           306
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 47(XP21.3) MUTATION ANALYSIS
D76V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 47(XP21.3) MUTATED    86  39
  DEL PEAK 47(XP21.3) WILD-TYPE 215  74
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          125                           289 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                           39                            74 
$`DEL PEAK 47(XP21.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-A4IH 
         462          415          276          248          384          622 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7862 
         850          182          623          142          133          536 
TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 
         428         1955         1157         1151          392         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 
         395          625         1988         1980         1081          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6024 TCGA-CN-6988 
         630          933          629           45          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A49B 
         611          394          432          429          391          904 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 
        1660         1393         1399          317         1253         1000 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C7 
        1959         1179         1560         1007         1950         1960 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-6493 
         950          358         1663         1050          234         1956 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
          30         1954          907          216          156          181 
TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 
        1955         1438          546         2437          406         1478 
TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6960 TCGA-CV-7095 
        1840         1970         1969         1952         1969         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7254 
        1939         1945         1952          954          797         1976 
TCGA-CV-7418 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A460 
        1955         1972         1937         1945         5480         1946 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 
         646          685          317          237          773          701 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A74Q TCGA-DQ-5625 
         154          106          539          232          338         1081 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 
         516          548         1965          622          299         1131 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-A6C5 TCGA-HD-7917 
         658           15           14           13          403           37 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A51X TCGA-P3-A5QE 
          25           11          360          552           34         1559 
TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B 
        1968          228          135          157         1663         1319 
TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS 
        1278          484          735          665          413 

$`DEL PEAK 47(XP21.3) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         102          283         1983          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-A4IF 
         644          451           63          113          236          895 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ 
         855          918          351          216         1976          314 
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-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 
         423          687          638         1153          436          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
           5            4          799          721          142         1230 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         817          993          642         1960         1330          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5365 
        1268         1007         1045          173         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 
        1966         1966         1975          683          628          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
         629          432           98         1970          202         1110 
TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T 
         735           46          443          535          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         526          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5333 
         298         1466         1207          654         1422          341 
TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7067 
         129         1057          985         1959         1750          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309         1274          877         1353          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
         893          998          785          391          303         2562 
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-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
         354          379          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-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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         898          930         1077          911         1472          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1950         3295          584         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 
        1958          519          701         2641          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 
        1665          641         1899         1948         1959         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-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 
        1959         1970         1936         1959         1987         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 
        1444         1095         1967         1960         1099         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 
        1948         1957         1947         1937         1973         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Y TCGA-CV-A45Z 
        1958         1959         1981          851         1960         1940 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 
        1959          670          110          714          606         1950 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         321          828          292           77          491          568 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         128          376          483          435          424          368 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 
         389         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-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 
         414          206            2            5           25           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          44           24           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H 
        1057          485          122          441          588          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
         440          351          360          224          378          168 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          14          392           56          111          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         240          910         1726         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-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         225          387          567          198          149          135 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
         168         1326         1252         1043         1894         1497 
TCGA-UF-A7JJ 
         214 

  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                           11                             2 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                         5480                          3837 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          658                           721 
[1] "11.0 - 5480.0 (658.0)" "2.0 - 3837.0 (721.0)" 
[1] "hr=" "1.4"
D76V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 47(XP21.3) MUTATED         5       22        21        72         6
  DEL PEAK 47(XP21.3) WILD-TYPE      21       53        53       163         6
                               vv
clus                            STAGE IVC
  DEL PEAK 47(XP21.3) MUTATED           1
  DEL PEAK 47(XP21.3) WILD-TYPE         0
D76V3, multiclass
           clus
vv          DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  STAGE I                             5                            21
  STAGE II                           22                            53
  STAGE III                          21                            53
  STAGE IVA                          72                           163
  STAGE IVB                           6                             6
  STAGE IVC                           1                             0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  DEL PEAK 47(XP21.3) MUTATED      10  37  38  46
  DEL PEAK 47(XP21.3) WILD-TYPE    37  90  56 116
D76V4, multiclass
       clus
vv      DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  T0+T1                          10                            37
  T2                             37                            90
  T3                             38                            56
  T4                             46                           116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 47(XP21.3) MUTATED    43  19  54   3
  DEL PEAK 47(XP21.3) WILD-TYPE 127  44  98   5
D76V5, multiclass
    clus
vv   DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  N0                          43                           127
  N1                          19                            44
  N2                          54                            98
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 47(XP21.3) MUTATED    48   1  11
  DEL PEAK 47(XP21.3) WILD-TYPE 119   0  47
D76V6, multiclass
    clus
vv   DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  M0                          48                           119
  M1                           1                             0
  MX                          11                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED    35 110
  DEL PEAK 47(XP21.3) WILD-TYPE  97 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     35  110
  DEL PEAK 47(XP21.3) WILD-TYPE   97  246
        clus
vv       DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  FEMALE                          35                            97
  MALE                           110                           246
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(XP21.3) MUTATED                                     140
  DEL PEAK 47(XP21.3) WILD-TYPE                                   337
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 47(XP21.3) MUTATED                                                             0
  DEL PEAK 47(XP21.3) WILD-TYPE                                                           1
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 47(XP21.3) MUTATED                                                     5
  DEL PEAK 47(XP21.3) WILD-TYPE                                                   5
D76V8, multiclass
                                                             clus
vv                                                            DEL PEAK 47(XP21.3) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                               140
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                           0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
                                                             clus
vv                                                            DEL PEAK 47(XP21.3) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 337
  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"
D76V9, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED    30 115
  DEL PEAK 47(XP21.3) WILD-TYPE  49 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     30  115
  DEL PEAK 47(XP21.3) WILD-TYPE   49  294
     clus
vv    DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  NO                           30                            49
  YES                         115                           294
[1] 2 2
[1] FALSE
D76V10, continuous
D76V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 47(XP21.3) MUTATED                                  1     3
  DEL PEAK 47(XP21.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(XP21.3) MUTATED                          14   123
  DEL PEAK 47(XP21.3) WILD-TYPE                        30   292
D76V12, multiclass
                                  clus
vv                                 DEL PEAK 47(XP21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    123
                                  clus
vv                                 DEL PEAK 47(XP21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   30
  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"
D76V13, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED     8 127
  DEL PEAK 47(XP21.3) WILD-TYPE  16 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED      8  127
  DEL PEAK 47(XP21.3) WILD-TYPE   16  304
                        clus
vv                       DEL PEAK 47(XP21.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         127
                        clus
vv                       DEL PEAK 47(XP21.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           304
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 48(XQ21.33) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(XQ21.33) MUTATED    48  19
  DEL PEAK 48(XQ21.33) WILD-TYPE 253  94
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            67                            347 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            19                             94 
$`DEL PEAK 48(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-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-4225 TCGA-BB-4227 
         622          850          182          623          140          133 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5360 
         536          687          428          392         1250         1081 
TCGA-CN-6011 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-6221 
         933          394          735          429          298         1000 
TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4CI TCGA-CR-5247 
        1959         1560         1007          509          950          358 
TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 
        1663         1050          234          105         1979           30 
TCGA-CR-7388 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6954 TCGA-CV-6960 
        1951         2641         1970         1969         1957         1969 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7418 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A460 
        3837         1970         1955         1972         1959         1946 
TCGA-CV-A6JU TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6827 TCGA-F7-7848 
         110          685          317          828          568         1131 
TCGA-F7-A50G TCGA-F7-A61W TCGA-IQ-A61G TCGA-IQ-A61J TCGA-P3-A5QA TCGA-P3-A5QE 
          15           14          360          440         1726         1559 
TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A7JA 
        1968          228          135          135          157         1894 
TCGA-UF-A7JC 
         484 

$`DEL PEAK 48(XQ21.33) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         102          283          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-A4IF TCGA-BA-A4IG 
         644          451           63          113          895          855 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP 
         918          351          216         1976          314          142 
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         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
        1151          817          993          642          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1045          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          683          290          630          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          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         1110          224          318          611 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         432           46          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         645          225          526          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1253         1057          985         1959         1179         1750 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         707         1963          893          998          785          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         303         2562         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-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          345          354          379          350          479 
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-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         759          889          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
        1954          997         1430          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-5430 TCGA-CV-5431 
         181         1077          911         1472         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-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-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
         641         1899         1948         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 
        1948         1969         1966         1959         1959         1970 
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-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 
        1960         1976         1099         1974         1948         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1947         1937         1973         1937         1984         1958 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 
        1959          670          646          714          606         1950 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         321          237          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          154          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         338         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-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
         368          324          340          490          658           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
         585            3          384           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            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-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H 
        1057          485          122          441          588          412 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
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-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         254          240          910         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-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3K 
         225          387          567          198          149          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1326         1663         1319         1252         1278         1043 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            14                              2 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                          3837                           5480 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                           685                            707 
[1] "14.0 - 3837.0 (685.0)" "2.0 - 5480.0 (707.0)" 
[1] "hr=" "1.1"
D77V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 48(XQ21.33) MUTATED         5        6        11        37         3
  DEL PEAK 48(XQ21.33) WILD-TYPE      21       69        63       198         9
                                vv
clus                             STAGE IVC
  DEL PEAK 48(XQ21.33) MUTATED           1
  DEL PEAK 48(XQ21.33) WILD-TYPE         0
D77V3, multiclass
           clus
vv          DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  STAGE I                              5                             21
  STAGE II                             6                             69
  STAGE III                           11                             63
  STAGE IVA                           37                            198
  STAGE IVB                            3                              9
  STAGE IVC                            1                              0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1  T2  T3  T4
  DEL PEAK 48(XQ21.33) MUTATED       7  17  18  23
  DEL PEAK 48(XQ21.33) WILD-TYPE    40 110  76 139
D77V4, multiclass
       clus
vv      DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  T0+T1                            7                             40
  T2                              17                            110
  T3                              18                             76
  T4                              23                            139
[1] 4 2
[1] TRUE
[1] "dimension 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 48(XQ21.33) MUTATED    18  14  25   1
  DEL PEAK 48(XQ21.33) WILD-TYPE 152  49 127   7
D77V5, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  N0                           18                            152
  N1                           14                             49
  N2                           25                            127
  N3                            1                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 48(XQ21.33) MUTATED    24   1   6
  DEL PEAK 48(XQ21.33) WILD-TYPE 143   0  52
D77V6, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  M0                           24                            143
  M1                            1                              0
  MX                            6                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    20  55
  DEL PEAK 48(XQ21.33) WILD-TYPE 112 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     20   55
  DEL PEAK 48(XQ21.33) WILD-TYPE  112  301
        clus
vv       DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  FEMALE                           20                            112
  MALE                             55                            301
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(XQ21.33) MUTATED                                      71
  DEL PEAK 48(XQ21.33) WILD-TYPE                                   406
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  DEL PEAK 48(XQ21.33) MUTATED                                                             0
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                           1
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                                     4
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                   6
D77V8, multiclass
                                                             clus
vv                                                            DEL PEAK 48(XQ21.33) MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                 71
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                            0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
                                                             clus
vv                                                            DEL PEAK 48(XQ21.33) WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                                  406
  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"
D77V9, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    10  65
  DEL PEAK 48(XQ21.33) WILD-TYPE  69 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     10   65
  DEL PEAK 48(XQ21.33) WILD-TYPE   69  344
     clus
vv    DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  NO                            10                             69
  YES                           65                            344
[1] 2 2
[1] FALSE
D77V10, continuous
D77V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 48(XQ21.33) MUTATED                                  0     2
  DEL PEAK 48(XQ21.33) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(XQ21.33) MUTATED                          10    60
  DEL PEAK 48(XQ21.33) WILD-TYPE                        34   355
D77V12, multiclass
                                  clus
vv                                 DEL PEAK 48(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      60
                                  clus
vv                                 DEL PEAK 48(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED     4  65
  DEL PEAK 48(XQ21.33) WILD-TYPE  20 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED      4   65
  DEL PEAK 48(XQ21.33) WILD-TYPE   20  366
                        clus
vv                       DEL PEAK 48(XQ21.33) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       DEL PEAK 48(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            366
[1] 2 2
[1] FALSE
