[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/15078978/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/15085744/transformed.cor.cli.txt"

nPatients in clinical file=522, in cluster file=522, common to both=516
[1]  77 516
[1] "AMP PEAK  1(2Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          106                           410 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          106                           410 
[1] "AMP PEAK  2(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          109                           407 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          109                           407 
[1] "AMP PEAK  3(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           375                            141 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           375                            141 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           237                            279 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           237                            279 
[1] "AMP PEAK  5(6P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                          109                           407 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                          109                           407 
[1] "AMP PEAK  6(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         94                         422 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         94                         422 
[1] "AMP PEAK  7(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                          218                           298 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                          218                           298 
[1] "AMP PEAK  8(7Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                          166                           350 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                          166                           350 
[1] "AMP PEAK  9(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                           159                            357 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                           159                            357 
[1] "AMP PEAK 10(8Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                           307                            209 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                           307                            209 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           380                            136 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           380                            136 
[1] "AMP PEAK 12(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                          124                           392 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                          124                           392 
[1] "AMP PEAK 13(9P23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                        122                         394 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                        122                         394 
[1] "AMP PEAK 14(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          138                           378 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          138                           378 
[1] "AMP PEAK 15(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                          174                           342 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                          174                           342 
[1] "AMP PEAK 16(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          99                          417 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          99                          417 
[1] "AMP PEAK 17(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                           225                            291 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                           225                            291 
[1] "AMP PEAK 18(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                            164                             352 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                            164                             352 
[1] "AMP PEAK 19(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         101                          415 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         101                          415 
[1] "AMP PEAK 20(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                           105                            411 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                           105                            411 
[1] "AMP PEAK 21(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                         106                          410 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                         106                          410 
[1] "AMP PEAK 22(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           103                            413 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           103                            413 
[1] "AMP PEAK 23(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          89                          427 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          89                          427 
[1] "AMP PEAK 24(18P11.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                            154                             362 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                            154                             362 
[1] "AMP PEAK 25(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                           104                            412 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                           104                            412 
[1] "AMP PEAK 26(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            58                            458 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            58                            458 
[1] "AMP PEAK 27(20P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           190                            326 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           190                            326 
[1] "AMP PEAK 28(20Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            225                             291 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            225                             291 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        146                         370 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        146                         370 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            93                            423 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            93                            423 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          130                           386 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          130                           386 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         47                         469 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         47                         469 
[1] "DEL PEAK  4(2Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           76                           440 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           76                           440 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          118                           398 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          118                           398 
[1] "DEL PEAK  6(2Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          154                           362 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          154                           362 
[1] "DEL PEAK  7(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          343                           173 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          343                           173 
[1] "DEL PEAK  8(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          363                           153 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          363                           153 
[1] "DEL PEAK  9(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          367                           149 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          367                           149 
[1] "DEL PEAK 10(3P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          338                           178 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          338                           178 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          207                           309 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          207                           309 
[1] "DEL PEAK 12(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                          153                           363 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                          153                           363 
[1] "DEL PEAK 13(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                          165                           351 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                          165                           351 
[1] "DEL PEAK 14(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          211                           305 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          211                           305 
[1] "DEL PEAK 15(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          212                           304 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          212                           304 
[1] "DEL PEAK 16(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                        223                         293 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                        223                         293 
[1] "DEL PEAK 17(5Q35.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                          197                           319 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                          197                           319 
[1] "DEL PEAK 18(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           95                           421 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           95                           421 
[1] "DEL PEAK 19(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           75                           441 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           75                           441 
[1] "DEL PEAK 20(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                          130                           386 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                          130                           386 
[1] "DEL PEAK 21(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          299                           217 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          299                           217 
[1] "DEL PEAK 22(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        235                         281 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        235                         281 
[1] "DEL PEAK 23(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          297                           219 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          297                           219 
[1] "DEL PEAK 24(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                           106                            410 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                           106                            410 
[1] "DEL PEAK 25(9Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           78                           438 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           78                           438 
[1] "DEL PEAK 26(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           167                            349 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           167                            349 
[1] "DEL PEAK 27(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                            160                             356 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                            160                             356 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            137                             379 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            137                             379 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           162                            354 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           162                            354 
[1] "DEL PEAK 30(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                           243                            273 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                           243                            273 
[1] "DEL PEAK 31(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             60                             456 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             60                             456 
[1] "DEL PEAK 32(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            229                             287 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            229                             287 
[1] "DEL PEAK 33(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                           213                            303 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                           213                            303 
[1] "DEL PEAK 34(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            73                            443 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            73                            443 
[1] "DEL PEAK 35(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             74                             442 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             74                             442 
[1] "DEL PEAK 36(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                           121                            395 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                           121                            395 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            95                            421 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            95                            421 
[1] "DEL PEAK 38(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                           102                            414 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                           102                            414 
[1] "DEL PEAK 39(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            97                            419 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            97                            419 
[1] "DEL PEAK 40(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            71                            445 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            71                            445 
[1] "DEL PEAK 41(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           264                            252 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           264                            252 
[1] "DEL PEAK 42(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         284                          232 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         284                          232 
[1] "DEL PEAK 43(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           172                            344 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           172                            344 
[1] "DEL PEAK 44(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             95                             421 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             95                             421 
[1] "DEL PEAK 45(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           205                            311 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           205                            311 
[1] "DEL PEAK 46(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          153                           363 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          153                           363 
[1] "DEL PEAK 47(XP21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          156                           360 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          156                           360 
[1] "DEL PEAK 48(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            80                            436 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            80                            436 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_PACK_YEARS_SMOKED"              
[18] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 516 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=185,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=330,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=23,	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=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 516 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [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] "NUMBER_PACK_YEARS_SMOKED"              
[10] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[11] "NUMBER_OF_LYMPH_NODES"                 
[12] "RACE"                                  
[13] "ETHNICITY"                             
YEARS_TO_BIRTH, 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  49 133  99 172 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   50   133    99   172 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  49 133  99 172 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   50   133    99   172 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
178  66 165   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
178  66 165   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
178  66 165   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
178  66 165   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=86, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=23, 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    56  50
  AMP PEAK  1(2Q11.2) WILD-TYPE 257 150
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          106                           407 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           50                           150 
$`AMP PEAK  1(2Q11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5555 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6DL 
        9.30        13.64        17.10        12.62        29.42        20.48 
TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4728 
       16.41        50.20        66.28        71.05        40.44        37.84 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 
       20.55        27.58        13.05        34.36        12.39        20.71 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 
       20.68        19.07        36.49        11.08        10.45        24.16 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7072 TCGA-CR-5247 
        7.40        11.44        10.42        13.25        64.11        11.77 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
       16.90         6.02        11.64        39.16        47.34         3.45 
TCGA-CR-7372 TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       24.95        17.13        29.82       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5973 TCGA-CV-6933 TCGA-CV-6936 
      108.95        19.20       107.51        86.83        90.12         5.46 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6960 
       20.52        26.43        11.24        15.09        30.08        28.34 
TCGA-CV-6962 TCGA-CV-7103 TCGA-CV-7178 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 
        4.14        52.31        71.21        36.00        26.20        18.97 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       95.34        47.97        36.13        18.41        35.54        17.85 
TCGA-CV-7414 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45U 
        0.46        34.09        14.89       153.86        16.64        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A465 TCGA-CV-A6JE TCGA-CX-7086 
       45.96         6.51        48.20         7.07        35.34        18.84 
TCGA-CX-7219 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7588 
       34.36        25.32        12.36        13.94        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-7229 TCGA-HD-A6HZ TCGA-HD-A6I0 
       18.90         9.83        20.25         0.07         3.65         6.90 
TCGA-IQ-A61K TCGA-KU-A66T TCGA-P3-A5Q6 TCGA-P3-A6T5 TCGA-QK-A6IJ TCGA-QK-A6VB 
        5.29        18.15        15.78        29.00        12.72        14.79 
TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-UF-A719 
        6.51        12.10        12.72        15.91        13.55        54.67 
TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JJ 
        2.83        44.65        49.22        16.11 

$`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 
        3.35        15.19        37.28         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        57.93        23.84        20.48        53.79        57.44 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83         3.55         4.01         7.76 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       28.11        20.45        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15        94.62         9.14         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
       22.42        36.72        33.70        44.98        24.66        38.40 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        26.27        23.70        38.04         4.67 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.65        21.11        41.10        12.99 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       14.33        43.73        41.69        33.11         8.58        35.54 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        8.52        22.45        56.94        30.67        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6989 
       20.68        14.20         6.74         9.07         9.24        20.09 
TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       12.95         3.68        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
       14.56        17.59        12.85        29.72        21.21        17.29 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       15.91         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        7.33         9.80         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       11.21         4.24        41.19        32.38        32.88        34.75 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       56.58         4.24        14.99        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       33.11        16.73        43.04        41.88        28.83        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        32.81        25.81        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        31.23        84.23        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.34         7.69        12.46        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       15.75         9.27        47.18        40.93        35.84         3.09 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       26.17        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5439 
        5.95        35.41        29.95        48.39        76.24        17.95 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       23.05        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 
       21.07        62.43         9.60         2.14         9.70         4.73 
TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 
       21.90       126.08        19.79        12.03        42.38         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 
       53.95        65.82        10.98         7.13         8.42         2.50 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       126.15       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 
        9.01         5.26         1.84        12.92        21.80        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 
      130.88        77.16         4.73        47.47        31.36        17.13 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
        4.96        11.87         2.10        57.47       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 
        9.67        22.85        25.08        25.94         0.07       100.57 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17         6.38        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A460 
      169.38       180.16       159.65         1.05        88.87        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
       67.86         0.76        56.61        15.25         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        22.03         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 
       19.92        22.52        10.42        10.42        10.55        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       18.67        24.95        17.72        15.88         7.63        14.30 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        11.11        58.45        35.54        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        25.48        20.45        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       11.18        37.18        16.11        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       19.23        18.94        12.62         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        6.77         0.16        25.74         1.22        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HL-7533 
       12.66        22.85         0.36        13.84         4.27        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
        0.07        14.47        11.54        11.84        13.35        12.43 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        3.68        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       56.75        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97         2.04        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       18.64        12.43         5.62        11.57         9.73         9.76 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ 
        8.32        16.96         6.87         7.10        32.45        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA 
       13.68        43.59        43.36        41.16        42.02        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       17.95        24.16        21.86        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                       153.86                        210.97 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                        19.02                         17.85 
[1] "0.1 - 153.9 (19.0)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.2"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  1(2Q11.2) MUTATED         2       11        17        60         2
  AMP PEAK  1(2Q11.2) WILD-TYPE      25       66        60       192        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                            25
  STAGE II                           11                            66
  STAGE III                          17                            60
  STAGE IVA                          60                           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  1(2Q11.2) MUTATED       5  19  26  44
  AMP PEAK  1(2Q11.2) WILD-TYPE    45 114  73 128
D1V4, multiclass
       clus
vv      AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  T0+T1                           5                            45
  T2                             19                           114
  T3                             26                            73
  T4                             44                           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  1(2Q11.2) MUTATED    36   9  41   2
  AMP PEAK  1(2Q11.2) WILD-TYPE 142  57 124   6
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  N0                          36                           142
  N1                           9                            57
  N2                          41                           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"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED    35   0
  AMP PEAK  1(2Q11.2) WILD-TYPE 148   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     35    0
  AMP PEAK  1(2Q11.2) WILD-TYPE  148    1
   clus
vv  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  0                          35                           148
  1                           0                             1
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED    22  84
  AMP PEAK  1(2Q11.2) WILD-TYPE 117 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     22   84
  AMP PEAK  1(2Q11.2) WILD-TYPE  117  293
        clus
vv       AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  FEMALE                          22                           117
  MALE                            84                           293
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(2Q11.2) MUTATED                                     105
  AMP PEAK  1(2Q11.2) WILD-TYPE                                   400
                               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                                               105
  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                                                 400
  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  88
  AMP PEAK  1(2Q11.2) WILD-TYPE  63 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     18   88
  AMP PEAK  1(2Q11.2) WILD-TYPE   63  347
     clus
vv    AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  NO                           18                            63
  YES                          88                           347
[1] 2 2
[1] FALSE
D1V10, continuous
D1V11, continuous
D1V12, 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    87
  AMP PEAK  1(2Q11.2) WILD-TYPE                        33   354
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     87
                                  clus
vv                                 AMP PEAK  1(2Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED     6  91
  AMP PEAK  1(2Q11.2) WILD-TYPE  19 363
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED      6   91
  AMP PEAK  1(2Q11.2) WILD-TYPE   19  363
                        clus
vv                       AMP PEAK  1(2Q11.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          91
                        clus
vv                       AMP PEAK  1(2Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           363
[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  53
  AMP PEAK  2(2Q31.2) WILD-TYPE 257 147
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          109                           404 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           53                           147 
$`AMP PEAK  2(2Q31.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4IG 
        9.30        13.64        37.28        12.62        29.42        28.11 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-8596 
       30.18        27.95        20.48        16.41        50.20        71.05 
TCGA-BB-A5HY TCGA-CN-4728 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-6012 TCGA-CN-6021 
       10.55        37.84        13.05        12.39        20.68         9.07 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5331 
       11.08        20.09        24.16         7.40        11.44        45.99 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 
       10.42        56.58        13.25        14.99        64.11        23.24 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 
       31.23        11.77        16.90        39.16         3.45         0.99 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       19.92        17.13        29.82       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6935 
      108.95        19.20       107.51         7.07        90.12         9.70 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 
       26.43        11.24        12.03        15.09        30.08         4.14 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7103 TCGA-CV-7178 TCGA-CV-7235 
      111.16        18.81        12.66        52.31        71.21        77.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
       36.00        26.20        18.97        95.34        47.97        36.13 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       18.41        35.54        25.94        34.09       100.57        14.89 
TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A6JM 
        3.52       153.86        16.64         6.51        48.20         6.38 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5629 
       18.84        34.36        23.05        25.32        12.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       14.04         9.83        20.25         4.27         3.65         6.90 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       11.84        13.55        18.15         1.84        17.98        15.78 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       29.00        12.99        13.15        14.79        11.57        12.10 
TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JF 
       15.91        54.67         2.83        43.36        44.65        49.22 
TCGA-UF-A7JJ 
       16.11 

$`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 
        3.35        15.19         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        53.79        57.44 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83         3.55         4.01         7.76 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        13.38         6.15        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        22.42        36.72        33.70 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU 
       44.98        66.28        24.66        38.40        20.52        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       27.19        12.92         8.81         6.28        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
       23.70        38.04         4.67        40.44        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       43.73        27.58        41.69        33.11        34.36         8.58 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       35.54         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        22.45        56.94        20.71        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       20.65        19.53        20.68        19.07        14.20         6.74 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 
        9.24        36.49        10.45        12.95         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21        17.29        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       46.75        45.80        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       32.88        34.75         4.24        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       33.11        16.73        43.04        41.88        28.83        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       11.61        29.36        32.81        25.81        14.14        12.46 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 
       39.52        34.52        36.99        18.54         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       10.22        11.34        11.64         7.69        12.46        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75         9.27        47.18        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        24.95        29.23        31.96         9.17        34.06 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       26.17        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5439 
        5.95        35.41        29.95        48.39        76.24        17.95 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
       23.05        86.83        48.59        60.49        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 
       21.07        62.43         9.60         2.14         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 
        4.73        21.90       126.08        19.79        42.38         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        2.50        64.83       126.15         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 
        1.84        12.92        21.80        10.75       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       47.47        31.36        17.13         4.96        11.87         2.10 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        17.85       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       22.85        25.08         0.07        56.48       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 
       16.27        84.49        19.76         7.17         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        24.99       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        1.05        45.96        88.87        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
       56.61         7.07        15.25         5.98        35.34        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.42        10.42        10.55        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       17.72        15.88         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        11.11        58.45        35.54        33.86        18.02 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       18.90        25.48        20.45        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       11.18        37.18        16.11        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       19.23        18.94        12.62         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HL-7533 
       22.03        12.66        22.85         0.36        13.84        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        12.76        14.50        19.33         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
        5.29        11.54        11.84        13.35        12.43        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       14.37         7.96        30.05        12.62         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        29.92        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        21.07        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        18.64        12.43         6.51         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        9.73         9.76         8.32        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       41.16        42.02        62.27        17.95        24.16        21.86 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                         0.99                          0.07 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                       153.86                        210.97 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                       18.840                        17.885 
[1] "1.0 - 153.9 (18.8)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  2(2Q31.2) MUTATED         2       17        13        58         3
  AMP PEAK  2(2Q31.2) WILD-TYPE      25       60        64       194         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                            25
  STAGE II                           17                            60
  STAGE III                          13                            64
  STAGE IVA                          58                           194
  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  23  41
  AMP PEAK  2(2Q31.2) WILD-TYPE    43 107  76 131
D2V4, multiclass
       clus
vv      AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  T0+T1                           7                            43
  T2                             26                           107
  T3                             23                            76
  T4                             41                           131
[1] 4 2
[1] TRUE
[1] "dimension of 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    34   8  41   2
  AMP PEAK  2(2Q31.2) WILD-TYPE 144  58 124   6
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  N0                          34                           144
  N1                           8                            58
  N2                          41                           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"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED    30   0
  AMP PEAK  2(2Q31.2) WILD-TYPE 153   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     30    0
  AMP PEAK  2(2Q31.2) WILD-TYPE  153    1
   clus
vv  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  0                          30                           153
  1                           0                             1
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED    22  87
  AMP PEAK  2(2Q31.2) WILD-TYPE 117 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     22   87
  AMP PEAK  2(2Q31.2) WILD-TYPE  117  290
        clus
vv       AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  FEMALE                          22                           117
  MALE                            87                           290
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2Q31.2) MUTATED                                     108
  AMP PEAK  2(2Q31.2) WILD-TYPE                                   397
                               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                                               108
  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                                                 397
  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  92
  AMP PEAK  2(2Q31.2) WILD-TYPE  64 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     17   92
  AMP PEAK  2(2Q31.2) WILD-TYPE   64  343
     clus
vv    AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  NO                           17                            64
  YES                          92                           343
[1] 2 2
[1] FALSE
D2V10, continuous
D2V11, continuous
D2V12, 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    89
  AMP PEAK  2(2Q31.2) WILD-TYPE                        33   352
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     89
                                  clus
vv                                 AMP PEAK  2(2Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED     8  91
  AMP PEAK  2(2Q31.2) WILD-TYPE  17 363
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED      8   91
  AMP PEAK  2(2Q31.2) WILD-TYPE   17  363
                        clus
vv                       AMP PEAK  2(2Q31.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                          91
                        clus
vv                       AMP PEAK  2(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           363
[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   224 148
  AMP PEAK  3(3Q26.33) WILD-TYPE  89  52
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           372                            141 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           148                             52 
$`AMP PEAK  3(3Q26.33) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        9.30        13.64        37.28         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       57.93        17.10        20.48        53.79        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01         7.76 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       29.42        28.11        20.45        30.18        27.95        11.54 
TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 
        5.69         2.27        11.05        20.48        16.41        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
        9.14         4.60         4.41        22.42        33.70        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
TCGA-BB-A5HY TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       10.55        12.92         6.28        12.69        23.70        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        40.44        37.84        12.89        26.86        32.65 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       35.54         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       22.45        56.94        20.71        20.68        20.65        19.53 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       11.08        10.45        20.09        12.95        24.16         3.68 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
       29.72        21.21         7.40        17.29        11.44        12.07 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5329 
        7.33         9.80         7.69         6.18        48.20        46.75 
TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       10.42        32.38        32.88        34.75        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        51.29        33.11        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        64.11        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       25.81        14.14        31.23        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       37.87        58.42        50.01        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 
       16.90         6.02        11.90        10.22        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
       12.46        11.51        15.75        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7377 
       35.84         3.45         3.09        24.95         0.99         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        19.92        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       12.89        29.82         7.10         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
       19.20        17.95       107.51        76.50        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
       13.35        86.83        60.49         7.07        54.74        21.07 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 
       90.12         2.14         9.70         5.46        20.52        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       26.43        11.24        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 
        6.08        65.82         7.13         8.42         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 
       64.83       126.15       111.16        12.66         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        47.47        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       36.13        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
        9.67         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
       34.09       100.57        14.89        16.27        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X 
      153.86        16.64       180.16        35.47        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JE 
       88.87        48.20        60.43        67.86         7.07        35.34 
TCGA-CV-A6JM TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        6.38         3.62        23.47        10.42        18.84        34.36 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        9.60        23.05        16.14        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       12.36         7.63        14.30        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
       11.11        58.45        30.94        33.86        18.02        18.90 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
       20.45         9.83        12.10        10.65        11.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7229 
        0.46        17.85        11.80        20.25        15.06         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        0.16        25.74         1.22        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61E 
       22.85        13.84         4.27         3.65        34.75        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67G TCGA-MT-A7BN 
       18.15        12.43        14.37         7.96         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        56.75 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       10.85        36.82        47.01        18.97         2.04        29.00 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ 
       16.01        13.15        21.07        11.74        16.70        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       18.64        14.79        12.43         6.51         5.62        11.57 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.10         9.76        12.72        16.96        15.91         7.10 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        13.68        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
       43.36        41.16        42.02        44.65        62.27        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ 
       49.22        21.86        13.94        20.75        32.65        20.55 

$`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 
        3.35        15.19        42.35        23.84         7.10        14.47 
TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7866 
        7.82        13.38         6.15        18.35        36.72        44.98 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-5369 TCGA-CN-5370 
       27.19         8.81        26.27        21.11        12.49         8.52 
TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       30.67        20.68        17.42        15.91         5.75         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        2.70        10.09        39.68        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-7063 
       45.80        45.99        11.21         4.24        41.19        70.13 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5250 TCGA-CR-6471 
       43.04        28.83        32.81        12.46        26.27        39.52 
TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7382 
       11.34         9.27        47.34        29.23        31.96        26.17 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 
       30.02        31.10        29.85        29.52        30.58         5.13 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 
       94.88        91.53        23.05        48.59        43.23        62.43 
TCGA-CV-6441 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 
        9.60         4.73       126.08        19.79        53.95        10.98 
TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7411 
       28.34        18.81         7.99       130.88        77.16        89.33 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7438 
       56.48       156.49        54.94         3.52        84.49         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
       22.19        27.98        24.99       169.38       159.65         1.05 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO 
        0.76        56.61        15.25         5.98        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       22.03        21.24        19.92        22.52        10.42        10.55 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK 
       13.25        25.41         2.53        11.44        18.67        15.88 
TCGA-DQ-5625 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-F7-7848 TCGA-F7-A624 
       35.54        14.04        25.48        12.13        37.18        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-A4C1 
       13.38        15.16        13.61        21.11         6.77         0.36 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S 
        6.90        15.95        12.76        14.50        11.84        13.35 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5QE TCGA-P3-A6T0 
       10.75        30.05         1.84        12.62        51.25        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A8ZB 
       75.55        12.99        17.65         7.30         9.34         9.73 
TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JS 
        8.32         6.87        32.45        17.95        16.11        22.36 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                          0.07                           0.36 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                        210.97                         169.38 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                        17.965                         18.670 
[1] "0.1 - 211.0 (18.0)" "0.4 - 169.4 (18.7)"
[1] "hr=" "1.1"
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  3(3Q26.33) MUTATED        16       49        59       185        11
  AMP PEAK  3(3Q26.33) WILD-TYPE      11       28        18        67         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                             11
  STAGE II                            49                             28
  STAGE III                           59                             18
  STAGE IVA                          185                             67
  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      35  92  74 127
  AMP PEAK  3(3Q26.33) WILD-TYPE    15  41  25  45
D3V4, multiclass
       clus
vv      AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  T0+T1                           35                             15
  T2                              92                             41
  T3                              74                             25
  T4                             127                             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
  AMP PEAK  3(3Q26.33) MUTATED   121  50 127   7
  AMP PEAK  3(3Q26.33) WILD-TYPE  57  16  38   1
D3V5, multiclass
    clus
vv   AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  N0                          121                             57
  N1                           50                             16
  N2                          127                             38
  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"
D3V6, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED   130   1
  AMP PEAK  3(3Q26.33) WILD-TYPE  53   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED    130    1
  AMP PEAK  3(3Q26.33) WILD-TYPE   53    0
   clus
vv  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  0                          130                             53
  1                            1                              0
[1] 2 2
[1] FALSE
D3V7, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED    88 287
  AMP PEAK  3(3Q26.33) WILD-TYPE  51  90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     88  287
  AMP PEAK  3(3Q26.33) WILD-TYPE   51   90
        clus
vv       AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  FEMALE                           88                             51
  MALE                            287                             90
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(3Q26.33) MUTATED                                     367
  AMP PEAK  3(3Q26.33) WILD-TYPE                                   138
                                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                                                367
  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                                                  138
  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    63 312
  AMP PEAK  3(3Q26.33) WILD-TYPE  18 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     63  312
  AMP PEAK  3(3Q26.33) WILD-TYPE   18  123
     clus
vv    AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  NO                            63                             18
  YES                          312                            123
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, continuous
D3V12, 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                          36   316
  AMP PEAK  3(3Q26.33) WILD-TYPE                         9   125
D3V13, multiclass
                                  clus
vv                                 AMP PEAK  3(3Q26.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                     316
                                  clus
vv                                 AMP PEAK  3(3Q26.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED    17 328
  AMP PEAK  3(3Q26.33) WILD-TYPE   8 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     17  328
  AMP PEAK  3(3Q26.33) WILD-TYPE    8  126
                        clus
vv                       AMP PEAK  3(3Q26.33) MUTATED
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          328
                        clus
vv                       AMP PEAK  3(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            126
[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   146  89
  AMP PEAK  4(5P15.33) WILD-TYPE 167 111
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           235                            278 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            89                            111 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
       17.10        23.84        53.79        57.44        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       14.83         3.55        12.62         4.01         7.76        29.42 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DI 
       28.11        30.18        27.95         7.10        14.47        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
       20.48        16.41         6.15        94.62         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-8596 TCGA-BB-8601 
       18.35        22.42        50.20        44.98        71.05        20.52 
TCGA-BB-A5HU TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 
       25.71         6.28        23.70        38.04        40.44        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       26.86        32.65        12.99        20.55        14.33        43.73 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 
       12.39         8.32        11.84        20.71        30.67        14.20 
TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
        6.74        36.49        10.45        12.95        24.16        14.10 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6UY 
       14.56        12.85        29.72        17.29        11.44        10.09 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5330 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 
        9.80         7.69        45.80        32.88        56.58        13.25 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 
       51.29        16.73        64.11        32.81        31.23        84.23 
TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       54.67        58.42        39.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
        6.02        12.46        15.75         9.27        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 
       40.93        35.84        34.06        19.92        17.13        12.89 
TCGA-CR-7390 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 
       29.82        31.10         7.10         5.13         5.95        48.39 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
       17.16       108.95        76.24        17.95       107.51        76.50 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6933 
       80.12        17.92        13.35        86.83         9.60        90.12 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 
        5.46        20.52        26.43        11.24        12.03        65.82 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        7.13         8.42         2.50       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
       12.66         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7254 
       71.21        10.75        77.16        36.00        26.20        47.97 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 
       35.54        17.85        25.08         0.07       100.57        14.89 
TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X 
        3.52       153.86        16.64       180.16        35.47         6.51 
TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM 
       48.20         0.76         7.07        15.25        35.34         6.38 
TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO 
       18.84         9.60        23.05        24.95        25.32        14.30 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A61S 
       25.48         9.83        12.10        11.18        19.23        18.94 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7753 
        0.46        17.85        20.25        15.06         6.77         0.16 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 
        1.22        14.66        22.85         3.65        34.75        15.95 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
       19.33        14.47        11.84        13.35        18.15        12.43 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 
       14.37         7.96         1.84        15.42         7.13        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 
       15.78        56.75        36.82        47.01        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        12.99        13.15        21.07        11.74 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        16.70        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K 
        6.51         5.62        11.57        12.10         9.76         8.32 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       12.72        15.91        13.55         2.83        43.36        41.16 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW 
       62.27        49.22        21.86        13.94        22.36        17.03 
TCGA-WA-A7GZ 
       20.55 

$`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 
       26.50        23.74        42.35        57.93        20.48        20.45 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4225 
       11.54         5.69         7.82         2.27        13.38         4.60 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HY 
       36.72        33.70        66.28        24.66        38.40        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 
       27.19        12.92         8.81        12.69        26.27         4.67 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       37.84        21.11        41.10        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       33.11        34.36         8.58        35.54        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 
       11.57        12.49         8.52        22.45        56.94        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 
       20.65        19.53        20.68        19.07         9.07         9.24 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       11.08        20.09         3.68        17.42        11.74        35.01 
TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       17.59        21.21         7.40        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       12.07         2.70         7.33         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        54.58        46.75        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6227 
       11.21         4.24        41.19        32.38        34.75         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
       14.99        38.76        70.13        33.11        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       28.83        44.48        11.61        23.24        29.36        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
       14.14        12.46        11.77        37.87        26.27        50.01 
TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       34.52        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       11.51        47.18         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        0.99        31.96         9.17        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 
       27.06        30.02        29.85        29.52        30.58        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 
       29.95       139.43       129.21        19.20        94.88        91.53 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       23.05        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6939 
       21.07        62.43         2.14         9.70         4.73        21.90 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      126.08        19.79        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 
       53.95        10.98        28.34         4.14        64.83         7.99 
TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 
        9.01       130.88         4.73        47.47        31.36        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 
       17.13        95.34         4.96        11.87         2.10        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       18.41        57.47       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       22.85        25.94        34.09        56.48       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 
       16.27        84.49        19.76         7.17         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W 
       27.98        24.99       169.38       159.65         1.05        45.96 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JD TCGA-CV-A6JN 
       88.87        60.43        67.86        56.61         5.98        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 
       22.52        10.42        10.42        10.55        34.36        13.25 
TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 
       25.41         2.53        16.14        11.44        18.67        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       12.36        15.88         7.63        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-F7-7848 
       11.11        35.54        20.45        12.13        10.65        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A622 
       16.11        21.63        20.25         3.02        12.62        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
       12.43        13.38        15.16        13.61        21.11         0.07 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       25.74        22.03        12.66         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
        6.90        12.76        14.50        11.84        13.55         0.07 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
        5.29        11.54        10.75        30.05        12.62         3.68 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T7 
       16.08        29.92        51.25        10.85        19.00        16.01 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A8ZB TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       17.65         9.34         9.73        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71E 
       32.45        13.25        13.68        43.59        54.67        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT 
       44.65        17.95        24.16        16.11        20.75        32.65 
TCGA-UF-A7JV TCGA-WA-A7H4 
        2.96        14.56 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        17.290                         19.365 
[1] "0.1 - 180.2 (17.3)" "0.1 - 211.0 (19.4)"
[1] "hr=" "1"  
D4V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  4(5P15.33) MUTATED         8       30        38       113         7
  AMP PEAK  4(5P15.33) WILD-TYPE      19       47        39       139         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                             19
  STAGE II                            30                             47
  STAGE III                           38                             39
  STAGE IVA                          113                            139
  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 63 46 75
  AMP PEAK  4(5P15.33) WILD-TYPE    32 70 53 97
D4V4, multiclass
       clus
vv      AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  T0+T1                           18                             32
  T2                              63                             70
  T3                              46                             53
  T4                              75                             97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  4(5P15.33) MUTATED    63  35  80   4
  AMP PEAK  4(5P15.33) WILD-TYPE 115  31  85   4
D4V5, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  N0                           63                            115
  N1                           35                             31
  N2                           80                             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"
D4V6, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    80   1
  AMP PEAK  4(5P15.33) WILD-TYPE 103   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     80    1
  AMP PEAK  4(5P15.33) WILD-TYPE  103    0
   clus
vv  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  0                           80                            103
  1                            1                              0
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    53 184
  AMP PEAK  4(5P15.33) WILD-TYPE  86 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     53  184
  AMP PEAK  4(5P15.33) WILD-TYPE   86  193
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                           53                             86
  MALE                            184                            193
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                     231
  AMP PEAK  4(5P15.33) WILD-TYPE                                   274
                                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                                                231
  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                                                  274
  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    43 194
  AMP PEAK  4(5P15.33) WILD-TYPE  38 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     43  194
  AMP PEAK  4(5P15.33) WILD-TYPE   38  241
     clus
vv    AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  NO                            43                             38
  YES                          194                            241
[1] 2 2
[1] FALSE
D4V10, continuous
D4V11, continuous
D4V12, 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                          28   198
  AMP PEAK  4(5P15.33) WILD-TYPE                        17   243
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     198
                                  clus
vv                                 AMP PEAK  4(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                       243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    15 207
  AMP PEAK  4(5P15.33) WILD-TYPE  10 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     15  207
  AMP PEAK  4(5P15.33) WILD-TYPE   10  247
                        clus
vv                       AMP PEAK  4(5P15.33) MUTATED
  HISPANIC OR LATINO                               15
  NOT HISPANIC OR LATINO                          207
                        clus
vv                       AMP PEAK  4(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            247
[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    66  41
  AMP PEAK  5(6P12.1) WILD-TYPE 247 159
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                          107                           406 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                           41                           159 
$`AMP PEAK  5(6P12.1) MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4II 
        9.30        17.10        15.52        12.62         4.01        30.18 
TCGA-BA-A6DI TCGA-BB-7870 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 
       11.05        66.28        25.71        10.55         6.28        23.70 
TCGA-CN-4725 TCGA-CN-4736 TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6020 
       38.04        12.99        34.36        11.54        11.57         6.74 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W 
        9.24        36.49        20.09        12.85        17.29        11.44 
TCGA-CN-A640 TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 
        4.41         7.69        46.75        45.99        10.42         4.24 
TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CR-5247 
       32.38        13.25        16.73        11.61        25.81        11.77 
TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7399 TCGA-CR-7402 
        7.69        40.93        12.89        31.10         5.95        29.95 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5977 
      139.43       129.21        76.24        94.88        76.50        60.49 
TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6959 
       54.74        90.12        20.52        12.03        65.82         8.42 
TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7253 
        5.26        71.21        77.16        31.36        17.13        11.87 
TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7435 TCGA-CV-7440 
        2.10        35.54        22.85        25.94       153.86        22.19 
TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A6JE TCGA-CV-A6JT TCGA-CV-A6JU TCGA-D6-6823 
      180.16        35.47        35.34        22.03         3.62        23.05 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7589 TCGA-F7-A623 
       13.94        11.11        58.45        35.54        18.90        20.25 
TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6I0 TCGA-IQ-A61E 
       15.06         0.16         1.22        14.66         6.90        19.33 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D TCGA-MZ-A5BI TCGA-P3-A6SW 
       11.54        18.15        14.37         1.84         7.13        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       75.55        18.97         7.30        14.79         6.51        11.57 
TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A7J9 
       12.10        12.72        15.91        13.25        54.67        44.65 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7H4 
       24.16        49.22        21.86        13.94        14.56 

$`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 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        53.79 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF 
       57.44        21.17        14.83         3.55         7.76        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
       14.47         7.82         2.27        13.38        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15        94.62         9.14         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       22.42        36.72        33.70        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       38.40        71.05        20.52        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       12.69        26.27         4.67        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.65        21.11        41.10        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       43.73        27.58        41.69        13.05        33.11         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 
       12.39        35.54         8.32        16.21        11.84        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        22.45        56.94        20.71        30.67        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
       20.65        19.53        20.68        19.07        14.20         9.07 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       11.08        10.45        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       14.10        11.74        35.01        14.56        17.59        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 
       21.21         7.40        15.91         5.75        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         9.80         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 
       21.50         2.93        54.58        45.80        11.21        41.19 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       32.88        34.75        56.58         4.24        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       70.13        51.29        33.11        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       64.11        44.48        23.24        29.36        32.81        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        31.23        84.23        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        11.90        10.22        11.34        11.64 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        11.51        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       47.34        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
       17.13        32.78        47.01        27.06        29.82        30.02 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
       29.85        29.52        30.58         7.10         5.13        35.41 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       48.39        17.16       108.95        19.20        17.95       107.51 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       91.53        80.12        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       48.59         7.07        43.23        21.07        62.43         9.60 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        2.14         9.70         5.46         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       11.24       126.08        19.79        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 
        6.08        53.95        10.98         7.13        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       126.15       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         1.84        52.31        12.92        21.80 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
       10.75       130.88         4.73        47.47        36.00        26.20 
TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       18.97        95.34         4.96        47.97        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        17.85       210.97        89.33         9.67         0.46 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.08         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64         6.38        27.98        24.99       169.38 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      159.65         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6JZ 
        5.98         6.38        29.79         6.48        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       34.36        13.25        25.41         9.60         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       11.44        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5629 
       15.88         7.63        14.30        12.10        12.79        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        14.04        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       12.13        12.10        10.65        11.18        37.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        12.43        13.38        15.16 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 
       13.61        21.11         6.77         0.07        25.74        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
       34.75        15.95        12.76        14.50        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
        0.07        14.47         5.29        11.84        13.35        12.43 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       10.75         7.96        30.05        12.62         3.68        15.42 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
       16.08        17.98        29.92        15.78        56.75        51.25 
TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       10.85        47.01        19.00         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       16.01        13.15        21.07        11.74        17.65        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB 
        9.34        12.72        18.64        12.43         5.62         9.73 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        9.76         8.32        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       13.55        13.68        43.59         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS 
       42.02        62.27        17.95        16.11        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       32.65         2.96        17.03        20.55 

  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                         0.16                          0.07 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                       180.16                        210.97 
  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE 
                        17.13                         18.38 
[1] "0.2 - 180.2 (17.1)" "0.1 - 211.0 (18.4)"
[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       17        17        53         4
  AMP PEAK  5(6P12.1) WILD-TYPE      23       60        60       199         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                            23
  STAGE II                           17                            60
  STAGE III                          17                            60
  STAGE IVA                          53                           199
  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  29  26  37
  AMP PEAK  5(6P12.1) WILD-TYPE    44 104  73 135
D5V4, multiclass
       clus
vv      AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  T0+T1                           6                            44
  T2                             29                           104
  T3                             26                            73
  T4                             37                           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  5(6P12.1) MUTATED    38  11  41   2
  AMP PEAK  5(6P12.1) WILD-TYPE 140  55 124   6
D5V5, multiclass
    clus
vv   AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  N0                          38                           140
  N1                          11                            55
  N2                          41                           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"
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P12.1) MUTATED    40   0
  AMP PEAK  5(6P12.1) WILD-TYPE 143   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P12.1) MUTATED     40    0
  AMP PEAK  5(6P12.1) WILD-TYPE  143    1
   clus
vv  AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  0                          40                           143
  1                           0                             1
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P12.1) MUTATED    26  83
  AMP PEAK  5(6P12.1) WILD-TYPE 113 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P12.1) MUTATED     26   83
  AMP PEAK  5(6P12.1) WILD-TYPE  113  294
        clus
vv       AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  FEMALE                          26                           113
  MALE                            83                           294
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(6P12.1) MUTATED                                     107
  AMP PEAK  5(6P12.1) WILD-TYPE                                   398
                               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                                               107
  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                                                 398
  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  98
  AMP PEAK  5(6P12.1) WILD-TYPE  70 337
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P12.1) MUTATED     11   98
  AMP PEAK  5(6P12.1) WILD-TYPE   70  337
     clus
vv    AMP PEAK  5(6P12.1) MUTATED AMP PEAK  5(6P12.1) WILD-TYPE
  NO                           11                            70
  YES                          98                           337
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, continuous
D5V12, 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    87
  AMP PEAK  5(6P12.1) WILD-TYPE                        29   354
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(6P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     87
                                  clus
vv                                 AMP PEAK  5(6P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P12.1) MUTATED     5  95
  AMP PEAK  5(6P12.1) WILD-TYPE  20 359
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P12.1) MUTATED      5   95
  AMP PEAK  5(6P12.1) WILD-TYPE   20  359
                        clus
vv                       AMP PEAK  5(6P12.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       AMP PEAK  5(6P12.1) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           359
[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  38
  AMP PEAK  6(6Q12) WILD-TYPE 259 162
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         92                         421 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                         38                         162 
$`AMP PEAK  6(6Q12) MUTATED`
TCGA-BA-4075 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4II TCGA-BA-A6DI TCGA-BA-A6DL 
        9.30        12.62         4.01        30.18        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A47Z 
       16.41        36.72        66.28        25.71        10.55         6.28 
TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5367 
       23.70        12.99        27.58        34.36        11.54        11.57 
TCGA-CN-6010 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 
       20.71         9.24        36.49        17.29        11.44         4.41 
TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6220 
        7.69        46.75        45.99        10.42         4.24        32.38 
TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-6491 
       16.73        25.81        11.77         6.02         7.69        11.51 
TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7397 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5440 
        3.45        12.89         7.10       139.43       129.21       107.51 
TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 
       76.50        86.83        60.49        54.74        90.12        20.52 
TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7243 
       65.82         8.42         4.14        71.21        77.16        31.36 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7407 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       17.13        11.87        35.54         7.17       153.86        16.64 
TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JM 
       22.19       180.16        67.86         7.07        35.34         6.38 
TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5624 
       10.42        34.36        23.05        13.94        12.10        58.45 
TCGA-DQ-5625 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6I0 TCGA-IQ-A61E 
       35.54         0.07         1.22        14.66         6.90        19.33 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D TCGA-MZ-A5BI 
        5.29        11.54        18.15        14.37         1.84         7.13 
TCGA-P3-A5Q6 TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO 
       15.78         7.30        14.79        11.57        12.10        12.72 
TCGA-T2-A6WZ TCGA-UF-A7JD 
       15.91        24.16 

$`AMP PEAK  6(6Q12) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       53.79        57.44        15.52        21.17        14.83         3.55 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        7.76        29.42        28.11        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
        7.10         5.69        14.47         7.82         2.27        13.38 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15        94.62         9.14         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
       22.42        33.70        50.20        44.98        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       71.05        20.52        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       26.27        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.65        21.11        41.10        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       43.73        41.69        13.05        33.11         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 
       35.54         8.32        16.21        11.84        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       22.45        56.94        30.67        20.68        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 
       20.68        19.07        14.20         6.74         9.07        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
       29.72        21.21         7.40        15.91         5.75        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        10.09         7.33         9.80         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5333 
       39.68        21.50         2.93        54.58        45.80        11.21 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       41.19        32.88        34.75        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        51.29        33.11        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        32.81        14.14        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       34.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.34        11.64        12.46        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
       26.17        17.13        32.78        47.01        27.06        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 
       30.02        31.10        29.85        29.52        30.58         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 
        5.95        35.41        29.95        48.39        17.16       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
       76.24        19.20        17.95        94.88        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       17.92        13.35        23.05        48.59         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60         2.14         9.70         5.46 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
       10.98         7.13        28.34         2.50        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 
        1.84        52.31        12.92        21.80        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 
        4.73        47.47        36.00        26.20        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        47.97         2.10        36.13        18.41        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       25.08        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
       19.76         6.38        27.98        24.99       169.38       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
       60.43         0.76        56.61        15.25         5.98        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.42        10.55        18.84        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       25.32        17.72        12.36        15.88         7.63        14.30 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       12.79        11.11        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       10.65        11.18        37.18        16.11        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        19.23        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 
       13.61        21.11         6.77         0.16        25.74        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
       34.75        15.95        12.76        14.50        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
        0.07        14.47        11.84        13.35        12.43        10.75 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
        7.96        30.05        12.62         3.68        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        56.75        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        11.74        17.65 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 
       16.70         9.34        12.72        18.64        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62         9.73         9.76         8.32        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       62.27        17.95        49.22        21.86        16.11        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                       0.07                        0.07 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                     180.16                      210.97 
  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE 
                     15.845                      18.810 
[1] "0.1 - 180.2 (15.8)" "0.1 - 211.0 (18.8)"
[1] "hr=" "1"  
D6V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  6(6Q12) MUTATED         3       13        16        44         2
  AMP PEAK  6(6Q12) WILD-TYPE      24       64        61       208        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                          24
  STAGE II                         13                          64
  STAGE III                        16                          61
  STAGE IVA                        44                         208
  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  25  22  30
  AMP PEAK  6(6Q12) WILD-TYPE    45 108  77 142
D6V4, multiclass
       clus
vv      AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  T0+T1                         5                          45
  T2                           25                         108
  T3                           22                          77
  T4                           30                         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
  AMP PEAK  6(6Q12) MUTATED    30  11  32   2
  AMP PEAK  6(6Q12) WILD-TYPE 148  55 133   6
D6V5, multiclass
    clus
vv   AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  N0                        30                         148
  N1                        11                          55
  N2                        32                         133
  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"
D6V6, binary
                             cls
clus                            0   1
  AMP PEAK  6(6Q12) MUTATED    30   0
  AMP PEAK  6(6Q12) WILD-TYPE 153   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(6Q12) MUTATED     30    0
  AMP PEAK  6(6Q12) WILD-TYPE  153    1
   clus
vv  AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  0                        30                         153
  1                         0                           1
[1] 2 2
[1] FALSE
D6V7, binary
                             cls
clus                            0   1
  AMP PEAK  6(6Q12) MUTATED    27  67
  AMP PEAK  6(6Q12) WILD-TYPE 112 310
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(6Q12) MUTATED     27   67
  AMP PEAK  6(6Q12) WILD-TYPE  112  310
        clus
vv       AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  FEMALE                        27                         112
  MALE                          67                         310
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(6Q12) MUTATED                                      94
  AMP PEAK  6(6Q12) WILD-TYPE                                   411
                             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                                              94
  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                                               411
  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  85
  AMP PEAK  6(6Q12) WILD-TYPE  72 350
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(6Q12) MUTATED      9   85
  AMP PEAK  6(6Q12) WILD-TYPE   72  350
     clus
vv    AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  NO                          9                          72
  YES                        85                         350
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, continuous
D6V12, 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    77
  AMP PEAK  6(6Q12) WILD-TYPE                        33   364
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                               12
  WHITE                                                   77
                                  clus
vv                                 AMP PEAK  6(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                    364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                             cls
clus                            0   1
  AMP PEAK  6(6Q12) MUTATED     7  81
  AMP PEAK  6(6Q12) WILD-TYPE  18 373
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(6Q12) MUTATED      7   81
  AMP PEAK  6(6Q12) WILD-TYPE   18  373
                        clus
vv                       AMP PEAK  6(6Q12) MUTATED AMP PEAK  6(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             7                          18
  NOT HISPANIC OR LATINO                        81                         373
[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  98
  AMP PEAK  7(7P11.2) WILD-TYPE 195 102
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                          216                           297 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                           98                           102 
$`AMP PEAK  7(7P11.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 
       15.19         9.30        13.64        26.50        17.10        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4II TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI 
       12.62         7.76        30.18        14.47         2.27        11.05 
TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
       20.48         9.14        33.70        66.28        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 
       25.71        10.55         6.28        26.27         4.67        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 
       26.86        32.65        20.55        14.33        43.73        34.36 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        8.58        12.39         8.32        11.54        11.84        11.57 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
       30.67        20.68        20.65         6.74         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A49A 
       11.08        10.45        12.95         3.68        14.10        12.85 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 
       29.72         7.40        15.91        11.44         4.41        12.07 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6229 
       46.75        45.80         4.24        32.38        13.25        38.76 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       16.73        43.04        41.88        64.11        11.61        23.24 
TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7364 
       12.46        18.54        16.90         6.02        11.64        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 
       39.16        47.34         3.45        29.23         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
       19.92        26.17        12.89        29.82         7.10         5.13 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
      139.43        17.16       129.21        17.95       107.51        76.50 
TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       80.12        48.59         7.07        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 
        5.46        26.43        11.24        12.03        15.09        30.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 
       53.95        65.82         8.42        28.34         4.14       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7180 
      111.16        18.81         5.26         1.84        21.80        10.75 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 
       17.13         2.10        18.41        35.54        17.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45V 
        3.52       153.86        16.64        22.19        35.47         1.05 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT 
        6.51        48.20         0.76         6.38         6.48        22.03 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
       23.47        19.92        18.84        34.36        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM 
       23.05        11.44        18.67        25.32        15.88         7.63 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 
       13.94        12.10        58.45        35.54        30.94        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I 
       14.04        18.90         9.83        37.18        16.11         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 
       19.23        18.94        11.80        13.61         0.07         0.16 
TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7631 TCGA-IQ-7632 
        1.22        12.66        13.84         3.65        12.76        14.50 
TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
       13.55         5.29        11.84        18.15        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       30.05         1.84         3.68        15.42        17.98        15.78 
TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A6IH 
       47.01        18.97         2.04        12.99        13.15        16.70 
TCGA-QK-A6II TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
        9.34        12.43         6.51         5.62        11.57        12.10 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-UF-A71A 
        8.32        12.72        15.91        32.45        13.25         2.83 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7GZ 
       42.02        44.65        24.16        21.86        13.94        20.55 

$`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 
        3.35        37.28         9.07        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
       23.84        20.48        53.79        57.44        15.52        21.17 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
        3.55         4.01        29.42        28.11        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BA-A8YP 
       11.54         7.10         5.69         7.82        13.38        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        6.15        94.62         4.60         4.41        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HZ 
       36.72        50.20        44.98        24.66        38.40        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 
       12.92         8.81        12.69        23.70        38.04        40.44 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 
       37.84        21.11        41.10        12.99        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5369 TCGA-CN-5370 
       13.05        33.11        35.54        16.21        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       22.45        56.94        20.71        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
       14.20         9.07        20.09        24.16        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y 
       35.01        14.56        17.59        21.21        17.29         5.75 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 
       48.20        39.68        21.50         2.93        54.58        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
       10.42        11.21        41.19        32.88        34.75        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 
        4.24        14.99        70.13        51.29        33.11        28.83 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
       44.48        29.36        32.81        25.81        14.14        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        34.52        36.99        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34         7.69        12.46        11.51        15.75         9.27 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
       40.93        35.84         3.09        24.95         0.99        31.96 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 
       17.13        32.78        47.01        27.06        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       29.85        29.52        30.58         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 
       48.39       108.95        76.24        19.20        94.88        91.53 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 
       17.92        13.35        23.05        86.83        60.49        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6938 
       54.74        21.07        62.43         9.60        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6955 
       21.90       126.08        19.79        42.38         6.08        10.98 
TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        7.13         2.50        64.83        12.66         7.99         9.01 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 
       52.31        12.92        71.21       130.88        47.47        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        4.96        11.87        47.97        36.13        57.47       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7427 TCGA-CV-7428 
       89.33         9.67         0.46        22.85       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45O 
       16.27        84.49        19.76         7.17         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45W TCGA-CV-A45Y 
       24.99       169.38       180.16       159.65        45.96        88.87 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        67.86        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 
       35.34        29.79         3.62        21.24        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 
       10.42        10.55        13.25         2.53        16.14        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5630 
       17.72        12.36        14.30        12.79        11.11        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       25.48        20.45        12.13        12.10        10.65        11.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       21.63        20.25        12.62         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        15.06        21.11         6.77 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
       25.74        14.66        22.03        22.85         0.36         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I 
        6.90        34.75        15.95        19.33        11.84         0.07 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67F 
       14.47        11.54        13.35        12.43        10.75        12.62 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        29.92        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z 
       36.82        19.00        75.55        29.00        16.01        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       11.74        17.65         7.30        12.72        18.64        14.79 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-TN-A7HI 
        9.73         9.76        16.96         6.87         7.10        13.55 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA 
       13.68        43.59        54.67        43.36        41.16        62.27 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       17.95        49.22        16.11        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                       153.86                        210.97 
  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE 
                       15.895                        20.450 
[1] "0.1 - 153.9 (15.9)" "0.1 - 211.0 (20.4)"
[1] "hr=" "1.6"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  7(7P11.2) MUTATED        10       34        33       113         7
  AMP PEAK  7(7P11.2) WILD-TYPE      17       43        44       139         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                            17
  STAGE II                           34                            43
  STAGE III                          33                            44
  STAGE IVA                         113                           139
  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 56 52 78
  AMP PEAK  7(7P11.2) WILD-TYPE    36 77 47 94
D7V4, multiclass
       clus
vv      AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  T0+T1                          14                            36
  T2                             56                            77
  T3                             52                            47
  T4                             78                            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
  AMP PEAK  7(7P11.2) MUTATED    75  27  77   4
  AMP PEAK  7(7P11.2) WILD-TYPE 103  39  88   4
D7V5, multiclass
    clus
vv   AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  N0                          75                           103
  N1                          27                            39
  N2                          77                            88
  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"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(7P11.2) MUTATED    74   1
  AMP PEAK  7(7P11.2) WILD-TYPE 109   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P11.2) MUTATED     74    1
  AMP PEAK  7(7P11.2) WILD-TYPE  109    0
   clus
vv  AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  0                          74                           109
  1                           1                             0
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(7P11.2) MUTATED    60 158
  AMP PEAK  7(7P11.2) WILD-TYPE  79 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P11.2) MUTATED     60  158
  AMP PEAK  7(7P11.2) WILD-TYPE   79  219
        clus
vv       AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  FEMALE                          60                            79
  MALE                           158                           219
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(7P11.2) MUTATED                                     215
  AMP PEAK  7(7P11.2) WILD-TYPE                                   290
                               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                                               215
  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                                                 290
  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    36 182
  AMP PEAK  7(7P11.2) WILD-TYPE  45 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P11.2) MUTATED     36  182
  AMP PEAK  7(7P11.2) WILD-TYPE   45  253
     clus
vv    AMP PEAK  7(7P11.2) MUTATED AMP PEAK  7(7P11.2) WILD-TYPE
  NO                           36                            45
  YES                         182                           253
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, continuous
D7V12, 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                          26   181
  AMP PEAK  7(7P11.2) WILD-TYPE                        19   260
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    181
                                  clus
vv                                 AMP PEAK  7(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                               cls
clus                              0   1
  AMP PEAK  7(7P11.2) MUTATED     9 195
  AMP PEAK  7(7P11.2) WILD-TYPE  16 259
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7P11.2) MUTATED      9  195
  AMP PEAK  7(7P11.2) WILD-TYPE   16  259
                        clus
vv                       AMP PEAK  7(7P11.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         195
                        clus
vv                       AMP PEAK  7(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           259
[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  79
  AMP PEAK  8(7Q21.3) WILD-TYPE 227 121
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                          165                           348 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                           79                           121 
$`AMP PEAK  8(7Q21.3) MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DE 
        9.30        15.52        14.83        12.62         7.76        14.47 
TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
       11.05        16.41        33.70        66.28        71.05        20.52 
TCGA-BB-A5HY TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4738 
       10.55        26.27        40.44        12.89        41.10        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       43.73        27.58        34.36         8.58        35.54         8.32 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       11.54        11.84        11.57        20.71        30.67        20.68 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
       20.65         6.74        36.49        11.08        10.45        20.09 
TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
        3.68        14.10        12.85        29.72         7.40        15.91 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7067 
       11.44        12.07         2.93        10.42        13.25        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-6478 
       41.88        64.11        11.61        23.24        11.77         6.02 
TCGA-CR-6491 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 
       11.51        47.34         3.45        17.13        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.82         5.95       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5978 
       76.24        17.95       107.51        76.50        80.12         7.07 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 
        9.60        90.12         9.70         5.46        26.43        11.24 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 
       12.03        15.09        30.08        28.34         4.14       126.15 
TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7247 
        5.26        21.80        71.21        77.16        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       17.13        47.97        36.13        18.41        35.54        17.85 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        9.67         0.46        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 
      100.57        14.89        56.48        19.76       153.86        22.19 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A6JE TCGA-CV-A6JM 
       35.47         1.05        48.20         0.76        35.34         6.38 
TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 
       23.47        18.84        34.36        25.41        11.44        18.67 
TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 
       25.32        15.88        14.30        13.94        11.11        35.54 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 
       30.94        18.02        14.04        18.90         9.83        16.11 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7753 
        3.02        19.23        18.94        20.25        15.06         0.16 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61H 
        1.22        14.66         3.65        34.75        12.76        13.55 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G 
        5.29        11.84        14.37         7.96        30.05         3.68 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-QK-A6VC 
       17.98        15.78        47.01         2.04        12.99        12.43 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7J9 
       12.10         9.76        12.72        54.67         2.83        44.65 
TCGA-UF-A7JA TCGA-UF-A7JS TCGA-WA-A7GZ 
       62.27        22.36        20.55 

$`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 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF 
       53.79        57.44        21.17         3.55         4.01        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       28.11        20.45        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
        5.69         7.82         2.27        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
       94.62         9.14         4.60         4.41        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU 
       36.72        50.20        44.98        24.66        38.40        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       27.19        12.92         8.81         6.28        12.69        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        37.84        26.86        32.65        21.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 
       12.99        20.55        41.69        13.05        33.11        12.39 
TCGA-CN-5364 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 
       16.21        12.49         8.52        22.45        56.94        19.53 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 
       20.68        19.07        14.20         9.07         9.24        12.95 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       24.16        17.42        11.74        35.01        14.56        17.59 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
       21.21        17.29         5.75         4.41         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        7.33         9.80         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50        54.58        46.75        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        34.75        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        51.29        33.11 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.04        28.83        44.48        29.36        32.81        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
        7.69        12.46        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       31.96         9.17        34.06        19.92        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       47.01        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 
        7.10         5.13        35.41        29.95        48.39        19.20 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       94.88        91.53        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49        43.23        54.74        21.07        62.43 
TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 
        2.14        20.52         4.73        21.90       126.08        19.79 
TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       42.38         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        8.42         2.50        64.83       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 
        7.99         9.01         1.84        52.31        12.92        10.75 
TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7250 
      130.88         4.73        47.47        36.00        31.36        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
        4.96        11.87         2.10        57.47       210.97        89.33 
TCGA-CV-7415 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       22.85       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64         6.38        27.98        24.99       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 
      180.16       159.65        45.96         6.51        88.87        60.43 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
       67.86        56.61         7.07        15.25         5.98        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        22.03         3.62        21.24        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.42        10.42        10.55        13.25         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM 
        2.53        16.14        24.95        17.72        12.36         7.63 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
       12.10        12.79        58.45        33.86        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       20.25        12.62         0.46        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        13.61        21.11         6.77         0.07 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       25.74        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        4.27         6.90        15.95        14.50        19.33        11.84 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
        0.07        14.47        11.54        13.35        18.15        12.43 
TCGA-KU-A6H8 TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       10.75         1.84        12.62        15.42         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       29.92        56.75        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55        18.97        29.00        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       18.64        14.79         6.51         5.62        11.57         9.73 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        16.96         6.87        15.91         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D 
       13.55        13.25        13.68        43.59        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       42.02        17.95        24.16        49.22        21.86        16.11 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       13.94        20.75        32.65         2.96        17.03        14.56 

  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                       153.86                        210.97 
  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE 
                       17.130                        18.985 
[1] "0.1 - 153.9 (17.1)" "0.1 - 211.0 (19.0)"
[1] "hr=" "1.5"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  8(7Q21.3) MUTATED         9       22        26        84         6
  AMP PEAK  8(7Q21.3) WILD-TYPE      18       55        51       168         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                            18
  STAGE II                           22                            55
  STAGE III                          26                            51
  STAGE IVA                          84                           168
  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  34  36  65
  AMP PEAK  8(7Q21.3) WILD-TYPE    37  99  63 107
D8V4, multiclass
       clus
vv      AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  T0+T1                          13                            37
  T2                             34                            99
  T3                             36                            63
  T4                             65                           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
  AMP PEAK  8(7Q21.3) MUTATED    57  19  54   5
  AMP PEAK  8(7Q21.3) WILD-TYPE 121  47 111   3
D8V5, multiclass
    clus
vv   AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  N0                          57                           121
  N1                          19                            47
  N2                          54                           111
  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"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q21.3) MUTATED    50   0
  AMP PEAK  8(7Q21.3) WILD-TYPE 133   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q21.3) MUTATED     50    0
  AMP PEAK  8(7Q21.3) WILD-TYPE  133    1
   clus
vv  AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  0                          50                           133
  1                           0                             1
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q21.3) MUTATED    42 124
  AMP PEAK  8(7Q21.3) WILD-TYPE  97 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q21.3) MUTATED     42  124
  AMP PEAK  8(7Q21.3) WILD-TYPE   97  253
        clus
vv       AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  FEMALE                          42                            97
  MALE                           124                           253
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(7Q21.3) MUTATED                                     164
  AMP PEAK  8(7Q21.3) WILD-TYPE                                   341
                               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                                               164
  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                                                 341
  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    32 134
  AMP PEAK  8(7Q21.3) WILD-TYPE  49 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q21.3) MUTATED     32  134
  AMP PEAK  8(7Q21.3) WILD-TYPE   49  301
     clus
vv    AMP PEAK  8(7Q21.3) MUTATED AMP PEAK  8(7Q21.3) WILD-TYPE
  NO                           32                            49
  YES                         134                           301
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, continuous
D8V12, 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                          25   137
  AMP PEAK  8(7Q21.3) WILD-TYPE                        20   304
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(7Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    137
                                  clus
vv                                 AMP PEAK  8(7Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   20
  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"
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK  8(7Q21.3) MUTATED     9 147
  AMP PEAK  8(7Q21.3) WILD-TYPE  16 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7Q21.3) MUTATED      9  147
  AMP PEAK  8(7Q21.3) WILD-TYPE   16  307
                        clus
vv                       AMP PEAK  8(7Q21.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         147
                        clus
vv                       AMP PEAK  8(7Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           307
[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   102  57
  AMP PEAK  9(8P11.23) WILD-TYPE 211 143
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                           159                            354 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                            57                            143 
$`AMP PEAK  9(8P11.23) MUTATED`
TCGA-BA-4075 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
        9.30        42.35        57.44        15.52        14.83         3.55 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 
        7.76        28.11        20.45         2.27        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
       94.62         9.14         4.60        18.35        22.42        36.72 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 
       50.20        66.28        24.66        71.05        20.52        26.27 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4739 TCGA-CN-4740 
       38.04        37.84        12.89        32.65        43.73        27.58 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 
       33.11        34.36        12.39        20.71        20.68        19.07 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A63T 
        6.74         9.24        12.95        24.16        17.59         7.40 
TCGA-CN-A63V TCGA-CQ-5324 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7068 TCGA-CQ-7069 
       15.91        39.68        13.25        38.76        43.04        41.88 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 
       23.24        25.81        14.14        31.23        84.23        58.42 
TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6487 
       50.01        18.54        16.90         6.02        11.34         7.69 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 
       47.18        39.16        47.34         3.45         0.99        34.06 
TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
       26.17        12.89        29.82         5.95       139.43        17.16 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 
      107.51        76.50        54.74        21.07         9.60         2.14 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6945 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-7090 
        5.46         4.73        12.03        53.95        65.82       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 
      111.16        18.81        12.66         7.99         9.01        10.75 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7407 
       36.00        31.36        11.87        47.97        18.41        35.54 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7435 
        0.46        25.08         0.07        34.09        16.27       153.86 
TCGA-CV-7440 TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45W TCGA-CV-A45X 
       22.19        24.99       180.16       159.65        45.96         6.51 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6K0 TCGA-CX-7082 
       48.20        67.86        15.25        35.34        19.92        10.42 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       18.84        25.41        11.44        24.95        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EP TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
       15.88        13.94        58.45        30.94        18.02        14.04 
TCGA-F7-A50J TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7917 
       19.23        20.25        12.43         6.77         0.16         1.22 
TCGA-HD-A634 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D 
        4.27        11.84        13.35        18.15        14.37         1.84 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-QK-A6VC 
        3.68         7.13        17.98        15.78        51.25        12.43 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WX TCGA-TN-A7HI 
        5.62         9.73         9.76         8.32         6.87        13.55 
TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH 
       13.25        54.67        44.65        17.95        49.22        21.86 
TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        20.55        14.56 

$`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 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        57.93        17.10        23.84        20.48        53.79 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 
       21.17        12.62         4.01        29.42        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI 
       11.54         7.10         5.69        14.47         7.82        11.05 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 
       13.38        16.41         4.41        33.70        44.98        38.40 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4733 
       12.69        23.70         4.67        40.44        26.86        21.11 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
       41.10        12.99        20.55        14.33        41.69        13.05 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        8.58        35.54         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
       11.57        12.49         8.52        22.45        56.94        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
       20.65        19.53        20.68        14.20         9.07        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       11.08        10.45        20.09         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        35.01        14.56        12.85        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       17.29        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       10.42        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 
       34.75        56.58         4.24        14.99        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       33.11        16.73        28.83        64.11        44.48        11.61 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       29.36        32.81        12.46        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
       26.27        39.52        34.52        36.99        11.90        10.22 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7368 
       11.64        12.46        11.51        15.75         9.27        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.09        24.95        29.23        31.96         9.17 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 
       19.92        17.13        32.78        47.01        27.06        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       35.41        29.95        48.39       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       19.20        17.95        94.88        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6939 
       43.23        62.43        90.12         9.70        20.52        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 
       26.43        11.24       126.08        19.79        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       30.08         6.08        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
        2.50         4.14        64.83         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       12.92        21.80        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       47.47        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
        2.10        36.13        57.47        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
        9.67        22.85        25.94       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94         3.52        84.49        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45V 
       16.64         6.38        27.98       169.38        35.47         1.05 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JD 
       88.87        60.43         0.76        56.61         7.07         5.98 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        22.03         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 
       23.47        22.52        10.42        10.55        34.36        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 
        9.60        23.05         2.53        16.14        18.67        25.32 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
        7.63        14.30        12.10        12.79        11.11        35.54 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       33.86        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       12.10        10.65        11.18        37.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       11.80        13.38        15.16        15.06        13.61        21.11 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
        0.07        25.74        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
       14.47         5.29        11.54        12.43        10.75         7.96 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
       30.05        12.62        15.42        16.08        29.92        56.75 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO 
       18.64        14.79         6.51        11.57        12.10        12.72 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HL TCGA-UF-A718 
       16.96        15.91         7.10        32.45        13.68        43.59 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
        2.83        43.36        41.16        42.02        62.27        24.16 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       16.11        13.94        20.75        32.65         2.96        17.03 

  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE 
                        18.840                         17.355 
[1] "0.1 - 180.2 (18.8)" "0.1 - 211.0 (17.4)"
[1] "hr=" "1.2"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  9(8P11.23) MUTATED         8       29        27        69         0
  AMP PEAK  9(8P11.23) WILD-TYPE      19       48        50       183        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                              8                             19
  STAGE II                            29                             48
  STAGE III                           27                             50
  STAGE IVA                           69                            183
  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      16  51  28  42
  AMP PEAK  9(8P11.23) WILD-TYPE    34  82  71 130
D9V4, multiclass
       clus
vv      AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  T0+T1                           16                             34
  T2                              51                             82
  T3                              28                             71
  T4                              42                            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  9(8P11.23) MUTATED    55  22  45   0
  AMP PEAK  9(8P11.23) WILD-TYPE 123  44 120   8
D9V5, multiclass
    clus
vv   AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  N0                           55                            123
  N1                           22                             44
  N2                           45                            120
  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"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED    53   1
  AMP PEAK  9(8P11.23) WILD-TYPE 130   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED     53    1
  AMP PEAK  9(8P11.23) WILD-TYPE  130    0
   clus
vv  AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  0                           53                            130
  1                            1                              0
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED    41 118
  AMP PEAK  9(8P11.23) WILD-TYPE  98 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED     41  118
  AMP PEAK  9(8P11.23) WILD-TYPE   98  259
        clus
vv       AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  FEMALE                           41                             98
  MALE                            118                            259
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(8P11.23) MUTATED                                     153
  AMP PEAK  9(8P11.23) WILD-TYPE                                   352
                                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                                                153
  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                                                  352
  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    27 132
  AMP PEAK  9(8P11.23) WILD-TYPE  54 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED     27  132
  AMP PEAK  9(8P11.23) WILD-TYPE   54  303
     clus
vv    AMP PEAK  9(8P11.23) MUTATED AMP PEAK  9(8P11.23) WILD-TYPE
  NO                            27                             54
  YES                          132                            303
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, continuous
D9V12, 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                          20   134
  AMP PEAK  9(8P11.23) WILD-TYPE                        25   307
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     134
                                  clus
vv                                 AMP PEAK  9(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                                cls
clus                               0   1
  AMP PEAK  9(8P11.23) MUTATED     8 137
  AMP PEAK  9(8P11.23) WILD-TYPE  17 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8P11.23) MUTATED      8  137
  AMP PEAK  9(8P11.23) WILD-TYPE   17  317
                        clus
vv                       AMP PEAK  9(8P11.23) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          137
                        clus
vv                       AMP PEAK  9(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            317
[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   187 118
  AMP PEAK 10(8Q11.21) WILD-TYPE 126  82
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                           305                            208 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                           118                             82 
$`AMP PEAK 10(8Q11.21) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
        3.35         9.30        26.50        17.10        20.48        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       57.44        15.52        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DG TCGA-BA-A6DI 
        7.76        28.11        20.45        30.18         2.27        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 
        4.41        18.35        22.42        33.70        50.20        66.28 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       38.40        71.05        20.52        25.71        10.55        27.19 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        26.27        23.70        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
        4.67        37.84        12.89        32.65        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        43.73        27.58        13.05        33.11        34.36 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
       12.39         8.32        11.84        11.57         8.52        22.45 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 
       20.68        20.65        19.53         6.74         9.24        11.08 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
       12.95        24.16         3.68        17.42        11.74        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       17.59        12.85        29.72         7.40        15.91        11.44 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
        4.41         2.70        39.68        21.50        46.75        45.80 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       56.58        13.25         4.24        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
       33.11        16.73        43.04        41.88        64.11        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
       11.61        23.24        29.36        25.81        14.14        31.23 
TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 
       84.23        58.42        50.01        39.52        36.99        16.90 
TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 
        6.02        11.34        11.64         7.69        12.46         9.27 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 
       39.16        47.34        35.84         3.45        24.95        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
        9.17        34.06        19.92        26.17        17.13        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 
       27.06        12.89        29.82         5.95        35.41       139.43 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      129.21        76.24        19.20       107.51        94.88        76.50 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 
       80.12        17.92        86.83        48.59        60.49        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 
       21.07        62.43        90.12         2.14         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        4.73        26.43        11.24       126.08        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6959 
       42.38        15.09        30.08         6.08        53.95         8.42 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
       28.34         4.14        64.83       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 
       12.66        12.92        71.21        10.75        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 
       47.47        31.36        26.20        18.97        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 
       18.41        35.54        22.85        25.08         0.07       100.57 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45P 
       14.89        54.94         7.17         6.38        22.19        24.99 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z 
      180.16       159.65        35.47        45.96         6.51        48.20 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.38        29.79         6.48        22.03        23.47        19.92 
TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       10.42        18.84        34.36        25.41         9.60        23.05 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        24.95        25.32        17.72        12.36        15.88 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       14.30        13.94        12.10        12.79        58.45        35.54 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 
       30.94        33.86        14.04        18.90         9.83        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       16.11        21.63        20.25         3.02        19.23        18.94 
TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
       17.85        20.25        12.43        15.16        15.06        13.61 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 
        6.77         0.07         1.22        14.66        12.66        22.85 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
        4.27        34.75        15.95        19.33        13.55        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
        5.29        11.54        11.84        13.35        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5QA 
        7.96         3.68        15.42         7.13        17.98        56.75 
TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       51.25        18.97        29.00        16.01        21.07        11.74 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8ZB 
        7.30        16.70         9.34        12.72        14.79         9.73 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HI 
        8.32        12.72         6.87        15.91        32.45        13.55 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 
       13.25        43.59        54.67         2.83        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JV TCGA-WA-A7H4 
       13.94        20.75        22.36         2.96        14.56 

$`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 
       15.19        13.64        37.28         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
       57.93        23.84        21.17        29.42        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BB-7862 
        7.10         5.69        14.47         7.82        13.38        36.72 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-A6UM TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4733 
       44.98        24.66        12.92        40.44        26.86        21.11 
TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       41.10        41.69         8.58        35.54        16.21        11.54 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 
       12.49        56.94        20.71        30.67        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 
       14.20         9.07        36.49        10.45        20.09        14.10 
TCGA-CN-A497 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY 
       35.01        21.21        17.29         5.75        12.07        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5326 
        7.33         9.80         7.69         6.18        48.20         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7071 TCGA-CQ-A4CD 
       32.38        32.88        34.75        14.99        28.83        32.81 
TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6472 
       12.46        11.77        54.67        37.87        26.27        34.52 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
       18.54        11.90        10.22        11.51        15.75        47.18 
TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7391 
       40.93         3.09        29.23         0.99        32.78        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5443 
       29.95        48.39        17.16       108.95        17.95        91.53 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6935 
       13.35        23.05         7.07        43.23         9.60         9.70 
TCGA-CV-6939 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-7099 
       21.90        65.82        10.98         7.13         2.50         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7183 
        9.01         5.26         1.84        52.31        21.80       130.88 
TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 
       36.00        17.13        95.34         4.96        11.87        36.13 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        17.85       210.97        89.33         9.67         0.46 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
       25.94        34.09        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45Q 
       84.49        19.76       153.86        16.64        27.98       169.38 
TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A6JU TCGA-CV-A6JY 
        1.05        88.87        60.43         0.76         3.62        21.24 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 
       22.52        10.42        10.55        13.25         2.53        16.14 
TCGA-D6-6827 TCGA-D6-A6EM TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       18.67         7.63        11.11        18.02        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A61V TCGA-F7-A61W 
       12.13        12.10        10.65        11.18        12.62         0.46 
TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 
       11.80        13.38        21.11         0.16        25.74        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 
        0.36        13.84         3.65         6.90        12.76        14.50 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D 
       11.84         0.07        12.43        10.75        30.05         1.84 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QF TCGA-P3-A6SW 
       12.62        16.08        29.92        15.78        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 
       47.01        19.00        75.55         2.04        12.99        13.15 
TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       17.65        18.64        12.43         6.51         5.62        11.57 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UF-A71B 
       12.10         9.76        16.96         7.10        13.68        43.36 
TCGA-UF-A71D TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       41.16        32.65        17.03        20.55 

  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                        18.970                         16.995 
[1] "0.1 - 180.2 (19.0)" "0.1 - 211.0 (17.0)"
[1] "hr=" "1.1"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 10(8Q11.21) MUTATED        18       45        56       144         7
  AMP PEAK 10(8Q11.21) WILD-TYPE       9       32        21       108         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                             18                              9
  STAGE II                            45                             32
  STAGE III                           56                             21
  STAGE IVA                          144                            108
  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      32 77 66 98
  AMP PEAK 10(8Q11.21) WILD-TYPE    18 56 33 74
D10V4, multiclass
       clus
vv      AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  T0+T1                           32                             18
  T2                              77                             56
  T3                              66                             33
  T4                              98                             74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 10(8Q11.21) MUTATED   104  45  98   4
  AMP PEAK 10(8Q11.21) WILD-TYPE  74  21  67   4
D10V5, multiclass
    clus
vv   AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  N0                          104                             74
  N1                           45                             21
  N2                           98                             67
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q11.21) MUTATED   119   0
  AMP PEAK 10(8Q11.21) WILD-TYPE  64   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED    119    0
  AMP PEAK 10(8Q11.21) WILD-TYPE   64    1
   clus
vv  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  0                          119                             64
  1                            0                              1
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q11.21) MUTATED    81 226
  AMP PEAK 10(8Q11.21) WILD-TYPE  58 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED     81  226
  AMP PEAK 10(8Q11.21) WILD-TYPE   58  151
        clus
vv       AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  FEMALE                           81                             58
  MALE                            226                            151
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(8Q11.21) MUTATED                                     301
  AMP PEAK 10(8Q11.21) WILD-TYPE                                   204
                                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                                                301
  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                                                  204
  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    44 263
  AMP PEAK 10(8Q11.21) WILD-TYPE  37 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED     44  263
  AMP PEAK 10(8Q11.21) WILD-TYPE   37  172
     clus
vv    AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  NO                            44                             37
  YES                          263                            172
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, continuous
D10V12, 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   263
  AMP PEAK 10(8Q11.21) WILD-TYPE                        22   178
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(8Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     263
                                  clus
vv                                 AMP PEAK 10(8Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q11.21) MUTATED    17 265
  AMP PEAK 10(8Q11.21) WILD-TYPE   8 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED     17  265
  AMP PEAK 10(8Q11.21) WILD-TYPE    8  189
                        clus
vv                       AMP PEAK 10(8Q11.21) MUTATED
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          265
                        clus
vv                       AMP PEAK 10(8Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            189
[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   223 155
  AMP PEAK 11(8Q24.21) WILD-TYPE  90  45
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           378                            135 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                           155                             45 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        3.35         9.30        13.64        26.50        23.74        42.35 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
       17.10        20.48        53.79        57.44        15.52        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
        3.55        12.62         4.01         7.76        29.42        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       20.45        30.18        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15        94.62         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
       18.35        33.70        50.20        66.28        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        25.71        10.55        27.19         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        26.27        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       37.84        12.89        32.65        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 
       43.73        27.58        13.05        33.11        34.36        12.39 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        8.32        16.21        11.54        11.84        11.57         8.52 
TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6022 
       22.45        20.68        20.65        19.53         6.74         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       36.49        11.08        10.45        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        14.10        11.74        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       12.85        29.72         7.40        17.29        15.91        11.44 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        4.41         2.70         9.80        39.68        21.50         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6218 
       46.75        45.80        45.99        10.42         4.24        41.19 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 
       51.29        33.11        16.73        43.04        41.88        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        32.81        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6470 
       14.14        31.23        84.23        11.77        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 
       39.52        36.99        18.54        16.90         6.02        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 
       11.64         7.69        12.46        11.51         9.27        39.16 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
       47.34        35.84         3.45        24.95         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
        9.17        34.06        19.92        26.17        17.13        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       27.06        12.89        29.82         7.10         5.95        35.41 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
       19.20       107.51        94.88        76.50        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       13.35        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        26.43        11.24       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        7.13         8.42         4.14        64.83       126.15       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       18.81        12.66         7.99         1.84        52.31        12.92 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 
       36.00        31.36        26.20        18.97        17.13        47.97 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7415 
        2.10        18.41        35.54        17.85         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 
       25.08        25.94         0.07       100.57        14.89       156.49 
TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       54.94        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       22.19        24.99       169.38       180.16       159.65        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 
       45.96         6.51        88.87        48.20        67.86        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 
        6.48        22.03         3.62        23.47        19.92        10.42 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        34.36        25.41         9.60        23.05         2.53 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        24.95        25.32        17.72        12.36        15.88 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       35.54        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
        9.83        37.18        16.11        21.63         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        15.06        13.61         6.77         0.07         0.16 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A634 
        1.22        14.66        22.03        12.66        22.85         4.27 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61K 
        3.65        34.75        15.95        19.33        11.84         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W 
       11.54        11.84        13.35        18.15        12.43        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        7.96         1.84         3.68        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T3 
       17.98        15.78        56.75        51.25        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB 
       11.74         7.30        16.70         9.34        12.72        14.79 
TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX 
       12.43        11.57         9.73         8.32        12.72         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
       15.91        32.45        13.55        13.25        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65         2.96        20.55        14.56 

$`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 
       15.19        37.28         9.07        57.93        23.84        21.17 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-A6UM TCGA-CN-4730 
       22.42        36.72        44.98        24.66        12.92        26.86 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5369 
       21.11        41.10        41.69         8.58        35.54        12.49 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       56.94        20.71        30.67        20.68        19.07        14.20 
TCGA-CN-6021 TCGA-CN-A497 TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY 
        9.07        35.01        21.21         5.75        12.07        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5333 
        7.33         7.69         6.18        48.20        54.58        11.21 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-7071 TCGA-CQ-A4CH TCGA-CR-5248 
       32.38        32.88        34.75        28.83        12.46        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6492 
       37.87        26.27        34.52        11.90        10.22        15.75 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7385 TCGA-CR-7391 
       47.18        40.93         3.09        29.23        32.78        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 
       31.10        29.85        29.52        30.58         5.13        29.95 
TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6939 
       17.95        91.53        23.05        86.83         9.60        21.90 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7101 
       65.82        10.98        28.34         2.50         9.01         5.26 
TCGA-CV-7177 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 
       21.80        95.34         4.96        11.87        36.13        57.47 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7429 
      210.97        89.33         9.67        34.09        56.48         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-A45O TCGA-CV-A45V TCGA-CV-A460 TCGA-CV-A463 
       16.27        84.49        27.98         1.05        60.43         0.76 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6825 
       21.24        22.52        10.42        10.55        13.25        16.14 
TCGA-D6-6827 TCGA-D6-A6EM TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
       18.67         7.63        25.48        20.45        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-A6C5 
       10.65        11.18        20.25        12.62        13.38        21.11 
TCGA-HD-7754 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 
       25.74         0.36        13.84         6.90        12.76        14.50 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
       13.55         0.07        14.47        10.75        30.05        12.62 
TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A6IF 
       29.92        10.85        36.82        47.01        75.55        17.65 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TP 
       18.64         6.51         5.62        12.10         9.76        16.96 
TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UP-A6WW 
        7.10        13.68        17.03 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                        17.885                         20.250 
[1] "0.1 - 180.2 (17.9)" "0.1 - 211.0 (20.2)"
[1] "hr=" "1.2"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 11(8Q24.21) MUTATED        20       51        57       194        11
  AMP PEAK 11(8Q24.21) WILD-TYPE       7       26        20        58         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                             20                              7
  STAGE II                            51                             26
  STAGE III                           57                             20
  STAGE IVA                          194                             58
  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      35  91  78 134
  AMP PEAK 11(8Q24.21) WILD-TYPE    15  42  21  38
D11V4, multiclass
       clus
vv      AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  T0+T1                           35                             15
  T2                              91                             42
  T3                              78                             21
  T4                             134                             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   123  47 133   7
  AMP PEAK 11(8Q24.21) WILD-TYPE  55  19  32   1
D11V5, multiclass
    clus
vv   AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  N0                          123                             55
  N1                           47                             19
  N2                          133                             32
  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"
D11V6, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED   143   0
  AMP PEAK 11(8Q24.21) WILD-TYPE  40   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED    143    0
  AMP PEAK 11(8Q24.21) WILD-TYPE   40    1
   clus
vv  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  0                          143                             40
  1                            0                              1
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED   103 277
  AMP PEAK 11(8Q24.21) WILD-TYPE  36 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED    103  277
  AMP PEAK 11(8Q24.21) WILD-TYPE   36  100
        clus
vv       AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  FEMALE                          103                             36
  MALE                            277                            100
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(8Q24.21) MUTATED                                     373
  AMP PEAK 11(8Q24.21) WILD-TYPE                                   132
                                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                                                373
  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                                                  132
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                              0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED    59 321
  AMP PEAK 11(8Q24.21) WILD-TYPE  22 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     59  321
  AMP PEAK 11(8Q24.21) WILD-TYPE   22  114
     clus
vv    AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  NO                            59                             22
  YES                          321                            114
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, continuous
D11V12, 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                          34   320
  AMP PEAK 11(8Q24.21) WILD-TYPE                        11   121
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  34
  WHITE                                                     320
                                  clus
vv                                 AMP PEAK 11(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    11
  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"
D11V14, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q24.21) MUTATED    21 329
  AMP PEAK 11(8Q24.21) WILD-TYPE   4 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     21  329
  AMP PEAK 11(8Q24.21) WILD-TYPE    4  125
                        clus
vv                       AMP PEAK 11(8Q24.21) MUTATED
  HISPANIC OR LATINO                               21
  NOT HISPANIC OR LATINO                          329
                        clus
vv                       AMP PEAK 11(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            125
[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    69  55
  AMP PEAK 12(9P24.1) WILD-TYPE 244 145
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                          124                           389 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                           55                           145 
$`AMP PEAK 12(9P24.1) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DI 
       23.84        20.48        57.44         4.01        11.54        11.05 
TCGA-BA-A6DJ TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-5355 
       13.38        66.28        27.19         8.81         6.28        33.11 
TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 
        8.32         8.52        22.45        20.71        30.67        19.07 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A640 
       36.49        24.16        17.42        17.59        21.21         4.41 
TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 
        2.70         7.69        21.50        46.75        45.80        34.75 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD 
       38.76        70.13        43.04        44.48        11.61        32.81 
TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7370 
       58.42         6.02         7.69         9.27        47.34         3.45 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7399 
        3.09        29.23        26.17        12.89        30.58         5.95 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       17.16       108.95       107.51        94.88        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 
       17.92        60.49        21.07        62.43         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6962 
       26.43        11.24       126.08         6.08         7.13         4.14 
TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7247 TCGA-CV-7254 
       64.83         7.99        12.92        71.21        18.97        47.97 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7425 TCGA-CV-7427 
       35.54        17.85        22.85        25.08        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A463 TCGA-CV-A6JD 
       54.94         3.52         7.17       169.38         0.76         5.98 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-D6-6516 TCGA-D6-A6EM TCGA-DQ-5625 
       29.79         6.48        23.47        25.41         7.63        35.54 
TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7229 
       20.25        18.94        11.80        13.38        15.06         0.07 
TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61E 
        1.22        12.66         4.27         6.90        34.75        19.33 
TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67A 
       13.55         5.29        11.54        12.43        14.37        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T5 
       12.62         3.68        16.08        36.82        75.55        29.00 
TCGA-P3-A6T7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX 
       16.01        11.57        12.10         8.32        12.72         6.87 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A7JT TCGA-UF-A7JV 
       13.55        13.68        32.65         2.96 

$`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 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        17.10        53.79 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       15.52        21.17        14.83         3.55        12.62         7.76 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
       29.42        28.11        20.45        30.18        27.95         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP 
        5.69        14.47         7.82         2.27        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15        94.62         9.14         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       22.42        36.72        33.70        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM 
       38.40        71.05        20.52        25.71        10.55        12.92 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        26.27        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       37.84        12.89        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 
       13.05        34.36         8.58        12.39        35.54        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6012 
       11.54        11.84        11.57        12.49        56.94        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       20.65        19.53        20.68        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 
        9.24        11.08        10.45        20.09        12.95         3.68 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       14.10        11.74        35.01        14.56        12.85        29.72 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
        7.40        17.29        15.91        11.44         5.75        12.07 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         9.80         6.18        48.20        39.68 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        2.93        54.58        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       41.19        32.38        32.88        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        51.29        33.11        16.73        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       64.11        23.24        29.36        25.81        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.34        11.64        12.46        11.51 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 
       15.75        47.18        39.16        40.93        35.84        24.95 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 
        0.99        31.96         9.17        34.06        19.92        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
       29.85        29.52         7.10         5.13        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       48.39       139.43       129.21        76.24        19.20        17.95 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       80.12        13.35        23.05        86.83        48.59         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        54.74         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
        5.46        20.52        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 
       30.08        53.95        65.82        10.98         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
        2.50       126.15       111.16        18.81        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 
        5.26         1.84        52.31        21.80        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 
       17.13        95.34         4.96        11.87         2.10        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       18.41        57.47       210.97        89.33         9.67         0.46 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7430 
       25.94         0.07        34.09       100.57        14.89        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76       153.86        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        24.99       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JT 
       56.61         7.07        15.25        35.34         6.38        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        21.24        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.55        18.84        34.36        13.25         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       17.72        12.36        15.88        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        11.11        58.45        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       14.04        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       12.10        10.65        11.18        37.18        16.11        21.63 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
        3.02        19.23        12.62         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 
       12.43        15.16        13.61        21.11         6.77         0.16 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       25.74        14.66        22.03        22.85         0.36        13.84 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I 
        3.65        15.95        12.76        14.50        11.84         0.07 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51X 
       14.47        11.84        13.35        18.15        10.75         7.96 
TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        1.84        15.42         7.13        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 
       56.75        51.25        10.85        47.01        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        2.04        12.99        13.15        21.07        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP 
       12.43         6.51         5.62         9.73         9.76        16.96 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
       15.91         7.10        32.45        13.25        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        17.03        20.55        14.56 

  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                       169.38                        210.97 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                        18.43                         18.02 
[1] "0.1 - 169.4 (18.4)" "0.1 - 211.0 (18.0)"
[1] "hr=" "1.2"
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 12(9P24.1) MUTATED         8       20        16        63         4
  AMP PEAK 12(9P24.1) WILD-TYPE      19       57        61       189         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                            19
  STAGE II                           20                            57
  STAGE III                          16                            61
  STAGE IVA                          63                           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 12(9P24.1) MUTATED      10  30  28  43
  AMP PEAK 12(9P24.1) WILD-TYPE    40 103  71 129
D12V4, multiclass
       clus
vv      AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  T0+T1                          10                            40
  T2                             30                           103
  T3                             28                            71
  T4                             43                           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 12(9P24.1) MUTATED    37  16  43   4
  AMP PEAK 12(9P24.1) WILD-TYPE 141  50 122   4
D12V5, multiclass
    clus
vv   AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  N0                          37                           141
  N1                          16                            50
  N2                          43                           122
  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"
D12V6, binary
                               cls
clus                              0   1
  AMP PEAK 12(9P24.1) MUTATED    39   0
  AMP PEAK 12(9P24.1) WILD-TYPE 144   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     39    0
  AMP PEAK 12(9P24.1) WILD-TYPE  144    1
   clus
vv  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  0                          39                           144
  1                           0                             1
[1] 2 2
[1] FALSE
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(9P24.1) MUTATED    51  73
  AMP PEAK 12(9P24.1) WILD-TYPE  88 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     51   73
  AMP PEAK 12(9P24.1) WILD-TYPE   88  304
        clus
vv       AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  FEMALE                          51                            88
  MALE                            73                           304
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(9P24.1) MUTATED                                     123
  AMP PEAK 12(9P24.1) WILD-TYPE                                   382
                               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                                               123
  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                                                 382
  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    15 109
  AMP PEAK 12(9P24.1) WILD-TYPE  66 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED     15  109
  AMP PEAK 12(9P24.1) WILD-TYPE   66  326
     clus
vv    AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  NO                           15                            66
  YES                         109                           326
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, continuous
D12V12, 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   107
  AMP PEAK 12(9P24.1) WILD-TYPE                        34   334
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    107
                                  clus
vv                                 AMP PEAK 12(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   34
  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"
D12V14, binary
                               cls
clus                              0   1
  AMP PEAK 12(9P24.1) MUTATED     9 111
  AMP PEAK 12(9P24.1) WILD-TYPE  16 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      9  111
  AMP PEAK 12(9P24.1) WILD-TYPE   16  343
                        clus
vv                       AMP PEAK 12(9P24.1) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         111
                        clus
vv                       AMP PEAK 12(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           343
[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  56
  AMP PEAK 13(9P23) WILD-TYPE 247 144
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                        122                         391 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                         56                         144 
$`AMP PEAK 13(9P23) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DI 
       23.84        20.48        57.44         4.01        11.54        11.05 
TCGA-BA-A6DJ TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-5355 
       13.38        27.19         8.81         6.28        38.04        33.11 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 
       12.39         8.32        11.57         8.52        20.71        30.67 
TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49C 
       19.07        36.49        24.16        17.42        17.59        21.21 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
        4.41         2.70         7.69        21.50        46.75        45.80 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 
       34.75        56.58        38.76        70.13        43.04        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-6493 
       11.61        32.81        58.42         6.02         7.69         9.27 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7399 
        3.45         3.09        26.17        12.89        30.58         5.95 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      139.43        17.16       108.95       107.51        94.88        76.50 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 
       17.92        60.49        21.07        62.43         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7089 
       26.43        11.24         6.08         7.13         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7243 TCGA-CV-7254 
      126.15        12.66         7.99         1.84        31.36        47.97 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       35.54        17.85        25.08        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JO 
        3.52         7.17       169.38         0.76         5.98         6.48 
TCGA-CV-A6JZ TCGA-D6-6516 TCGA-D6-A6EM TCGA-DQ-5625 TCGA-DQ-7589 TCGA-F7-A50G 
       23.47        25.41         7.63        35.54        18.90        20.25 
TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-8634 
       18.94        11.80        13.38        15.06         1.22        12.66 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61K 
        4.27         6.90        34.75        19.33        13.55         5.29 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW 
       14.37        30.05        12.62         3.68        16.08        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IJ 
       75.55        29.00        16.01        17.65         7.30        12.72 
TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-TN-A7HI TCGA-TN-A7HL 
       11.57         8.32        12.72         6.87        13.55        13.68 
TCGA-UF-A7JT TCGA-UF-A7JV 
       32.65         2.96 

$`AMP PEAK 13(9P23) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        17.10        53.79 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       15.52        21.17        14.83         3.55        12.62         7.76 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
       29.42        28.11        20.45        30.18        27.95         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP 
        5.69        14.47         7.82         2.27        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15        94.62         9.14         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       22.42        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY 
       24.66        38.40        71.05        20.52        25.71        10.55 
TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
       12.92        12.69        26.27        23.70         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       37.84        12.89        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       13.05        34.36         8.58        35.54        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
       11.84        12.49        22.45        56.94        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       19.53        20.68        14.20         6.74         9.07         9.24 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6997 
       11.08        10.45        20.09        12.95         3.68        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        35.01        14.56        12.85        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY 
       17.29        15.91        11.44         5.75        12.07        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5326 
        7.33         9.80         6.18        48.20        39.68         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 
       32.38        32.88        13.25         4.24        14.99        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 
       33.11        16.73        41.88        28.83        64.11        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        25.81        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
       11.77        54.67        37.87        26.27        50.01        39.52 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       34.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
       11.34        11.64        12.46        11.51        15.75        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 
       39.16        47.34        40.93        35.84        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 
        0.99        31.96         9.17        34.06        19.92        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
       29.85        29.52         7.10         5.13        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5443 
       48.39       129.21        76.24        19.20        17.95        91.53 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       80.12        13.35        23.05        86.83        48.59         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        54.74         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
        5.46        20.52       126.08        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 
       15.09        30.08        53.95        65.82        10.98         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7100 TCGA-CV-7101 
       28.34         2.50       111.16        18.81         9.01         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        47.47        36.00        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 
       17.13        95.34         4.96        11.87         2.10        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       18.41        57.47       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       22.85        25.94         0.07        34.09       100.57        14.89 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       16.27        84.49        19.76       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       22.19        27.98        24.99       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1.05        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM 
       67.86        56.61         7.07        15.25        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
       29.79        22.03         3.62        21.24        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       10.42        10.42        10.55        18.84        34.36        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
       24.95        25.32        17.72        12.36        15.88        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
       13.94        12.10        12.79        11.11        58.45        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        14.04        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       12.13        12.10        10.65        11.18        37.18        16.11 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       21.63         3.02        19.23        12.62         0.46        17.85 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       20.25        12.43        15.16        13.61        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
        0.07         0.16        25.74        14.66        22.03        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        0.36        13.84         3.65        15.95        12.76        14.50 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
       11.84         0.07        14.47        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN 
       18.15        12.43        10.75         7.96         1.84        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        17.98        29.92        15.78        56.75        51.25 
TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 
       10.85        47.01        19.00        18.97         2.04        12.99 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
       13.15        21.07        11.74        16.70         9.34        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       14.79        12.43         6.51         5.62        12.10         9.73 
TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ 
        9.76        16.96        15.91         7.10        32.45        13.25 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ 
       16.11        13.94        20.75        22.36        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                       0.76                        0.07 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                     169.38                      210.97 
  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE 
                      17.62                       18.41 
[1] "0.8 - 169.4 (17.6)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.2"
D13V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 13(9P23) MUTATED         7       21        17        59         4
  AMP PEAK 13(9P23) WILD-TYPE      20       56        60       193         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                          20
  STAGE II                         21                          56
  STAGE III                        17                          60
  STAGE IVA                        59                         193
  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  32  27  40
  AMP PEAK 13(9P23) WILD-TYPE    41 101  72 132
D13V4, multiclass
       clus
vv      AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  T0+T1                         9                          41
  T2                           32                         101
  T3                           27                          72
  T4                           40                         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
  AMP PEAK 13(9P23) MUTATED    32  17  43   4
  AMP PEAK 13(9P23) WILD-TYPE 146  49 122   4
D13V5, multiclass
    clus
vv   AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  N0                        32                         146
  N1                        17                          49
  N2                        43                         122
  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"
D13V6, binary
                             cls
clus                            0   1
  AMP PEAK 13(9P23) MUTATED    39   0
  AMP PEAK 13(9P23) WILD-TYPE 144   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(9P23) MUTATED     39    0
  AMP PEAK 13(9P23) WILD-TYPE  144    1
   clus
vv  AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  0                        39                         144
  1                         0                           1
[1] 2 2
[1] FALSE
D13V7, binary
                             cls
clus                            0   1
  AMP PEAK 13(9P23) MUTATED    47  75
  AMP PEAK 13(9P23) WILD-TYPE  92 302
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(9P23) MUTATED     47   75
  AMP PEAK 13(9P23) WILD-TYPE   92  302
        clus
vv       AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  FEMALE                        47                          92
  MALE                          75                         302
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(9P23) MUTATED                                     121
  AMP PEAK 13(9P23) WILD-TYPE                                   384
                             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                                             121
  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                                               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"
D13V9, binary
                             cls
clus                            0   1
  AMP PEAK 13(9P23) MUTATED    16 106
  AMP PEAK 13(9P23) WILD-TYPE  65 329
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(9P23) MUTATED     16  106
  AMP PEAK 13(9P23) WILD-TYPE   65  329
     clus
vv    AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  NO                         16                          65
  YES                       106                         329
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, continuous
D13V12, 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   108
  AMP PEAK 13(9P23) WILD-TYPE                        36   333
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                9
  WHITE                                                  108
                                  clus
vv                                 AMP PEAK 13(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 36
  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"
D13V14, binary
                             cls
clus                            0   1
  AMP PEAK 13(9P23) MUTATED     8 110
  AMP PEAK 13(9P23) WILD-TYPE  17 344
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 13(9P23) MUTATED      8  110
  AMP PEAK 13(9P23) WILD-TYPE   17  344
                        clus
vv                       AMP PEAK 13(9P23) MUTATED AMP PEAK 13(9P23) WILD-TYPE
  HISPANIC OR LATINO                             8                          17
  NOT HISPANIC OR LATINO                       110                         344
[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    81  56
  AMP PEAK 14(9P13.3) WILD-TYPE 232 144
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          137                           376 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           56                           144 
$`AMP PEAK 14(9P13.3) MUTATED`
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DA 
       23.84        20.48        57.44        12.62         4.01        11.54 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4728 
       13.38        20.48         9.14        66.28        27.19        37.84 
TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6010 
       20.55        33.11        12.39         8.32         8.52        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6995 
       30.67        20.68        36.49        11.08        24.16         3.68 
TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V3 
       17.42        17.59         7.40         4.41         2.70         9.80 
TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 
        7.69        46.75        45.80        56.58        38.76        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-6467 TCGA-CR-6488 
       43.04        44.48        11.61        31.23        58.42        12.46 
TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       40.93         3.45         3.09        24.95        29.23        31.96 
TCGA-CR-7380 TCGA-CR-7390 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5431 
       19.92        29.82        30.58         5.95        35.41        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      129.21       108.95        17.95       107.51        94.88        76.50 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 
       80.12        17.92        13.35        60.49        21.07        62.43 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-6962 
        4.73        21.90        26.43        11.24         6.08         4.14 
TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7235 
       64.83        18.81         7.99        12.92        10.75        77.16 
TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 
       47.47        18.97        47.97         2.10        18.41        35.54 
TCGA-CV-7409 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-A45Q 
       17.85        56.48       156.49         3.52         7.17       169.38 
TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CX-7219 
        0.76        15.25         5.98         6.48        23.47        34.36 
TCGA-D6-6516 TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5629 TCGA-F7-8298 
       25.41         7.63        12.10        35.54        30.94        16.11 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8502 
       20.25         3.02        18.94        11.80        13.38        15.06 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 
        1.22        14.66        12.66         4.27         6.90        15.95 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
       11.54        14.37         7.96        30.05        12.62         3.68 
TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A8Z7 
       36.82        75.55        29.00        21.07         7.30         6.51 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ 
       11.57        12.10         8.32        12.72         6.87        15.91 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71D TCGA-UF-A7JT TCGA-WA-A7H4 
       13.55        13.25        41.16        32.65        14.56 

$`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 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        17.10        53.79 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF 
       15.52        21.17        14.83         3.55         7.76        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        30.18        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4217 
       14.47         7.82         2.27        11.05        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
       94.62         4.60         4.41        18.35        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        44.98        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       20.52        25.71        10.55        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        26.27        23.70        38.04         4.67        40.44 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.65        21.11        41.10        12.99 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       14.33        43.73        27.58        41.69        13.05        34.36 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        8.58        35.54        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       12.49        22.45        56.94        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6988 
       19.07        14.20         6.74         9.07         9.24        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       20.09        12.95        14.10        11.74        35.01        14.56 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       12.85        29.72        21.21        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V7 TCGA-CQ-5323 
        5.75        12.07        10.09         7.33         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 
       39.68        21.50         2.93        54.58        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       11.21         4.24        41.19        32.38        32.88        34.75 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       13.25         4.24        14.99        51.29        33.11        16.73 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.88        28.83        64.11        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       25.81        14.14        12.46        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       37.87        26.27        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64         7.69        11.51        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 
       39.16        47.34        35.84         0.99         9.17        34.06 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 
       30.02        31.10        29.85        29.52         7.10         5.13 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5443 
       29.95        48.39       139.43        76.24        19.20        91.53 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       23.05        86.83        48.59         7.07        43.23        54.74 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 
        2.50       126.15       111.16        12.66         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 
        1.84        52.31        21.80        71.21       130.88         4.73 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       36.00        31.36        26.20        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       11.87        36.13        57.47       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
      100.57        14.89        54.94        16.27        84.49        19.76 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        24.99 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        60.43        67.86        56.61         7.07 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34         6.38        29.79        22.03         3.62        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        15.88 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 
       14.30        13.94        12.79        11.11        58.45        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        37.18        21.63 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       19.23        12.62         0.46        17.85        20.25        12.43 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.16        13.61        21.11         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       25.74        22.03        22.85         0.36        13.84         3.65 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       34.75        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
        0.07        14.47         5.29        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       12.43        10.75         1.84        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        56.75        51.25        10.85 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 
       47.01        19.00        18.97         2.04        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       13.15        11.74        17.65        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J 
       18.64        14.79        12.43         5.62         9.73         9.76 
TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       16.96         7.10        32.45        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        43.36        42.02        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.16        49.22        21.86        16.11        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       22.36         2.96        17.03        20.55 

  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                         0.76                          0.07 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                       169.38                        210.97 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                        17.92                         18.25 
[1] "0.8 - 169.4 (17.9)" "0.1 - 211.0 (18.2)"
[1] "hr=" "1.1"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 14(9P13.3) MUTATED         8       26        16        73         5
  AMP PEAK 14(9P13.3) WILD-TYPE      19       51        61       179         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                            19
  STAGE II                           26                            51
  STAGE III                          16                            61
  STAGE IVA                          73                           179
  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  39  29  50
  AMP PEAK 14(9P13.3) WILD-TYPE    38  94  70 122
D14V4, multiclass
       clus
vv      AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  T0+T1                          12                            38
  T2                             39                            94
  T3                             29                            70
  T4                             50                           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 14(9P13.3) MUTATED    45  19  49   4
  AMP PEAK 14(9P13.3) WILD-TYPE 133  47 116   4
D14V5, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  N0                          45                           133
  N1                          19                            47
  N2                          49                           116
  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"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED    51   0
  AMP PEAK 14(9P13.3) WILD-TYPE 132   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     51    0
  AMP PEAK 14(9P13.3) WILD-TYPE  132    1
   clus
vv  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  0                          51                           132
  1                           0                             1
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED    45  93
  AMP PEAK 14(9P13.3) WILD-TYPE  94 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     45   93
  AMP PEAK 14(9P13.3) WILD-TYPE   94  284
        clus
vv       AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  FEMALE                          45                            94
  MALE                            93                           284
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P13.3) MUTATED                                     135
  AMP PEAK 14(9P13.3) WILD-TYPE                                   370
                               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                                               135
  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                                                 370
  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    21 117
  AMP PEAK 14(9P13.3) WILD-TYPE  60 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     21  117
  AMP PEAK 14(9P13.3) WILD-TYPE   60  318
     clus
vv    AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  NO                           21                            60
  YES                         117                           318
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, continuous
D14V12, 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   121
  AMP PEAK 14(9P13.3) WILD-TYPE                        34   320
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(9P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    121
                                  clus
vv                                 AMP PEAK 14(9P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   34
  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"
D14V14, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED    10 121
  AMP PEAK 14(9P13.3) WILD-TYPE  15 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     10  121
  AMP PEAK 14(9P13.3) WILD-TYPE   15  333
                        clus
vv                       AMP PEAK 14(9P13.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         121
                        clus
vv                       AMP PEAK 14(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           333
[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    95  78
  AMP PEAK 15(9Q34.3) WILD-TYPE 218 122
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                          173                           340 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                           78                           122 
$`AMP PEAK 15(9Q34.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
        9.30        37.28        26.50        17.10        23.84        20.48 
TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DJ 
       57.44        14.83         4.01        11.54         5.69        13.38 
TCGA-BB-4224 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4727 
        9.14        38.40        20.52        10.55        23.70        40.44 
TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 
       37.84        32.65        41.69        33.11        12.39         8.32 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6021 
       16.21        11.84        11.57        20.71        30.67         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 
       36.49        11.08        24.16         3.68        17.42        17.59 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 
       12.85        21.21         7.40        11.44         4.41         2.70 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5332 
        9.80         7.69        48.20        21.50        45.80        10.42 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
       32.88        34.75        13.25        38.76        70.13        43.04 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6491 
       44.48        11.61        32.81        58.42        16.90        11.51 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7379 
       39.16        40.93        35.84         3.45        29.23        34.06 
TCGA-CR-7380 TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 
       19.92        29.95       129.21       108.95        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 
      107.51        76.50        80.12        17.92        13.35        60.49 
TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6938 
        7.07        21.07        62.43         9.60        90.12         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7089 
       21.90        26.43        15.09         6.08         4.14        64.83 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 
        7.99         9.01        21.80        10.75        77.16         4.73 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       26.20        18.97        36.13        18.41        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7415 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
      210.97        22.85        34.09        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A45Z TCGA-CV-A461 
       16.27        84.49         7.17       169.38        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-CX-7082 
        0.76         7.07        15.25         5.98        23.47        10.42 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EP 
       34.36        25.41        23.05        25.32         7.63        13.94 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-7589 TCGA-F7-A61S TCGA-F7-A622 
       12.10        11.11        35.54        18.90        18.94        11.80 
TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       13.38        15.06         0.07         1.22        14.66        22.03 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-A61J TCGA-IQ-A61L TCGA-MT-A51W 
        4.27         3.65         6.90        14.47        11.54        14.37 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SW 
       30.05         1.84         3.68        17.98        15.78        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A6II 
       75.55        29.00        13.15        21.07         7.30         9.34 
TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ 
       12.43        11.57         8.32        12.72         6.87        15.91 
TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        7.10        13.55        42.02        44.65        62.27        17.95 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       49.22        21.86        22.36        32.65        17.03 

$`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 
        3.35        15.19        13.64         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
       57.93        53.79        15.52        21.17         3.55        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        7.76        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL 
        7.10        14.47         7.82         2.27        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       16.41         6.15        94.62         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       22.42        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        71.05        25.71        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 
        6.28        12.69        26.27        38.04         4.67        12.89 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       26.86        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
       43.73        27.58        13.05        34.36         8.58        35.54 
TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 
       11.54        12.49         8.52        22.45        56.94        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       20.65        19.53        20.68        19.07        14.20         6.74 
TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 
        9.24        10.45        20.09        12.95        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       35.01        14.56        29.72        17.29        15.91         5.75 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 
       12.07        10.09         7.33         6.18        39.68         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        46.75        45.99        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       32.38        56.58         4.24        14.99        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       16.73        41.88        28.83        64.11        23.24        29.36 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       25.81        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       54.67        37.87        26.27        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64         7.69        12.46        15.75         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       47.34         3.09        24.95         0.99        31.96         9.17 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
        7.10         5.13         5.95        35.41        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 
       17.16        76.24        94.88        91.53        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       48.59        43.23        54.74         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       20.52        11.24       126.08        19.79        12.03        42.38 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       30.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       28.34         2.50       126.15       111.16        18.81        12.66 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7183 
        5.26         1.84        52.31        12.92        71.21       130.88 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       47.47        36.00        31.36        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7411 TCGA-CV-7413 
       11.87        47.97         2.10        57.47        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 
        0.46        25.08        25.94         0.07       100.57        14.89 
TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       54.94        19.76       153.86        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        24.99       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JE 
       45.96         6.51        88.87        60.43        56.61        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        22.03         3.62        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 
       19.92        22.52        10.42        10.55        18.84        13.25 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6ES TCGA-DQ-5624 
       17.72        12.36        15.88        14.30        12.79        58.45 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 
       30.94        33.86        18.02        14.04        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V 
       16.11        21.63        20.25         3.02        19.23        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A6C4 
        0.46        17.85        20.25        12.43        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-8635 
       21.11         6.77         0.16        25.74        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        0.36        13.84        34.75        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61O 
       19.33        11.84        13.55         0.07         5.29        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67F 
       13.35        18.15        12.43        10.75         7.96        12.62 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
       15.42         7.13        16.08        29.92        56.75        51.25 
TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 
       10.85        47.01        19.00        18.97         2.04        12.99 
TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
       16.01        11.74        17.65        16.70        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       14.79         6.51         5.62        12.10         9.73         9.76 
TCGA-RS-A6TP TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       16.96        32.45        13.25        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JK 
        2.83        43.36        41.16        24.16        16.11        13.94 
TCGA-UF-A7JO TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75         2.96        20.55        14.56 

  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                       210.97                        180.16 
  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE 
                       17.980                        18.085 
[1] "0.1 - 211.0 (18.0)" "0.1 - 180.2 (18.1)"
[1] "hr=" "1.2"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 15(9Q34.3) MUTATED         7       24        22        97         7
  AMP PEAK 15(9Q34.3) WILD-TYPE      20       53        55       155         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                            20
  STAGE II                           24                            53
  STAGE III                          22                            55
  STAGE IVA                          97                           155
  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 36 37 75
  AMP PEAK 15(9Q34.3) WILD-TYPE    39 97 62 97
D15V4, multiclass
       clus
vv      AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  T0+T1                          11                            39
  T2                             36                            97
  T3                             37                            62
  T4                             75                            97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 15(9Q34.3) MUTATED    57  22  62   5
  AMP PEAK 15(9Q34.3) WILD-TYPE 121  44 103   3
D15V5, multiclass
    clus
vv   AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  N0                          57                           121
  N1                          22                            44
  N2                          62                           103
  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"
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.3) MUTATED    58   0
  AMP PEAK 15(9Q34.3) WILD-TYPE 125   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.3) MUTATED     58    0
  AMP PEAK 15(9Q34.3) WILD-TYPE  125    1
   clus
vv  AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  0                          58                           125
  1                           0                             1
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.3) MUTATED    48 126
  AMP PEAK 15(9Q34.3) WILD-TYPE  91 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.3) MUTATED     48  126
  AMP PEAK 15(9Q34.3) WILD-TYPE   91  251
        clus
vv       AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  FEMALE                          48                            91
  MALE                           126                           251
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(9Q34.3) MUTATED                                     171
  AMP PEAK 15(9Q34.3) WILD-TYPE                                   334
                               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                                               171
  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                                                 334
  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    25 149
  AMP PEAK 15(9Q34.3) WILD-TYPE  56 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.3) MUTATED     25  149
  AMP PEAK 15(9Q34.3) WILD-TYPE   56  286
     clus
vv    AMP PEAK 15(9Q34.3) MUTATED AMP PEAK 15(9Q34.3) WILD-TYPE
  NO                           25                            56
  YES                         149                           286
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, continuous
D15V12, 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                          18   150
  AMP PEAK 15(9Q34.3) WILD-TYPE                        27   291
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    150
                                  clus
vv                                 AMP PEAK 15(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      291
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                               cls
clus                              0   1
  AMP PEAK 15(9Q34.3) MUTATED    12 150
  AMP PEAK 15(9Q34.3) WILD-TYPE  13 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9Q34.3) MUTATED     12  150
  AMP PEAK 15(9Q34.3) WILD-TYPE   13  304
                        clus
vv                       AMP PEAK 15(9Q34.3) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         150
                        clus
vv                       AMP PEAK 15(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           304
[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    54  45
  AMP PEAK 16(11P13) WILD-TYPE 259 155
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          99                          414 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                          45                          155 
$`AMP PEAK 16(11P13) MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        9.30        23.84        15.52        12.62         4.01         7.76 
TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4225 
       27.95         5.69        11.05        20.48        16.41         4.60 
TCGA-BB-7861 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-4737 
       22.42        10.55         6.28        23.70        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-6018 TCGA-CN-6994 
       14.33        13.05        33.11         8.32        19.07        24.16 
TCGA-CN-6995 TCGA-CN-A63T TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5333 
        3.68         7.40        48.20         2.93        46.75        11.21 
TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6225 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        32.88        13.25        70.13        33.11        41.88 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 
       44.48        11.61        23.24        25.81        14.14        11.64 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7380 TCGA-CR-7382 
       12.46        39.16        47.34         3.45        19.92        26.17 
TCGA-CR-7392 TCGA-CV-5430 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 
       31.10       139.43       107.51        13.35        60.49        54.74 
TCGA-CV-6433 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6950 TCGA-CV-6959 
       21.07        20.52        21.90       126.08        15.09         8.42 
TCGA-CV-6962 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7409 
        4.14        18.97        47.97         2.10        36.13        17.85 
TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-7219 
      100.57         3.52        60.43        21.24        23.47        34.36 
TCGA-D6-6517 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5624 
        9.60        18.67        25.32        13.94        11.11        58.45 
TCGA-DQ-7588 TCGA-F7-A50J TCGA-F7-A622 TCGA-IQ-7630 TCGA-IQ-A61K TCGA-IQ-A61L 
       14.04        19.23        11.80        15.95         5.29        11.54 
TCGA-MT-A67D TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T2 
        1.84        15.78        56.75        10.85        36.82        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6VB 
       18.97         2.04        12.99         7.30        12.72        14.79 
TCGA-T2-A6WX TCGA-UF-A7JV TCGA-WA-A7GZ 
        6.87         2.96        20.55 

$`AMP PEAK 16(11P13) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        20.48        53.79 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG 
       57.44        21.17        14.83         3.55        29.42        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        30.18        11.54         7.10        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
        2.27        13.38         6.15        94.62         9.14         4.41 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.35        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        25.71        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 
       12.92         8.81        12.69        26.27        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 
       41.10        43.73        27.58        41.69        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       12.39        35.54        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       20.68        20.65        19.53        20.68        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        9.07         9.24        36.49        11.08        10.45        20.09 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       12.95        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       17.59        12.85        29.72        21.21        17.29        15.91 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       11.44         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        7.33         9.80         7.69         6.18        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       54.58        45.80        45.99        10.42        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       34.75        56.58         4.24        14.99        38.76        51.29 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       16.73        43.04        28.83        64.11        29.36        32.81 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 
        7.69        11.51        15.75         9.27        47.18        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        9.17        34.06        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        29.82        30.02        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 
       94.88        76.50        91.53        80.12        17.92        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 
       86.83        48.59         7.07        43.23        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6940 
       90.12         2.14         9.70         5.46         4.73        26.43 
TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
       11.24        19.79        12.03        42.38        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 
       53.95        65.82        10.98         7.13        28.34         2.50 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       126.15       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       36.00        31.36        26.20        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
       11.87        18.41        57.47        35.54       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
        9.67         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
       34.09        14.89        56.48       156.49        54.94        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        24.99       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        22.03         3.62 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
       19.92        22.52        10.42        10.42        10.55        18.84 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41        23.05         2.53        16.14        11.44 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       24.95        17.72        12.36        15.88         7.63        14.30 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       12.10        12.79        35.54        30.94        33.86        18.02 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       10.65        11.18        37.18        16.11        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
        3.02        18.94        12.62         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        34.75        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
       11.84        13.55         0.07        14.47        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        10.75        14.37         7.96        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         3.68        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T5 TCGA-P3-A6T7 
       29.92        51.25        47.01        19.00        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        11.74        17.65        16.70         9.34 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       18.64        12.43         6.51         5.62        11.57        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ 
        9.73         9.76         8.32        12.72        16.96        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
       54.67         2.83        43.36        41.16        42.02        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       62.27        17.95        24.16        49.22        21.86        16.11 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 
       13.94        20.75        22.36        32.65        17.03        14.56 

  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                        1.84                         0.07 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                      139.43                       210.97 
  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE 
                       16.41                        18.25 
[1] "1.8 - 139.4 (16.4)" "0.1 - 211.0 (18.2)"
[1] "hr=" "1.3"
D16V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 16(11P13) MUTATED         4       19        17        42         5
  AMP PEAK 16(11P13) WILD-TYPE      23       58        60       210         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                           23
  STAGE II                          19                           58
  STAGE III                         17                           60
  STAGE IVA                         42                          210
  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  28  20  35
  AMP PEAK 16(11P13) WILD-TYPE    42 105  79 137
D16V4, multiclass
       clus
vv      AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  T0+T1                          8                           42
  T2                            28                          105
  T3                            20                           79
  T4                            35                          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 16(11P13) MUTATED    39  10  28   4
  AMP PEAK 16(11P13) WILD-TYPE 139  56 137   4
D16V5, multiclass
    clus
vv   AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  N0                         39                          139
  N1                         10                           56
  N2                         28                          137
  N3                          4                            4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                              cls
clus                             0   1
  AMP PEAK 16(11P13) MUTATED    39   0
  AMP PEAK 16(11P13) WILD-TYPE 144   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED     39    0
  AMP PEAK 16(11P13) WILD-TYPE  144    1
   clus
vv  AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  0                         39                          144
  1                          0                            1
[1] 2 2
[1] FALSE
D16V7, binary
                              cls
clus                             0   1
  AMP PEAK 16(11P13) MUTATED    24  75
  AMP PEAK 16(11P13) WILD-TYPE 115 302
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED     24   75
  AMP PEAK 16(11P13) WILD-TYPE  115  302
        clus
vv       AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  FEMALE                         24                          115
  MALE                           75                          302
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(11P13) MUTATED                                      98
  AMP PEAK 16(11P13) WILD-TYPE                                   407
                              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                                               98
  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                                                407
  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  83
  AMP PEAK 16(11P13) WILD-TYPE  65 352
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED     16   83
  AMP PEAK 16(11P13) WILD-TYPE   65  352
     clus
vv    AMP PEAK 16(11P13) MUTATED AMP PEAK 16(11P13) WILD-TYPE
  NO                          16                           65
  YES                         83                          352
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, continuous
D16V12, 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    81
  AMP PEAK 16(11P13) WILD-TYPE                        35   360
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(11P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                    81
                                  clus
vv                                 AMP PEAK 16(11P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  35
  WHITE                                                     360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                              cls
clus                             0   1
  AMP PEAK 16(11P13) MUTATED     7  86
  AMP PEAK 16(11P13) WILD-TYPE  18 368
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(11P13) MUTATED      7   86
  AMP PEAK 16(11P13) WILD-TYPE   18  368
                        clus
vv                       AMP PEAK 16(11P13) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                         86
                        clus
vv                       AMP PEAK 16(11P13) WILD-TYPE
  HISPANIC OR LATINO                               18
  NOT HISPANIC OR LATINO                          368
[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   128  95
  AMP PEAK 17(11Q13.3) WILD-TYPE 185 105
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                           223                            290 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                            95                            105 
$`AMP PEAK 17(11Q13.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
       17.10        23.84        53.79        15.52        14.83         3.55 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DG 
       12.62         7.76        30.18        11.54         5.69         2.27 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 
       20.48        16.41         6.15         4.60         4.41        22.42 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A6UO TCGA-C9-A47Z 
       66.28        24.66        71.05        25.71         8.81         6.28 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 
       23.70        40.44        37.84        32.65        41.10        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5364 
       14.33        43.73        13.05        33.11         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       11.54        11.84        11.57         8.52        22.45        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6989 
       30.67        20.68        20.65        19.07         6.74        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A 
       12.95        24.16         3.68        14.10        14.56        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5326 
       29.72        21.21        17.29         6.18        48.20         2.93 
TCGA-CQ-5329 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6225 TCGA-CQ-6227 
       46.75        11.21         4.24        32.88        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
       14.99        38.76        70.13        33.11        16.73        41.88 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        11.61        29.36        32.81        25.81        14.14 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6488 
       11.77        54.67        18.54        16.90         6.02        12.46 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
       11.51         9.27        39.16        47.34        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 
        3.09        24.95         9.17        34.06        19.92        17.13 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5440 
       27.06        29.82         5.95       139.43        17.16       107.51 
TCGA-CV-5441 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       94.88        13.35        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       43.23        54.74        90.12         9.70         5.46        20.52 
TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6956 TCGA-CV-6959 
       26.43        12.03        15.09        30.08         7.13         8.42 
TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7178 
       28.34       111.16        18.81        12.66         1.84        71.21 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 
       77.16        31.36        18.97         2.10        36.13        35.54 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.08        25.94        34.09       100.57 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U 
       84.49        19.76       153.86        22.19       180.16        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A460 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       45.96         6.51        60.43        35.34         6.38        29.79 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
       21.24        23.47        10.42        18.84        34.36        25.41 
TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
        9.60        16.14        11.44        18.67        24.95        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 
       12.36        13.94        12.79        35.54        18.02        14.04 
TCGA-DQ-7589 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V 
       18.90        37.18        16.11         3.02        19.23        12.62 
TCGA-F7-A622 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-IQ-7630 TCGA-IQ-7631 
       11.80        15.06         0.07         0.16        15.95        12.76 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66T 
       11.84        13.55        14.47         5.29        11.54        18.15 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       10.75        14.37         7.96         1.84        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 
       56.75        47.01        18.97         2.04        29.00        16.01 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J 
        7.30        16.70        12.72        11.57        12.10         9.76 
TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
        8.32        15.91        43.59        54.67        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JS 
       42.02        62.27        17.95        24.16        16.11        22.36 
TCGA-UF-A7JV 
        2.96 

$`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 
        3.35        23.74        42.35        57.93        20.48        57.44 
TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
       21.17         4.01        29.42        28.11        20.45        27.95 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4223 
        7.10        14.47         7.82        11.05        13.38        94.62 
TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        9.14        18.35        36.72        33.70        50.20        44.98 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A480 
       38.40        20.52        10.55        27.19        12.92        12.69 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 
       26.27        38.04         4.67        12.89        26.86        21.11 
TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       12.99        27.58        41.69        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       35.54        12.49        56.94        19.53        20.68        14.20 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 
        9.07         9.24        36.49        11.08        10.45        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       11.74        35.01        17.59         7.40        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 
        9.80         7.69        39.68        21.50        54.58        45.80 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       45.99        10.42        41.19        32.38        34.75        56.58 
TCGA-CQ-7064 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CH 
       51.29        43.04        28.83        64.11        23.24        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       31.23        84.23        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       39.52        34.52        36.99        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7373 
       11.64         7.69        15.75        47.18        40.93        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
        0.99        31.96        26.17        32.78        47.01        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
        5.13        35.41        29.95        48.39       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       76.24        19.20        17.95        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       17.92        23.05        21.07        62.43         9.60         2.14 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        4.73        21.90        11.24       126.08        19.79        42.38 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-6962 
        6.08        53.95        65.82        10.98         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 
       64.83       126.15         7.99         9.01         5.26        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       12.92        21.80        10.75       130.88         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       36.00        26.20        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       47.97        18.41        57.47        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
        9.67         0.07        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O 
        3.52        16.27         7.17        16.64         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z 
       24.99       169.38       159.65         1.05        88.87        48.20 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        6.48        22.03         3.62        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-8569 TCGA-D6-A6EK 
       10.55        13.25        23.05         2.53        25.32        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
        7.63        14.30        12.10        11.11        58.45        30.94 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       33.86        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61W 
       10.65        11.18        21.63        20.25        18.94         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
       17.85        20.25        12.43        13.38        15.16        13.61 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       21.11         6.77        25.74         1.22        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61O 
        6.90        34.75        14.50        19.33         0.07        11.84 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       13.35        12.43        30.05        12.62         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
        7.13        16.08        29.92        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       19.00        75.55        12.99        13.15        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       17.65         9.34        18.64        14.79        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        5.62         9.73        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A7J9 
       32.45        13.55        13.25        13.68         2.83        44.65 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW 
       49.22        21.86        13.94        20.75        32.65        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE 
                         17.98                          18.38 
[1] "0.1 - 180.2 (18.0)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.2"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 17(11Q13.3) MUTATED        15       30        32       115         7
  AMP PEAK 17(11Q13.3) WILD-TYPE      12       47        45       137         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                             12
  STAGE II                            30                             47
  STAGE III                           32                             45
  STAGE IVA                          115                            137
  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 53 46 82
  AMP PEAK 17(11Q13.3) WILD-TYPE    29 80 53 90
D17V4, multiclass
       clus
vv      AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  T0+T1                           21                             29
  T2                              53                             80
  T3                              46                             53
  T4                              82                             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 17(11Q13.3) MUTATED    77  25  85   4
  AMP PEAK 17(11Q13.3) WILD-TYPE 101  41  80   4
D17V5, multiclass
    clus
vv   AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  N0                           77                            101
  N1                           25                             41
  N2                           85                             80
  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"
D17V6, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    81   0
  AMP PEAK 17(11Q13.3) WILD-TYPE 102   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     81    0
  AMP PEAK 17(11Q13.3) WILD-TYPE  102    1
   clus
vv  AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  0                           81                            102
  1                            0                              1
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    56 169
  AMP PEAK 17(11Q13.3) WILD-TYPE  83 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     56  169
  AMP PEAK 17(11Q13.3) WILD-TYPE   83  208
        clus
vv       AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  FEMALE                           56                             83
  MALE                            169                            208
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(11Q13.3) MUTATED                                     223
  AMP PEAK 17(11Q13.3) WILD-TYPE                                   282
                                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                                                223
  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                                                  282
  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    42 183
  AMP PEAK 17(11Q13.3) WILD-TYPE  39 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     42  183
  AMP PEAK 17(11Q13.3) WILD-TYPE   39  252
     clus
vv    AMP PEAK 17(11Q13.3) MUTATED AMP PEAK 17(11Q13.3) WILD-TYPE
  NO                            42                             39
  YES                          183                            252
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, continuous
D17V12, 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   190
  AMP PEAK 17(11Q13.3) WILD-TYPE                        22   251
D17V13, multiclass
                                  clus
vv                                 AMP PEAK 17(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     190
                                  clus
vv                                 AMP PEAK 17(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    22
  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"
D17V14, binary
                                cls
clus                               0   1
  AMP PEAK 17(11Q13.3) MUTATED    10 197
  AMP PEAK 17(11Q13.3) WILD-TYPE  15 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(11Q13.3) MUTATED     10  197
  AMP PEAK 17(11Q13.3) WILD-TYPE   15  257
                        clus
vv                       AMP PEAK 17(11Q13.3) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          197
                        clus
vv                       AMP PEAK 17(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            257
[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   101  62
  AMP PEAK 18(12P13.33) WILD-TYPE 212 138
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                            163                             350 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                             62                             138 
$`AMP PEAK 18(12P13.33) MUTATED`
TCGA-4P-AA8J TCGA-BA-4077 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-6873 
        3.35        37.28        17.10        57.44         3.55         4.01 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       29.42        28.11        20.45        11.05        20.48        16.41 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-A5HY 
       94.62         9.14         4.60        36.72        66.28        10.55 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 
        6.28        38.04         4.67        37.84        12.89        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6012 
       14.33        43.73        12.39         8.32        11.84        20.68 
TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
       20.65        19.07        36.49        11.08        10.45        20.09 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       24.16         3.68        35.01        12.85        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6221 
       17.29         7.69        46.75        10.42        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-5247 
       34.75        56.58        16.73        25.81        84.23        11.77 
TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 
       58.42         7.69        12.46        47.18        39.16        24.95 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
        9.17        34.06        17.13        29.82         7.10         5.13 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 
        5.95       139.43        17.16       129.21       108.95       107.51 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6940 
       86.83         7.07        54.74        90.12        20.52        26.43 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7091 
       11.24        12.03        30.08         8.42         4.14       111.16 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7242 TCGA-CV-7243 
        1.84        52.31        21.80        71.21        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
       26.20        18.97        17.13        47.97        36.13        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
       35.54        17.85        25.08        25.94         0.07        34.09 
TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R 
       16.27         7.17       153.86        16.64        22.19       180.16 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JM TCGA-CX-7086 
       35.47        45.96        48.20        60.43         6.38        18.84 
TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6823 TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q 
       34.36        13.25        23.05        13.94        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        30.94        14.04        18.90        20.45         9.83 
TCGA-F7-7848 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 TCGA-HD-7753 
       37.18        19.23        18.94        12.43        13.38         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A51W 
       25.74         1.22        22.03         3.65        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q6 
        7.96        30.05         1.84         3.68        17.98        15.78 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6VB 
       75.55        13.15        21.07        17.65         7.30        14.79 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71B 
       11.57        12.10        12.72        13.55         2.83        43.36 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       42.02        44.65        17.95        24.16        49.22        21.86 
TCGA-UF-A7JK 
       13.94 

$`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 
       15.19         9.30        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
       42.35        57.93        23.84        20.48        53.79        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4II TCGA-BA-A6D8 
       21.17        14.83        12.62         7.76        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
       13.38         6.15         4.41        18.35        22.42        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        44.98        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       25.71        27.19        12.92         8.81        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       23.70        40.44        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       12.99        27.58        41.69        13.05        33.11        34.36 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 
        8.58        35.54        16.21        11.54        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 
        8.52        22.45        56.94        20.71        30.67        19.53 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 
       20.68        14.20         6.74         9.07         9.24        12.95 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C 
       17.42        14.10        11.74        14.56        17.59        21.21 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         9.80         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50         2.93        54.58        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        4.24        41.19        13.25         4.24        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       70.13        51.29        33.11        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       64.11        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       14.14        12.46        31.23        54.67        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 
        6.02        11.90        10.22        11.34        11.64        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       15.75         9.27        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7380 TCGA-CR-7382 
        3.09        29.23         0.99        31.96        19.92        26.17 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       29.85        29.52        30.58        35.41        29.95        48.39 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       76.24        19.20        17.95        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 
       80.12        17.92        13.35        23.05        48.59        60.49 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
       43.23        21.07        62.43         9.60         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        5.46         4.73        21.90       126.08        19.79        42.38 
TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
       28.34         2.50        64.83       126.15        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7183 
        7.99         9.01         5.26        12.92        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       77.16         4.73        47.47        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
        2.10        18.41       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       22.85       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
        3.52        84.49        19.76         6.38        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 
      169.38       159.65         1.05         6.51        88.87        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        22.03         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 
       19.92        22.52        10.42        10.42        10.55        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       25.32        17.72        12.36        15.88         7.63        14.30 
TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7593 
       12.10        35.54        33.86        18.02        25.48        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        11.18        16.11        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
        3.02        12.62         0.46        17.85        11.80        20.25 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11         6.77         0.07 
TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       14.66        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MT-A7BN 
       11.84        13.35        12.43        10.75        12.62        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        29.92        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        19.00        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       12.99        16.01        11.74        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J 
       18.64        12.43         6.51         5.62         9.73         9.76 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        16.96         6.87        15.91         7.10        32.45 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JA 
       13.25        13.68        43.59        54.67        41.16        62.27 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       16.11        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                         180.16                          210.97 
  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE 
                         19.230                          17.225 
[1] "0.1 - 180.2 (19.2)" "0.1 - 211.0 (17.2)"
[1] "hr=" "1.1"
D18V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 18(12P13.33) MUTATED         8       22        25        86
  AMP PEAK 18(12P13.33) WILD-TYPE      19       55        52       166
                                 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                              19
  STAGE II                             22                              55
  STAGE III                            25                              52
  STAGE IVA                            86                             166
  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      16  42  32  59
  AMP PEAK 18(12P13.33) WILD-TYPE    34  91  67 113
D18V4, multiclass
       clus
vv      AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  T0+T1                            16                              34
  T2                               42                              91
  T3                               32                              67
  T4                               59                             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
  AMP PEAK 18(12P13.33) MUTATED    56  19  59   4
  AMP PEAK 18(12P13.33) WILD-TYPE 122  47 106   4
D18V5, multiclass
    clus
vv   AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  N0                            56                             122
  N1                            19                              47
  N2                            59                             106
  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"
D18V6, binary
                                 cls
clus                                0   1
  AMP PEAK 18(12P13.33) MUTATED    55   0
  AMP PEAK 18(12P13.33) WILD-TYPE 128   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED     55    0
  AMP PEAK 18(12P13.33) WILD-TYPE  128    1
   clus
vv  AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  0                            55                             128
  1                             0                               1
[1] 2 2
[1] FALSE
D18V7, binary
                                 cls
clus                                0   1
  AMP PEAK 18(12P13.33) MUTATED    35 129
  AMP PEAK 18(12P13.33) WILD-TYPE 104 248
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED     35  129
  AMP PEAK 18(12P13.33) WILD-TYPE  104  248
        clus
vv       AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  FEMALE                            35                             104
  MALE                             129                             248
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(12P13.33) MUTATED                                     161
  AMP PEAK 18(12P13.33) WILD-TYPE                                   344
                                 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                                                 161
  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                                                   344
  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    25 139
  AMP PEAK 18(12P13.33) WILD-TYPE  56 296
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED     25  139
  AMP PEAK 18(12P13.33) WILD-TYPE   56  296
     clus
vv    AMP PEAK 18(12P13.33) MUTATED AMP PEAK 18(12P13.33) WILD-TYPE
  NO                             25                              56
  YES                           139                             296
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, continuous
D18V12, 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   140
  AMP PEAK 18(12P13.33) WILD-TYPE                        28   301
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      140
                                  clus
vv                                 AMP PEAK 18(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     28
  WHITE                                                        301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                                 cls
clus                                0   1
  AMP PEAK 18(12P13.33) MUTATED     6 146
  AMP PEAK 18(12P13.33) WILD-TYPE  19 308
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(12P13.33) MUTATED      6  146
  AMP PEAK 18(12P13.33) WILD-TYPE   19  308
                        clus
vv                       AMP PEAK 18(12P13.33) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           146
                        clus
vv                       AMP PEAK 18(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                  19
  NOT HISPANIC OR LATINO                             308
[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    63  37
  AMP PEAK 19(12Q15) WILD-TYPE 250 163
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         100                          413 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                          37                          163 
$`AMP PEAK 19(12Q15) MUTATED`
TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BB-4223 
       57.44        14.83         3.55        27.95        20.48        94.62 
TCGA-BB-4225 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 
        4.60        66.28        38.40        10.55         6.28        38.04 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-6010 
       40.44        37.84        20.55        43.73        34.36        20.71 
TCGA-CN-6012 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 
       20.68        36.49        11.08        10.45        20.09         3.68 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A6V6 TCGA-CQ-6220 
       17.59        12.85        29.72         7.40         7.69        32.38 
TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 
       56.58        16.73        25.81        11.77        58.42         6.02 
TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5434 
       39.16        34.06        17.13        29.82       139.43       108.95 
TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6959 TCGA-CV-7091 TCGA-CV-7101 
        9.70        26.43        42.38         8.42       111.16         5.26 
TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        1.84        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7428 TCGA-CV-7430 
       35.54        25.08         0.07        34.09        54.94        16.27 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45X TCGA-CV-A45Y 
       16.64         6.38        22.19       180.16         6.51        88.87 
TCGA-CV-A45Z TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4ZB 
       48.20        13.25        25.41        23.05        11.44        12.36 
TCGA-D6-A74Q TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A50J 
       11.11        14.04        18.90         9.83        12.10        19.23 
TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 TCGA-HD-7753 TCGA-HD-A6HZ TCGA-KU-A66T 
       18.94        12.43        13.38         0.16         3.65        18.15 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6T4 TCGA-QK-A6IF 
       14.37        30.05         1.84         3.68         2.04        17.65 
TCGA-QK-A6VB TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-UF-A71A 
       14.79        12.10        12.72         7.10        13.55         2.83 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JH TCGA-UF-A7JO 
       42.02        44.65        21.86        20.75 

$`AMP PEAK 19(12Q15) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       20.48        53.79        15.52        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
        7.76        29.42        28.11        20.45        30.18        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
       13.38        16.41         6.15         9.14         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       22.42        36.72        33.70        50.20        44.98        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        25.71        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
       12.69        26.27        23.70         4.67        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 
       32.65        21.11        41.10        12.99        14.33        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       41.69        13.05        33.11         8.58        12.39        35.54 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        8.52        22.45        56.94        30.67        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       20.68        19.07        14.20         6.74         9.07         9.24 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       12.95        24.16        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       14.56        21.21        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       41.19        32.88        34.75        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
       38.76        70.13        51.29        33.11        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       28.83        64.11        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
       32.81        14.14        12.46        31.23        84.23        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       37.87        26.27        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        11.51        15.75         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 
       29.23         0.99        31.96         9.17        19.92        26.17 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 
       35.41        29.95        48.39        17.16       129.21        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       60.49         7.07        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
        9.60        90.12         2.14         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
       21.90        11.24       126.08        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 
       28.34         2.50         4.14        64.83       126.15        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
       12.66         7.99         9.01        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
        0.46        22.85        25.94       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
      156.49         3.52        84.49        19.76         7.17       153.86 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        24.99       169.38       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       45.96        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       22.03         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 
       10.42        10.42        10.55        18.84        34.36         9.60 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        16.14        18.67        24.95        25.32        17.72 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       15.88         7.63        14.30        13.94        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       58.45        35.54        30.94        33.86        18.02        25.48 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       20.45        12.13        10.65        11.18        37.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       21.63        20.25         3.02        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       11.80        20.25        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        6.77         0.07        25.74         1.22        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       12.66        22.85         0.36        13.84         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        15.95        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67F TCGA-MT-A7BN 
       13.35        12.43        10.75         7.96        12.62        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        56.75 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       11.74         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.43         6.51         5.62        11.57         9.73         9.76 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HJ 
        8.32        16.96         6.87        15.91        32.45        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA 
       13.68        43.59        54.67        43.36        41.16        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS 
       17.95        24.16        49.22        16.11        13.94        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                      180.16                       210.97 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                       18.92                        17.95 
[1] "0.1 - 180.2 (18.9)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.1"
D19V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 19(12Q15) MUTATED         9       14        14        49         2
  AMP PEAK 19(12Q15) WILD-TYPE      18       63        63       203        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                           18
  STAGE II                          14                           63
  STAGE III                         14                           63
  STAGE IVA                         49                          203
  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  26  16  35
  AMP PEAK 19(12Q15) WILD-TYPE    38 107  83 137
D19V4, multiclass
       clus
vv      AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  T0+T1                         12                           38
  T2                            26                          107
  T3                            16                           83
  T4                            35                          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 19(12Q15) MUTATED    44   9  28   1
  AMP PEAK 19(12Q15) WILD-TYPE 134  57 137   7
D19V5, multiclass
    clus
vv   AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  N0                         44                          134
  N1                          9                           57
  N2                         28                          137
  N3                          1                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED    33   0
  AMP PEAK 19(12Q15) WILD-TYPE 150   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED     33    0
  AMP PEAK 19(12Q15) WILD-TYPE  150    1
   clus
vv  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  0                         33                          150
  1                          0                            1
[1] 2 2
[1] FALSE
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED    28  73
  AMP PEAK 19(12Q15) WILD-TYPE 111 304
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED     28   73
  AMP PEAK 19(12Q15) WILD-TYPE  111  304
        clus
vv       AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  FEMALE                         28                          111
  MALE                           73                          304
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(12Q15) MUTATED                                     100
  AMP PEAK 19(12Q15) WILD-TYPE                                   405
                              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                                              100
  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                                                405
  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  82
  AMP PEAK 19(12Q15) WILD-TYPE  62 353
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED     19   82
  AMP PEAK 19(12Q15) WILD-TYPE   62  353
     clus
vv    AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  NO                          19                           62
  YES                         82                          353
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, continuous
D19V12, 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    86
  AMP PEAK 19(12Q15) WILD-TYPE                        37   355
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    86
                                  clus
vv                                 AMP PEAK 19(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  37
  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"
D19V14, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED     4  87
  AMP PEAK 19(12Q15) WILD-TYPE  21 367
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED      4   87
  AMP PEAK 19(12Q15) WILD-TYPE   21  367
                        clus
vv                       AMP PEAK 19(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         87
                        clus
vv                       AMP PEAK 19(12Q15) WILD-TYPE
  HISPANIC OR LATINO                               21
  NOT HISPANIC OR LATINO                          367
[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    54  50
  AMP PEAK 20(13Q22.1) WILD-TYPE 259 150
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                           104                            409 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                            50                            150 
$`AMP PEAK 20(13Q22.1) MUTATED`
TCGA-BA-4075 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BB-4224 TCGA-BB-4225 
        9.30        14.83         3.55        29.42         9.14         4.60 
TCGA-BB-4227 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4737 
        4.41         4.67        37.84        12.89        12.99        20.55 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6989 
       27.58        41.69        13.05         8.52        20.65        20.09 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.42        14.10        29.72        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-7065 TCGA-CQ-7072 
        5.75        32.38        13.25         4.24        33.11        64.11 
TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 
       12.46        11.77        34.52        11.64        12.46        39.16 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7380 
       47.34        35.84         3.45        24.95         0.99        19.92 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6441 
       29.82       139.43        17.16       107.51        54.74         9.60 
TCGA-CV-6933 TCGA-CV-6939 TCGA-CV-6956 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
       90.12        21.90         7.13       126.15        18.81        12.66 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7247 
        9.01         1.84        71.21        10.75        31.36        18.97 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7416 TCGA-CV-7423 
       17.13        11.87         2.10        36.13        25.08       100.57 
TCGA-CV-7424 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A463 
       14.89        16.64        22.19        45.96         6.51         0.76 
TCGA-CV-A6JM TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EQ 
        6.38        34.36        23.05        25.32        17.72        12.10 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        30.94        18.02        14.04        20.45         9.83 
TCGA-F7-A50J TCGA-HD-7753 TCGA-IQ-A61G TCGA-IQ-A61K TCGA-MT-A51W TCGA-MT-A51X 
       19.23         0.16        11.84         5.29        14.37         7.96 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-QK-A6VB TCGA-QK-A8Z7 
       18.97         2.04        29.00        16.70        14.79         6.51 
TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JH 
       15.91        13.25        54.67        62.27        17.95        21.86 
TCGA-UF-A7JK TCGA-WA-A7GZ 
       13.94        20.55 

$`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 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       53.79        57.44        15.52        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
        7.76        28.11        20.45        30.18        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4228 
       13.38        20.48        16.41         6.15        94.62        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       22.42        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY 
       24.66        38.40        71.05        20.52        25.71        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       27.19        12.92         8.81         6.28        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       23.70        38.04        40.44        26.86        32.65        21.11 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       41.10        14.33        43.73        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        35.54         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       11.57        12.49        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       20.68        19.53        20.68        19.07        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
        9.07         9.24        36.49        11.08        10.45        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       24.16         3.68        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       12.85        21.21         7.40         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
       45.99        10.42        11.21         4.24        41.19        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       34.75        56.58        14.99        38.76        70.13        51.29 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       16.73        43.04        41.88        28.83        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
       23.24        29.36        32.81        25.81        14.14        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        36.99        18.54        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       10.22        11.34         7.69        11.51        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
       47.18        40.93         3.09        29.23        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
        7.10         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
      129.21       108.95        76.24        19.20        17.95        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       86.83        48.59        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       62.43         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 
        8.42        28.34         2.50         4.14        64.83       111.16 
TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7183 
        7.99         5.26        52.31        12.92        21.80       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
       77.16         4.73        47.47        36.00        26.20        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
        4.96        47.97        18.41        57.47        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
        0.07        34.09        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 
       16.27        84.49        19.76         7.17       153.86         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        24.99       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        1.05        88.87        48.20        60.43        67.86        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        7.07        15.25         5.98        35.34        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       22.03         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.42        10.55        18.84        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES 
       12.36        15.88         7.63        14.30        13.94        12.79 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 
       11.11        35.54        33.86        18.90        25.48        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       12.10        10.65        11.18        37.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
       13.61        21.11         6.77         0.07        25.74         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        4.27         3.65         6.90        34.75        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L 
       14.50        19.33        13.55         0.07        14.47        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A 
       11.84        13.35        18.15        12.43        10.75        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         3.68        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 
       36.82        47.01        19.00        75.55        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       13.15        21.07        11.74        17.65         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       12.72        18.64        12.43         5.62        11.57        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        9.73         9.76         8.32        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
        7.10        32.45        13.55        13.68        43.59         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF 
       43.36        41.16        42.02        44.65        24.16        49.22 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       16.11        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7H4 
       14.56 

  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                          0.16                           0.07 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                        139.43                         210.97 
  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE 
                        17.145                         18.670 
[1] "0.2 - 139.4 (17.1)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.5"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 20(13Q22.1) MUTATED         3       16        14        52         2
  AMP PEAK 20(13Q22.1) WILD-TYPE      24       61        63       200        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                             24
  STAGE II                            16                             61
  STAGE III                           14                             63
  STAGE IVA                           52                            200
  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  25  24  36
  AMP PEAK 20(13Q22.1) WILD-TYPE    45 108  75 136
D20V4, multiclass
       clus
vv      AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  T0+T1                            5                             45
  T2                              25                            108
  T3                              24                             75
  T4                              36                            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
  AMP PEAK 20(13Q22.1) MUTATED    33  12  36   0
  AMP PEAK 20(13Q22.1) WILD-TYPE 145  54 129   8
D20V5, multiclass
    clus
vv   AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  N0                           33                            145
  N1                           12                             54
  N2                           36                            129
  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"
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q22.1) MUTATED    32   0
  AMP PEAK 20(13Q22.1) WILD-TYPE 151   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED     32    0
  AMP PEAK 20(13Q22.1) WILD-TYPE  151    1
   clus
vv  AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  0                           32                            151
  1                            0                              1
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q22.1) MUTATED    25  80
  AMP PEAK 20(13Q22.1) WILD-TYPE 114 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED     25   80
  AMP PEAK 20(13Q22.1) WILD-TYPE  114  297
        clus
vv       AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  FEMALE                           25                            114
  MALE                             80                            297
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(13Q22.1) MUTATED                                     104
  AMP PEAK 20(13Q22.1) WILD-TYPE                                   401
                                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                                                104
  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                                                  401
  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  83
  AMP PEAK 20(13Q22.1) WILD-TYPE  59 352
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED     22   83
  AMP PEAK 20(13Q22.1) WILD-TYPE   59  352
     clus
vv    AMP PEAK 20(13Q22.1) MUTATED AMP PEAK 20(13Q22.1) WILD-TYPE
  NO                            22                             59
  YES                           83                            352
[1] 2 2
[1] FALSE
D20V10, continuous
D20V11, continuous
D20V12, 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    86
  AMP PEAK 20(13Q22.1) WILD-TYPE                        36   355
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      86
                                  clus
vv                                 AMP PEAK 20(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  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"
D20V14, binary
                                cls
clus                               0   1
  AMP PEAK 20(13Q22.1) MUTATED     7  88
  AMP PEAK 20(13Q22.1) WILD-TYPE  18 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(13Q22.1) MUTATED      7   88
  AMP PEAK 20(13Q22.1) WILD-TYPE   18  366
                        clus
vv                       AMP PEAK 20(13Q22.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       AMP PEAK 20(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            366
[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    55  49
  AMP PEAK 21(13Q34) WILD-TYPE 258 151
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                         104                          409 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                          49                          151 
$`AMP PEAK 21(13Q34) MUTATED`
TCGA-BA-4075 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-4225 
        9.30        14.83        29.42        20.48         9.14         4.60 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 
       10.55        27.19         4.67        37.84        12.89        20.55 
TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6989 
       13.05         8.58         8.52        20.65         6.74        20.09 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       17.42        14.10        29.72        15.91        11.44         5.75 
TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7072 
        7.69        46.75        32.38        13.25        14.99        64.11 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 
       11.61        23.24        12.46        31.23        11.77        54.67 
TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
       58.42        11.64        12.46        39.16        47.34         3.45 
TCGA-CR-7372 TCGA-CR-7380 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7392 TCGA-CV-5431 
       24.95        19.92        27.06        29.82        31.10        17.16 
TCGA-CV-5440 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6950 TCGA-CV-6956 
      107.51        17.92        54.74        90.12        15.09         7.13 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7178 TCGA-CV-7243 
        2.50       126.15        18.81        12.66        71.21        31.36 
TCGA-CV-7247 TCGA-CV-7255 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 
       18.97         2.10         0.46        25.08       100.57        14.89 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A463 
       16.64        22.19       180.16        35.47         6.51         0.76 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8569 
        7.07         6.38        34.36         9.60        23.05        25.32 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J 
       12.10        12.79        30.94        18.02        14.04        19.23 
TCGA-HD-8314 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A5Q6 
       22.03        15.95        11.84        14.37         7.96        15.78 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-QK-A6VC TCGA-QK-A8ZA 
       18.97         2.04        29.00        16.70        12.43        12.10 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A7JC 
       12.72        16.96        15.91        13.25        54.67        17.95 
TCGA-UF-A7JH TCGA-WA-A7GZ 
       21.86        20.55 

$`AMP PEAK 21(13Q34) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
       53.79        57.44        15.52        21.17         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        4.01         7.76        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 
       11.05        13.38        16.41         6.15        94.62         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.35        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       12.92         8.81         6.28        12.69        26.27        23.70 
TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       38.04        40.44        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
       12.99        14.33        43.73        27.58        41.69        33.11 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       34.36        12.39        35.54         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.84        11.57        12.49        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        20.68        19.53        20.68        19.07        14.20 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
        9.07         9.24        36.49        11.08        10.45        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       24.16         3.68        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A640 TCGA-CN-A641 
       12.85        21.21         7.40        17.29         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 
        2.70        10.09         7.33         9.80         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 
       39.68        21.50         2.93        54.58        45.80        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.88        34.75 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58         4.24        38.76        70.13        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       16.73        43.04        41.88        28.83        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 
       32.81        25.81        14.14        84.23        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 
        6.02        11.90        10.22        11.34         7.69        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       15.75         9.27        47.18        40.93        35.84         3.09 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
       29.23         0.99        31.96         9.17        34.06        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7393 
       17.13        32.78        47.01        12.89        30.02        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       29.52        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.95        48.39       139.43       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95        94.88        76.50        91.53        80.12 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
       43.23        21.07        62.43         9.60         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 
      126.08        19.79        12.03        42.38        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 
       53.95        65.82        10.98         8.42        28.34         4.14 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       64.83       111.16         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       52.31        12.92        21.80        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        4.73        47.47        36.00        26.20        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87        47.97        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 
       35.54        17.85       210.97        89.33         9.67        22.85 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.94         0.07        34.09        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        3.52        16.27        84.49        19.76         7.17       153.86 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
        6.38        27.98        24.99       169.38       159.65         1.05 
TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
       45.96        88.87        48.20        60.43        67.86        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 
       10.42        10.55        18.84        13.25        25.41         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        24.95        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5624 
       15.88         7.63        14.30        13.94        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       35.54        33.86        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       12.13        12.10        10.65        11.18        37.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63        20.25         3.02        18.94        12.62         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.06        13.61        21.11         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       25.74         1.22        14.66        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
       13.84         4.27         3.65         6.90        34.75        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        19.33        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        10.75 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         3.68        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        29.92        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 
       36.82        47.01        19.00        75.55        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       13.15        21.07        11.74        17.65         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       12.72        18.64        14.79         6.51         5.62        11.57 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        9.73         9.76         8.32         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       13.55        13.68        43.59         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
       42.02        44.65        62.27        24.16        49.22        16.11 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7H4 
       14.56 

  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                        0.46                         0.07 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                      180.16                       210.97 
  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE 
                       16.83                        18.67 
[1] "0.5 - 180.2 (16.8)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.4"
D21V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 21(13Q34) MUTATED         2       19        21        48         2
  AMP PEAK 21(13Q34) WILD-TYPE      25       58        56       204        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                           25
  STAGE II                          19                           58
  STAGE III                         21                           56
  STAGE IVA                         48                          204
  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  33  25  31
  AMP PEAK 21(13Q34) WILD-TYPE    44 100  74 141
D21V4, multiclass
       clus
vv      AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  T0+T1                          6                           44
  T2                            33                          100
  T3                            25                           74
  T4                            31                          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
  AMP PEAK 21(13Q34) MUTATED    34  20  34   0
  AMP PEAK 21(13Q34) WILD-TYPE 144  46 131   8
D21V5, multiclass
    clus
vv   AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  N0                         34                          144
  N1                         20                           46
  N2                         34                          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"
D21V6, binary
                              cls
clus                             0   1
  AMP PEAK 21(13Q34) MUTATED    39   0
  AMP PEAK 21(13Q34) WILD-TYPE 144   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(13Q34) MUTATED     39    0
  AMP PEAK 21(13Q34) WILD-TYPE  144    1
   clus
vv  AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  0                         39                          144
  1                          0                            1
[1] 2 2
[1] FALSE
D21V7, binary
                              cls
clus                             0   1
  AMP PEAK 21(13Q34) MUTATED    24  82
  AMP PEAK 21(13Q34) WILD-TYPE 115 295
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(13Q34) MUTATED     24   82
  AMP PEAK 21(13Q34) WILD-TYPE  115  295
        clus
vv       AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  FEMALE                         24                          115
  MALE                           82                          295
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(13Q34) MUTATED                                     104
  AMP PEAK 21(13Q34) WILD-TYPE                                   401
                              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                                              104
  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                                                401
  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  87
  AMP PEAK 21(13Q34) WILD-TYPE  62 348
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(13Q34) MUTATED     19   87
  AMP PEAK 21(13Q34) WILD-TYPE   62  348
     clus
vv    AMP PEAK 21(13Q34) MUTATED AMP PEAK 21(13Q34) WILD-TYPE
  NO                          19                           62
  YES                         87                          348
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, continuous
D21V12, 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                           8    89
  AMP PEAK 21(13Q34) WILD-TYPE                        37   352
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    89
                                  clus
vv                                 AMP PEAK 21(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  37
  WHITE                                                     352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                              cls
clus                             0   1
  AMP PEAK 21(13Q34) MUTATED     8  92
  AMP PEAK 21(13Q34) WILD-TYPE  17 362
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(13Q34) MUTATED      8   92
  AMP PEAK 21(13Q34) WILD-TYPE   17  362
                        clus
vv                       AMP PEAK 21(13Q34) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         92
                        clus
vv                       AMP PEAK 21(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          362
[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    56  47
  AMP PEAK 22(15Q26.3) WILD-TYPE 257 153
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           103                            410 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            47                            153 
$`AMP PEAK 22(15Q26.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A6D8 
        9.30        37.28        14.83         3.55         4.01        27.95 
TCGA-BA-A8YP TCGA-BB-7861 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4729 
       16.41        22.42        71.05         6.28        37.84        12.89 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5365 
       20.55        43.73        27.58        34.36        12.39        11.54 
TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6995 
       11.84        20.71        20.65         9.24        12.95         3.68 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
       13.25        14.99        16.73        41.88        23.24        31.23 
TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7364 
       11.77        18.54        16.90        11.64        11.51        47.18 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7390 
       39.16         3.45         0.99        34.06        19.92        29.82 
TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 
       54.74         2.14        10.98         7.13         8.42         4.14 
TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7254 
      126.15         5.26        71.21        77.16        36.00        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
        2.10        36.13         9.67        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7437 
        0.07        14.89       156.49         3.52        19.76        16.64 
TCGA-CV-A45X TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6K2 TCGA-D6-6516 TCGA-D6-8569 
        6.51         5.98         6.38        10.42        25.41        25.32 
TCGA-D6-A6EM TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-7848 
        7.63        30.94        18.02        14.04        18.90        37.18 
TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ 
       15.16         0.16         1.22        14.66        13.84         3.65 
TCGA-HD-A6I0 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-MT-A67A TCGA-MT-A67G TCGA-P3-A5QA 
        6.90        14.50        13.55        30.05         3.68        56.75 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-T2-A6WZ 
       12.99        16.01        16.70         6.51         9.76        15.91 
TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A71E TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
        7.10        13.25        42.02        49.22        21.86        13.94 
TCGA-WA-A7GZ 
       20.55 

$`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 
        3.35        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       42.35        57.93        17.10        23.84        20.48        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       57.44        15.52        21.17        12.62         7.76        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        30.18        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15        94.62         9.14         4.60         4.41        18.35 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       36.72        33.70        50.20        44.98        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       38.40        20.52        25.71        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        8.81        12.69        26.27        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       40.44        26.86        32.65        21.11        41.10        12.99 
TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       14.33        41.69        13.05        33.11         8.58        35.54 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
        8.32        16.21        11.57        12.49         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        30.67        20.68        19.53        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       14.20         6.74         9.07        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 
       20.09        24.16        17.42        14.10        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       14.56        17.59        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       17.29        15.91        11.44         5.75         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
       32.38        32.88        34.75        56.58         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 
       70.13        51.29        33.11        43.04        28.83        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        11.61        29.36        32.81        25.81        14.14 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       12.46        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 
       50.01        39.52        34.52        36.99         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
       10.22        11.34         7.69        12.46        15.75         9.27 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       47.34        40.93        35.84         3.09        24.95        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49         7.07        43.23        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
       90.12         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6960 
       15.09        30.08         6.08        53.95        65.82        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        2.50        64.83       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 
        9.01         1.84        52.31        12.92        21.80        10.75 
TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
      130.88         4.73        47.47        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7406 
       17.13        95.34         4.96        11.87        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7422 
       35.54        17.85       210.97        89.33         0.46        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
      100.57        56.48        54.94        16.27        84.49         7.17 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
      153.86         6.38        22.19        27.98        24.99       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
      180.16       159.65        35.47         1.05        45.96        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       15.25        35.34        29.79         6.48        22.03         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        34.36        13.25         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        11.44        18.67        24.95        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       15.88        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        35.54        33.86        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        19.23        18.94        12.62         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 
       17.85        11.80        20.25        12.43        13.38        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 
       13.61        21.11         6.77         0.07        25.74        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 
       12.66        22.85         0.36         4.27        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       12.76        19.33        11.84         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI 
       14.37         7.96         1.84        12.62        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        17.98        29.92        15.78        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       29.00        13.15        21.07        11.74        17.65         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        18.64        14.79        12.43         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       11.57        12.10         9.73         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        6.87        32.45        13.55        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        43.36        41.16        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       24.16        16.11        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7H4 
       17.03        14.56 

  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                        156.49                         210.97 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                        15.160                         18.955 
[1] "0.1 - 156.5 (15.2)" "0.1 - 211.0 (19.0)"
[1] "hr=" "1.5"
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 22(15Q26.3) MUTATED         6       14        13        51         4
  AMP PEAK 22(15Q26.3) WILD-TYPE      21       63        64       201         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                             21
  STAGE II                            14                             63
  STAGE III                           13                             64
  STAGE IVA                           51                            201
  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  25  13  43
  AMP PEAK 22(15Q26.3) WILD-TYPE    41 108  86 129
D22V4, multiclass
       clus
vv      AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  T0+T1                            9                             41
  T2                              25                            108
  T3                              13                             86
  T4                              43                            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 22(15Q26.3) MUTATED    33  13  31   2
  AMP PEAK 22(15Q26.3) WILD-TYPE 145  53 134   6
D22V5, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  N0                           33                            145
  N1                           13                             53
  N2                           31                            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"
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED    35   0
  AMP PEAK 22(15Q26.3) WILD-TYPE 148   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED     35    0
  AMP PEAK 22(15Q26.3) WILD-TYPE  148    1
   clus
vv  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  0                           35                            148
  1                            0                              1
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED    29  74
  AMP PEAK 22(15Q26.3) WILD-TYPE 110 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED     29   74
  AMP PEAK 22(15Q26.3) WILD-TYPE  110  303
        clus
vv       AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  FEMALE                           29                            110
  MALE                             74                            303
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(15Q26.3) MUTATED                                      99
  AMP PEAK 22(15Q26.3) WILD-TYPE                                   406
                                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                                                 99
  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                                                  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"
D22V9, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED    17  86
  AMP PEAK 22(15Q26.3) WILD-TYPE  64 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED     17   86
  AMP PEAK 22(15Q26.3) WILD-TYPE   64  349
     clus
vv    AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  NO                            17                             64
  YES                           86                            349
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, continuous
D22V12, 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    84
  AMP PEAK 22(15Q26.3) WILD-TYPE                        34   357
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      84
                                  clus
vv                                 AMP PEAK 22(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  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"
D22V14, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED     4  89
  AMP PEAK 22(15Q26.3) WILD-TYPE  21 365
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED      4   89
  AMP PEAK 22(15Q26.3) WILD-TYPE   21  365
                        clus
vv                       AMP PEAK 22(15Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           89
                        clus
vv                       AMP PEAK 22(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            365
[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  39
  AMP PEAK 23(17Q12) WILD-TYPE 263 161
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          89                          424 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                          39                          161 
$`AMP PEAK 23(17Q12) MUTATED`
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BB-4225 TCGA-BB-4227 
       12.62         7.76        29.42        11.05         4.60         4.41 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-5356 TCGA-CN-5366 TCGA-CN-6023 TCGA-CN-6988 
       20.52         6.28        34.36        11.84        36.49        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-6220 
       20.09        24.16        21.21        17.29        11.44        32.38 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       13.25        14.99        41.88        64.11        23.24        25.81 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7370 
       11.77        58.42         6.02        12.46        39.16         3.45 
TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       17.13        29.82         5.95       139.43        17.16       129.21 
TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6940 
      107.51        13.35        60.49        54.74        90.12        26.43 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7101 
       11.24        12.03        15.09        30.08         4.14         5.26 
TCGA-CV-7102 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7414 
        1.84        17.13        95.34        47.97        36.13         0.46 
TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W 
       22.85         0.07        14.89       180.16        35.47        45.96 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-D6-8569 TCGA-D6-A6EP TCGA-D6-A6ES 
        7.07         6.38        23.47        25.32        13.94        12.79 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-8298 TCGA-HD-7753 TCGA-HD-7917 
       30.94        14.04        18.90        16.11         0.16         1.22 
TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-IQ-A61O TCGA-MT-A67D TCGA-P3-A6T7 TCGA-QK-A6IG 
        3.65        11.54        11.84         1.84        16.01         7.30 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3K TCGA-RS-A6TO 
       14.79        12.43         6.51         5.62         8.32        12.72 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JH TCGA-UF-A7JO 
       54.67         2.83        42.02        21.86        20.75 

$`AMP PEAK 23(17Q12) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        53.79        57.44        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        3.55         4.01        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15        94.62         9.14 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.35        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        25.71        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19        12.92         8.81        12.69        26.27        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       43.73        27.58        41.69        13.05        33.11         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
       12.39        35.54         8.32        16.21        11.54        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6995 
        6.74         9.07         9.24        11.08        12.95         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       12.85        29.72         7.40        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
       41.19        32.88        34.75        56.58         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
       70.13        51.29        33.11        16.73        43.04        28.83 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
       44.48        11.61        29.36        32.81        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
       31.23        84.23        54.67        37.87        26.27        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       39.52        34.52        36.99        18.54        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34        11.64         7.69        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        9.27        47.18        47.34        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       19.92        26.17        32.78        47.01        27.06        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5435 
        5.13        35.41        29.95        48.39       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20        17.95        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       17.92        23.05        86.83        48.59         7.07        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
       20.52         4.73        21.90       126.08        19.79        42.38 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
       28.34         2.50        64.83       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
       12.66         7.99         9.01        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7252 TCGA-CV-7253 
       36.00        31.36        26.20        18.97         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 
       89.33         9.67        25.08        25.94        34.09       100.57 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X 
       27.98        24.99       169.38       159.65         1.05         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        21.24        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ 
       17.72        12.36        15.88         7.63        14.30        12.10 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       11.11        58.45        35.54        33.86        18.02        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       37.18        21.63        20.25         3.02        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
        0.07        25.74        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       12.76        14.50        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       14.47         5.29        13.35        18.15        12.43        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       14.37         7.96        30.05        12.62         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        56.75 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        29.00        12.99        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       11.74        17.65        16.70         9.34        12.72        18.64 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX 
       11.57        12.10         9.73         9.76        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.55        13.25        13.68 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       43.59        43.36        41.16        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       24.16        49.22        16.11        13.94        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                      180.16                       210.97 
  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE 
                       15.09                        18.74 
[1] "0.1 - 180.2 (15.1)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.2"
D23V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 23(17Q12) MUTATED         3       13        18        42         0
  AMP PEAK 23(17Q12) WILD-TYPE      24       64        59       210        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                           24
  STAGE II                          13                           64
  STAGE III                         18                           59
  STAGE IVA                         42                          210
  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  29
  AMP PEAK 23(17Q12) WILD-TYPE    46 110  78 143
D23V4, multiclass
       clus
vv      AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  T0+T1                          4                           46
  T2                            23                          110
  T3                            21                           78
  T4                            29                          143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 23(17Q12) MUTATED    32  13  29   0
  AMP PEAK 23(17Q12) WILD-TYPE 146  53 136   8
D23V5, multiclass
    clus
vv   AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  N0                         32                          146
  N1                         13                           53
  N2                         29                          136
  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"
D23V6, binary
                              cls
clus                             0   1
  AMP PEAK 23(17Q12) MUTATED    34   1
  AMP PEAK 23(17Q12) WILD-TYPE 149   0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED     34    1
  AMP PEAK 23(17Q12) WILD-TYPE  149    0
   clus
vv  AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  0                         34                          149
  1                          1                            0
[1] 2 2
[1] FALSE
D23V7, binary
                              cls
clus                             0   1
  AMP PEAK 23(17Q12) MUTATED    20  69
  AMP PEAK 23(17Q12) WILD-TYPE 119 308
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED     20   69
  AMP PEAK 23(17Q12) WILD-TYPE  119  308
        clus
vv       AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  FEMALE                         20                          119
  MALE                           69                          308
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(17Q12) MUTATED                                      86
  AMP PEAK 23(17Q12) WILD-TYPE                                   419
                              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                                               86
  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                                                419
  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  77
  AMP PEAK 23(17Q12) WILD-TYPE  69 358
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED     12   77
  AMP PEAK 23(17Q12) WILD-TYPE   69  358
     clus
vv    AMP PEAK 23(17Q12) MUTATED AMP PEAK 23(17Q12) WILD-TYPE
  NO                          12                           69
  YES                         77                          358
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, continuous
D23V12, 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                          10    74
  AMP PEAK 23(17Q12) WILD-TYPE                        35   367
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                    74
                                  clus
vv                                 AMP PEAK 23(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  35
  WHITE                                                     367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                              cls
clus                             0   1
  AMP PEAK 23(17Q12) MUTATED     8  74
  AMP PEAK 23(17Q12) WILD-TYPE  17 380
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(17Q12) MUTATED      8   74
  AMP PEAK 23(17Q12) WILD-TYPE   17  380
                        clus
vv                       AMP PEAK 23(17Q12) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         74
                        clus
vv                       AMP PEAK 23(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          380
[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    87  66
  AMP PEAK 24(18P11.31) WILD-TYPE 226 134
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                            153                             360 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                             66                             134 
$`AMP PEAK 24(18P11.31) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 
        9.30        13.64        23.74        17.10        53.79        57.44 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A6DL 
       21.17         3.55        12.62         4.01        28.11        20.48 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
       94.62         9.14         4.60        18.35        22.42        36.72 
TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO 
       66.28        20.52        25.71        10.55        27.19         8.81 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        6.28        38.04        40.44        37.84        12.89        26.86 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6012 
       12.99        20.55         8.32        11.84        11.57        20.68 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A63T 
        6.74         9.24        11.08        10.45        35.01         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY TCGA-CQ-5332 TCGA-CQ-6225 
       17.29        11.44        12.07        10.09        10.42        13.25 
TCGA-CQ-6227 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CG TCGA-CR-5247 
        4.24        16.73        64.11        23.24        14.14        11.77 
TCGA-CR-6467 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 
       58.42        18.54         6.02        11.34         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 
       39.16         3.45        24.95        29.82         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 
       29.95        48.39       129.21       108.95        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 
       94.88        17.92        86.83        60.49        43.23        21.07 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 
        9.60         9.70        20.52        11.24        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6962 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
       30.08        53.95         4.14         5.26         1.84        10.75 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7255 
       77.16        31.36        26.20        18.97        11.87         2.10 
TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7434 
       17.85        22.85        25.94         0.07        34.09         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 
      153.86        16.64        22.19        45.96        48.20        67.86 
TCGA-CV-A6JM TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO 
        6.38        18.84        23.05        24.95        25.32        14.30 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7595 
       13.94        11.11        18.02        14.04        25.48        10.65 
TCGA-F7-8298 TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 
       16.11        20.25        15.06        21.11         6.77        25.74 
TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61K TCGA-KU-A66S 
       22.03         4.27         3.65        11.84         5.29        13.35 
TCGA-KU-A66T TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T3 TCGA-P3-A6T6 TCGA-QK-A8Z7 
       18.15        17.98        15.78        18.97        12.99         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T2-A6X2 
        5.62        12.10         9.73        12.72        15.91        32.45 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
       54.67         2.83        41.16        42.02        62.27        24.16 
TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JS 
       49.22        13.94        22.36 

$`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 
        3.35        15.19        37.28         9.07        26.50        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 
       57.93        23.84        20.48        15.52        14.83         7.76 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        20.45        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       16.41         6.15         4.41        33.70        50.20        44.98 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 
       24.66        38.40        71.05        12.92        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 
       23.70         4.67        32.65        21.11        41.10        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       43.73        27.58        41.69        13.05        33.11        34.36 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5369 
        8.58        12.39        35.54        16.21        11.54        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        8.52        22.45        56.94        20.71        30.67        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
       19.53        20.68        19.07        14.20         9.07        36.49 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 
       15.91         5.75         4.41         2.70         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.80        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
       41.19        32.38        32.88        34.75        56.58        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
       38.76        70.13        51.29        33.11        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       28.83        44.48        11.61        29.36        32.81        25.81 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        31.23        84.23        54.67        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        34.52        36.99        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.64         7.69        12.46        11.51        15.75 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
       47.34        40.93        35.84         3.09        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 
       29.85        29.52        30.58         7.10         5.13       139.43 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.16        76.24        19.20        76.50        91.53        80.12 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6436 
       13.35        23.05        48.59         7.07        54.74        62.43 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
       90.12         2.14         5.46         4.73        21.90        26.43 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 
      126.08        19.79        42.38         6.08        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
        7.13         8.42        28.34         2.50        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 
      111.16        18.81        12.66         7.99         9.01        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       12.92        21.80        71.21       130.88         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 
       36.00        17.13        95.34         4.96        47.97        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.46        25.08       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7438 
       54.94         3.52        16.27        84.49        19.76         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        24.99       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 
        1.05         6.51        88.87        60.43         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        7.07        15.25         5.98        35.34        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       22.03         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.42        10.55        34.36        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 
        9.60         2.53        16.14        11.44        18.67        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       12.36        15.88         7.63        12.10        12.79        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
       35.54        30.94        33.86        18.90        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       12.13        12.10        11.18        37.18        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        19.23        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-HD-7229 
       11.80        12.43        13.38        15.16        13.61         0.07 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        0.16         1.22        14.66        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
       13.84         6.90        34.75        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
       19.33        13.55         0.07        14.47        11.54        11.84 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       12.62         3.68        15.42         7.13        16.08        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       56.75        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55         2.04        29.00        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K 
       18.64        14.79        12.43        11.57         9.76         8.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       16.96         6.87         7.10        13.55        13.25        13.68 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JJ 
       43.59        43.36        44.65        17.95        21.86        16.11 
TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        32.65         2.96        17.03        20.55        14.56 

  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                         153.86                          210.97 
  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE 
                         17.950                          18.655 
[1] "0.1 - 153.9 (17.9)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.3"
D24V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 24(18P11.31) MUTATED         4       16        28        80
  AMP PEAK 24(18P11.31) WILD-TYPE      23       61        49       172
                                 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                              23
  STAGE II                             16                              61
  STAGE III                            28                              49
  STAGE IVA                            80                             172
  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      13  30  40  52
  AMP PEAK 24(18P11.31) WILD-TYPE    37 103  59 120
D24V4, multiclass
       clus
vv      AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  T0+T1                            13                              37
  T2                               30                             103
  T3                               40                              59
  T4                               52                             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 24(18P11.31) MUTATED    45  22  58   2
  AMP PEAK 24(18P11.31) WILD-TYPE 133  44 107   6
D24V5, multiclass
    clus
vv   AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  N0                            45                             133
  N1                            22                              44
  N2                            58                             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"
D24V6, binary
                                 cls
clus                                0   1
  AMP PEAK 24(18P11.31) MUTATED    46   1
  AMP PEAK 24(18P11.31) WILD-TYPE 137   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(18P11.31) MUTATED     46    1
  AMP PEAK 24(18P11.31) WILD-TYPE  137    0
   clus
vv  AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  0                            46                             137
  1                             1                               0
[1] 2 2
[1] FALSE
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(18P11.31) MUTATED    25 129
  AMP PEAK 24(18P11.31) WILD-TYPE 114 248
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(18P11.31) MUTATED     25  129
  AMP PEAK 24(18P11.31) WILD-TYPE  114  248
        clus
vv       AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  FEMALE                            25                             114
  MALE                             129                             248
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(18P11.31) MUTATED                                     150
  AMP PEAK 24(18P11.31) WILD-TYPE                                   355
                                 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                                                 150
  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                                                   355
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                                 cls
clus                                0   1
  AMP PEAK 24(18P11.31) MUTATED    21 133
  AMP PEAK 24(18P11.31) WILD-TYPE  60 302
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(18P11.31) MUTATED     21  133
  AMP PEAK 24(18P11.31) WILD-TYPE   60  302
     clus
vv    AMP PEAK 24(18P11.31) MUTATED AMP PEAK 24(18P11.31) WILD-TYPE
  NO                             21                              60
  YES                           133                             302
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, continuous
D24V12, 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   130
  AMP PEAK 24(18P11.31) WILD-TYPE                        28   311
D24V13, multiclass
                                  clus
vv                                 AMP PEAK 24(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      130
                                  clus
vv                                 AMP PEAK 24(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     28
  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"
D24V14, binary
                                 cls
clus                                0   1
  AMP PEAK 24(18P11.31) MUTATED     5 137
  AMP PEAK 24(18P11.31) WILD-TYPE  20 317
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(18P11.31) MUTATED      5  137
  AMP PEAK 24(18P11.31) WILD-TYPE   20  317
                        clus
vv                       AMP PEAK 24(18P11.31) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           137
                        clus
vv                       AMP PEAK 24(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                  20
  NOT HISPANIC OR LATINO                             317
[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    63  41
  AMP PEAK 25(18Q11.2) WILD-TYPE 250 159
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                           104                            409 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                            41                            159 
$`AMP PEAK 25(18Q11.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 
        3.35        15.19         9.30        13.64        23.74        17.10 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DL 
       53.79        57.44        29.42        28.11        30.18        20.48 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
       16.41        94.62         9.14         4.60        18.35        22.42 
TCGA-CN-4723 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5367 TCGA-CN-6012 
       23.70        26.86        12.99        20.55        11.57        20.68 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY 
        6.74         9.24        11.08        11.44        12.07        10.09 
TCGA-CQ-5326 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CR-5247 TCGA-CR-6467 
        2.93        51.29        33.11        16.73        11.77        58.42 
TCGA-CR-6482 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7383 
       11.34        47.34         3.45        24.95         0.99        17.13 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5432 
       29.82         5.13         5.95        35.41        48.39       129.21 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 
      108.95        17.95       107.51        60.49        43.23        21.07 
TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6962 
       20.52        11.24        15.09        30.08        65.82         4.14 
TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 
      126.15        12.66         5.26        52.31        12.92        10.75 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       11.87         2.10        57.47        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7437 TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM 
        0.07        16.64        45.96        48.20        67.86         6.38 
TCGA-CX-7219 TCGA-D6-A6EO TCGA-D6-A6ES TCGA-DQ-7589 TCGA-DQ-7590 TCGA-H7-A76A 
       34.36        14.30        12.79        18.90        25.48         6.77 
TCGA-HD-7917 TCGA-HD-A634 TCGA-IQ-7630 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
        1.22         4.27        15.95        11.84        13.35        18.15 
TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A8Z7 
        7.96        15.42        17.98        21.07         7.30         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-UF-A71B TCGA-UF-A71E 
        5.62        12.10        15.91        32.45        43.36        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA 
       44.65        62.27 

$`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 
       37.28         9.07        26.50        42.35        57.93        23.84 
TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       20.48        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01         7.76        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        6.15         4.41        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       26.27        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       32.65        21.11        41.10        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 
       35.54         8.32        16.21        11.54        11.84        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        8.52        22.45        56.94        20.71        30.67        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
       19.53        20.68        19.07        14.20         9.07        36.49 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       29.72        21.21         7.40        17.29        15.91         5.75 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41         2.70         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       48.20        39.68        21.50        54.58        46.75        45.80 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        34.75        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        70.13        43.04        41.88        28.83        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        32.81        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       26.27        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 
       16.90         6.02        11.90        10.22        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        11.51        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
       40.93        35.84         3.09        29.23        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        19.92        26.17        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
        7.10        29.95       139.43        17.16        76.24        19.20 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6436 
       23.05        86.83        48.59         7.07        54.74        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
        9.60        90.12         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       21.90        26.43       126.08        19.79        12.03        42.38 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
        6.08        53.95        10.98         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 
        2.50        64.83       111.16        18.81         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
        1.84        21.80        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       47.47        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 
       95.34         4.96        47.97        36.13        18.41        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7422 
       17.85       210.97        89.33         9.67         0.46        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
      100.57        14.89        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 
       16.27        84.49        19.76         7.17       153.86         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        24.99       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 
       35.47         1.05         6.51        88.87        60.43         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
       56.61         7.07        15.25         5.98        35.34        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 
       22.52        10.42        10.42        10.55        18.84        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        15.88 
TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
        7.63        13.94        12.10        11.11        58.45        35.54 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 
       30.94        33.86        18.02        14.04        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       12.13        12.10        10.65        11.18        37.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
       15.16        15.06        13.61        21.11         0.07         0.16 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       25.74        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
       13.84         3.65         6.90        34.75        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
       11.54        12.43        10.75        14.37        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       12.62         3.68         7.13        16.08        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       56.75        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       13.15        11.74        17.65        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       18.64        14.79        12.43        11.57         9.73         9.76 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-TN-A7HI 
        8.32        12.72        16.96         6.87         7.10        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D 
       13.25        13.68        43.59        54.67         2.83        41.16 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                        129.21                         210.97 
  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE 
                         17.54                          18.54 
[1] "0.1 - 129.2 (17.5)" "0.1 - 211.0 (18.5)"
[1] "hr=" "1.1"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 25(18Q11.2) MUTATED         4       15        11        53         1
  AMP PEAK 25(18Q11.2) WILD-TYPE      23       62        66       199        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                             23
  STAGE II                            15                             62
  STAGE III                           11                             66
  STAGE IVA                           53                            199
  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  17  33
  AMP PEAK 25(18Q11.2) WILD-TYPE    39 106  82 139
D25V4, multiclass
       clus
vv      AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  T0+T1                           11                             39
  T2                              27                            106
  T3                              17                             82
  T4                              33                            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
  AMP PEAK 25(18Q11.2) MUTATED    31  11  34   1
  AMP PEAK 25(18Q11.2) WILD-TYPE 147  55 131   7
D25V5, multiclass
    clus
vv   AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  N0                           31                            147
  N1                           11                             55
  N2                           34                            131
  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"
D25V6, binary
                                cls
clus                               0   1
  AMP PEAK 25(18Q11.2) MUTATED    28   1
  AMP PEAK 25(18Q11.2) WILD-TYPE 155   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED     28    1
  AMP PEAK 25(18Q11.2) WILD-TYPE  155    0
   clus
vv  AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  0                           28                            155
  1                            1                              0
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                               0   1
  AMP PEAK 25(18Q11.2) MUTATED    18  86
  AMP PEAK 25(18Q11.2) WILD-TYPE 121 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED     18   86
  AMP PEAK 25(18Q11.2) WILD-TYPE  121  291
        clus
vv       AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  FEMALE                           18                            121
  MALE                             86                            291
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(18Q11.2) MUTATED                                     100
  AMP PEAK 25(18Q11.2) WILD-TYPE                                   405
                                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                                                100
  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                                                  405
  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  90
  AMP PEAK 25(18Q11.2) WILD-TYPE  67 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED     14   90
  AMP PEAK 25(18Q11.2) WILD-TYPE   67  345
     clus
vv    AMP PEAK 25(18Q11.2) MUTATED AMP PEAK 25(18Q11.2) WILD-TYPE
  NO                            14                             67
  YES                           90                            345
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, continuous
D25V12, 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    87
  AMP PEAK 25(18Q11.2) WILD-TYPE                        30   354
D25V13, multiclass
                                  clus
vv                                 AMP PEAK 25(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      87
                                  clus
vv                                 AMP PEAK 25(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                                cls
clus                               0   1
  AMP PEAK 25(18Q11.2) MUTATED     3  94
  AMP PEAK 25(18Q11.2) WILD-TYPE  22 360
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(18Q11.2) MUTATED      3   94
  AMP PEAK 25(18Q11.2) WILD-TYPE   22  360
                        clus
vv                       AMP PEAK 25(18Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 25(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            360
[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    40  18
  AMP PEAK 26(19P13.2) WILD-TYPE 273 182
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            58                            455 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                            18                            182 
$`AMP PEAK 26(19P13.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-4223 
        3.35        57.44        15.52        29.42        14.47        94.62 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-6013 TCGA-CN-6021 
        4.60        22.42        24.66        20.52        20.65         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A63V TCGA-CN-A6V6 TCGA-CN-A6V7 
       36.49        11.08        20.09        15.91         7.69         6.18 
TCGA-CQ-7067 TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7370 TCGA-CR-7389 
       16.73        58.42         7.69        12.46         3.45        12.89 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6441 
       48.39        17.16       107.51        76.50        60.49         9.60 
TCGA-CV-6933 TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7421 
       90.12        77.16        18.97        47.97        36.13         0.07 
TCGA-CV-7428 TCGA-CV-A45U TCGA-CV-A45Z TCGA-CV-A6JM TCGA-CV-A6K2 TCGA-CX-7086 
       54.94        35.47        48.20         6.38        10.42        18.84 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-F7-8298 TCGA-H7-A76A TCGA-HL-7533 TCGA-IQ-A61K 
       34.36        30.94        16.11         6.77        34.75         5.29 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-QK-A6V9 TCGA-QK-A6VC 
        3.68         7.13        15.78        56.75        18.64        12.43 
TCGA-QK-AA3J TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
        9.76        13.55        13.68        43.59 

$`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 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       53.79        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
        7.76        28.11        20.45        30.18        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        7.10         5.69         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
       20.48        16.41         6.15         9.14         4.41        18.35 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
       36.72        33.70        50.20        44.98        66.28        38.40 
TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        25.71        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        26.27        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       40.44        37.84        12.89        26.86        32.65        21.11 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       35.54         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       12.49         8.52        22.45        56.94        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       20.68        19.53        20.68        19.07        14.20         6.74 
TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        9.24        10.45        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21         7.40        17.29        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       32.38        32.88        34.75        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        51.29        33.11        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
       84.23        11.77        54.67        37.87        26.27        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       39.52        34.52        36.99        18.54        16.90         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 
       11.90        10.22        11.34        11.64        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.09        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        29.82        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58         7.10         5.13         5.95        35.41        29.95 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
      139.43       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       94.88        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       86.83        48.59         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       62.43         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       126.08        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       126.15       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21        10.75       130.88         4.73        47.47        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        17.13        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       89.33         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
       34.09       100.57        14.89        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       16.27        84.49        19.76         7.17       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        22.19        27.98        24.99       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 
      159.65         1.05        45.96         6.51        88.87        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34        29.79         6.48        22.03         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 
       23.47        19.92        22.52        10.42        10.55        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        35.54        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       11.18        37.18        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       18.94        12.62         0.46        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        15.95        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
       13.55         0.07        14.47        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        1.84        12.62        15.42        16.08        17.98        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       51.25        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       12.72        14.79         6.51         5.62        11.57        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
        9.73         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
        7.10        32.45        13.25        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        17.03        20.55        14.56 

  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                        107.51                         210.97 
  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE 
                         17.90                          18.02 
[1] "0.1 - 107.5 (17.9)" "0.1 - 211.0 (18.0)"
[1] "hr=" "1.3"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 26(19P13.2) MUTATED         5        6         7        27         0
  AMP PEAK 26(19P13.2) WILD-TYPE      22       71        70       225        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                             22
  STAGE II                             6                             71
  STAGE III                            7                             70
  STAGE IVA                           27                            225
  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  11  11  15
  AMP PEAK 26(19P13.2) WILD-TYPE    42 122  88 157
D26V4, multiclass
       clus
vv      AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  T0+T1                            8                             42
  T2                              11                            122
  T3                              11                             88
  T4                              15                            157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 26(19P13.2) MUTATED    15   6  22   0
  AMP PEAK 26(19P13.2) WILD-TYPE 163  60 143   8
D26V5, multiclass
    clus
vv   AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  N0                           15                            163
  N1                            6                             60
  N2                           22                            143
  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"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(19P13.2) MUTATED    16   0
  AMP PEAK 26(19P13.2) WILD-TYPE 167   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19P13.2) MUTATED     16    0
  AMP PEAK 26(19P13.2) WILD-TYPE  167    1
   clus
vv  AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  0                           16                            167
  1                            0                              1
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(19P13.2) MUTATED    10  48
  AMP PEAK 26(19P13.2) WILD-TYPE 129 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19P13.2) MUTATED     10   48
  AMP PEAK 26(19P13.2) WILD-TYPE  129  329
        clus
vv       AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  FEMALE                           10                            129
  MALE                             48                            329
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(19P13.2) MUTATED                                      57
  AMP PEAK 26(19P13.2) WILD-TYPE                                   448
                                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                                                 57
  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                                                  448
  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  49
  AMP PEAK 26(19P13.2) WILD-TYPE  72 386
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19P13.2) MUTATED      9   49
  AMP PEAK 26(19P13.2) WILD-TYPE   72  386
     clus
vv    AMP PEAK 26(19P13.2) MUTATED AMP PEAK 26(19P13.2) WILD-TYPE
  NO                             9                             72
  YES                           49                            386
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, continuous
D26V12, 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                           8    49
  AMP PEAK 26(19P13.2) WILD-TYPE                        37   392
D26V13, multiclass
                                  clus
vv                                 AMP PEAK 26(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      49
                                  clus
vv                                 AMP PEAK 26(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       392
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                                cls
clus                               0   1
  AMP PEAK 26(19P13.2) MUTATED     3  53
  AMP PEAK 26(19P13.2) WILD-TYPE  22 401
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19P13.2) MUTATED      3   53
  AMP PEAK 26(19P13.2) WILD-TYPE   22  401
                        clus
vv                       AMP PEAK 26(19P13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       AMP PEAK 26(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            401
[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   113  76
  AMP PEAK 27(20P12.2) WILD-TYPE 200 124
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           189                            324 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                            76                            124 
$`AMP PEAK 27(20P12.2) MUTATED`
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 
        9.07        26.50        23.74        23.84        57.44        15.52 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BB-4224 
       12.62         7.76         7.10         2.27        11.05         9.14 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HY 
        4.60        22.42        36.72        38.40        25.71        10.55 
TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        6.28        37.84        26.86        32.65        21.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 
       34.36        12.39        35.54         8.32        11.84        56.94 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       20.68        20.65         6.74         9.24        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6220 
       10.45        20.09         7.40        46.75        45.80        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 
       34.75        56.58        13.25        38.76        51.29        16.73 
TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       41.88        44.48        11.61        23.24        29.36        25.81 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 
       31.23        84.23        11.77        58.42        11.64        12.46 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7380 
       39.16        47.34         3.45        24.95         9.17        19.92 
TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5431 
       12.89        31.10         7.10         5.95        35.41        17.16 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
      108.95        76.24        19.20        76.50        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
       13.35        23.05        86.83        60.49         7.07        54.74 
TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6945 
       90.12         5.46        20.52        21.90        26.43        12.03 
TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7090 
       42.38        65.82         7.13         8.42         4.14       126.15 
TCGA-CV-7095 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 
       18.81        21.80        71.21        10.75        77.16        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7416 
       31.36        26.20        17.13         2.10        18.41        25.08 
TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45R 
      100.57         3.52        16.27       153.86        16.64       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A464 
      159.65        35.47         6.51        88.87        48.20        56.61 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        7.07        35.34        29.79         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CX-7082 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-8569 
       19.92        10.42        25.41         9.60        16.14        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7592 
       12.36        13.94        12.10        58.45        14.04         9.83 
TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-8501 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ 
       19.23        18.94        15.16        22.03         4.27         3.65 
TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K 
       15.95        14.50        19.33        11.84         0.07         5.29 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN 
       11.54        18.15        30.05         1.84         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 
        7.13        16.08        56.75        19.00        18.97         2.04 
TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
       29.00        11.74        17.65         7.30         9.34        12.72 
TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HJ 
       14.79         6.51        12.10        15.91        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF 
       13.68         2.83        42.02        44.65        62.27        49.22 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JV 
       16.11        13.94         2.96 

$`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 
        3.35        15.19         9.30        13.64        37.28        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       57.93        17.10        20.48        53.79        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        3.55         4.01        29.42        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ 
       27.95        11.54         5.69        14.47         7.82        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 
       20.48        16.41         6.15        94.62         4.41        18.35 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
       33.70        50.20        44.98        66.28        24.66        71.05 
TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       20.52        27.19        12.92         8.81        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 
       23.70        38.04         4.67        40.44        12.89        41.10 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 
       33.11         8.58        16.21        11.54        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 
        8.52        22.45        20.71        30.67        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
       19.07        14.20         9.07        12.95        24.16         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       17.42        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       12.85        29.72        21.21        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        2.93        54.58        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 
       41.19        32.88         4.24        14.99        70.13        33.11 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
       43.04        28.83        64.11        32.81        14.14        12.46 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       54.67        37.87        26.27        50.01        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.34         7.69        11.51        15.75         9.27        47.18 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       40.93        35.84         3.09        29.23         0.99        31.96 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       34.06        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 
       29.82        30.02        29.85        29.52        30.58         5.13 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 
       29.95        48.39       139.43       129.21        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       94.88        91.53        48.59        43.23        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6941 TCGA-CV-6942 
        9.60         2.14         9.70         4.73        11.24       126.08 
TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       19.79        15.09        30.08         6.08        53.95        10.98 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
       28.34         2.50        64.83       111.16        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7183 
        9.01         5.26         1.84        52.31        12.92       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
        4.73        47.47        18.97        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       47.97        36.13        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67         0.46        22.85        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
       34.09        14.89        56.48       156.49        54.94        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17         6.38        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
      169.38         1.05        45.96        60.43        67.86         0.76 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6K1 
       15.25         5.98         6.38         6.48        22.03        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6823 
       10.42        10.55        18.84        34.36        13.25        23.05 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK 
        2.53        11.44        18.67        24.95        17.72        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 
        7.63        14.30        12.79        11.11        35.54        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
       33.86        18.02        18.90        25.48        20.45        12.13 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       12.10        10.65        11.18        37.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       20.25         3.02        12.62         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       20.25        12.43        13.38        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
        6.77         0.07         0.16        25.74         1.22        14.66 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 
       12.66        22.85         0.36        13.84         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
       12.76        13.55        14.47        11.84        13.35        12.43 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       10.75        14.37         7.96        12.62        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       15.78        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6V9 
       12.99        16.01        13.15        21.07        16.70        18.64 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       12.43         5.62        11.57         9.73         9.76         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-UF-A718 
       12.72        16.96         6.87         7.10        32.45        43.59 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       54.67        43.36        41.16        17.95        24.16        21.86 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.75        22.36        32.65        17.03        20.55        14.56 

  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                         18.97                          17.85 
[1] "0.1 - 180.2 (19.0)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1"  
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 27(20P12.2) MUTATED        10       25        35        94         5
  AMP PEAK 27(20P12.2) WILD-TYPE      17       52        42       158         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                             17
  STAGE II                            25                             52
  STAGE III                           35                             42
  STAGE IVA                           94                            158
  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  45  38  67
  AMP PEAK 27(20P12.2) WILD-TYPE    30  88  61 105
D27V4, multiclass
       clus
vv      AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  T0+T1                           20                             30
  T2                              45                             88
  T3                              38                             61
  T4                              67                            105
[1] 4 2
[1] TRUE
[1] "dimension of 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    61  32  62   3
  AMP PEAK 27(20P12.2) WILD-TYPE 117  34 103   5
D27V5, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  N0                           61                            117
  N1                           32                             34
  N2                           62                            103
  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"
D27V6, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    77   0
  AMP PEAK 27(20P12.2) WILD-TYPE 106   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     77    0
  AMP PEAK 27(20P12.2) WILD-TYPE  106    1
   clus
vv  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  0                           77                            106
  1                            0                              1
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    50 140
  AMP PEAK 27(20P12.2) WILD-TYPE  89 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     50  140
  AMP PEAK 27(20P12.2) WILD-TYPE   89  237
        clus
vv       AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  FEMALE                           50                             89
  MALE                            140                            237
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                     186
  AMP PEAK 27(20P12.2) WILD-TYPE                                   319
                                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                                                186
  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                                                  319
  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    33 157
  AMP PEAK 27(20P12.2) WILD-TYPE  48 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     33  157
  AMP PEAK 27(20P12.2) WILD-TYPE   48  278
     clus
vv    AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  NO                            33                             48
  YES                          157                            278
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, continuous
D27V12, 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   159
  AMP PEAK 27(20P12.2) WILD-TYPE                        30   282
D27V13, multiclass
                                  clus
vv                                 AMP PEAK 27(20P12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     159
                                  clus
vv                                 AMP PEAK 27(20P12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    14 158
  AMP PEAK 27(20P12.2) WILD-TYPE  11 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     14  158
  AMP PEAK 27(20P12.2) WILD-TYPE   11  296
                        clus
vv                       AMP PEAK 27(20P12.2) MUTATED
  HISPANIC OR LATINO                               14
  NOT HISPANIC OR LATINO                          158
                        clus
vv                       AMP PEAK 27(20P12.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            296
[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   140  84
  AMP PEAK 28(20Q11.22) WILD-TYPE 173 116
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                            224                             289 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                             84                             116 
$`AMP PEAK 28(20Q11.22) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5559 
        9.30         9.07        26.50        23.74        23.84        57.44 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       15.52        14.83        12.62         4.01         7.76        29.42 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
        7.10         2.27        11.05        94.62         9.14         4.60 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 
       18.35        22.42        36.72        50.20        44.98        38.40 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 
       25.71        10.55         6.28        38.04        37.84        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       32.65        21.11        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 
       27.58        41.69        13.05        34.36        12.39         8.32 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6022 TCGA-CN-6023 
       11.84        56.94        30.67        20.65         9.24        36.49 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A49A 
       10.45        20.09        12.95        24.16         3.68        12.85 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CQ-5329 TCGA-CQ-5330 
        7.40        17.29        10.09         9.80        46.75        45.80 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 
       32.38        34.75        56.58        13.25        38.76        51.29 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       16.73        41.88        64.11        44.48        11.61        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6473 
       25.81        14.14        84.23        11.77        58.42        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6493 
       18.54        16.90         6.02        11.64        12.46         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
       47.18        39.16        47.34         3.45        24.95        29.23 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 
        9.17        34.06        19.92        17.13        12.89        31.10 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        7.10        35.41        29.95       139.43       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
       76.24        19.20        76.50        91.53        80.12        13.35 
TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6933 
       23.05        60.49         7.07        54.74        21.07        90.12 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 
        5.46        20.52        21.90        26.43        12.03        42.38 
TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 
       30.08        65.82         7.13         8.42        28.34         4.14 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7242 
      126.15        18.81        21.80        71.21        10.75        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       31.36        26.20        17.13        47.97         2.10        18.41 
TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7437 
       17.85        25.08         0.07       100.57         3.52        16.64 
TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z 
        6.38       180.16       159.65        35.47         6.51        48.20 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY 
       56.61         7.07        35.34        29.79         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 
       23.47        19.92        18.84        25.41        23.05        16.14 
TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       25.32        13.94        58.45        18.02        14.04        18.90 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 
       20.45         9.83        16.11        19.23        18.94        20.25 
TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ 
       15.16         0.16         1.22        22.03         4.27         3.65 
TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L 
       15.95        14.50        19.33         0.07         5.29        11.54 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       18.15        12.43        14.37         7.96        30.05         1.84 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        3.68        15.42         7.13        17.98        15.78        56.75 
TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IG 
       19.00        18.97         2.04        29.00        11.74         7.30 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       12.72        18.64        14.79        12.43         6.51        11.57 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71D 
       16.96        15.91        13.55        13.25         2.83        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       42.02        44.65        62.27        49.22        16.11        13.94 
TCGA-UF-A7JV TCGA-WA-A7GZ 
        2.96        20.55 

$`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 
        3.35        15.19        13.64        37.28        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG 
       17.10        20.48        53.79        21.17         3.55        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        30.18        27.95        11.54         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4227 
        7.82        13.38        20.48        16.41         6.15         4.41 
TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ 
       33.70        66.28        24.66        71.05        20.52        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
       12.92         8.81        12.69        26.27        23.70         4.67 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       40.44        12.89        41.10        33.11         8.58        35.54 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.57        12.49         8.52        22.45 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.71        20.68        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
        6.74         9.07        11.08        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V 
       35.01        14.56        17.59        29.72        21.21        15.91 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 
       11.44         5.75         4.41        12.07         2.70         7.33 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 
       32.88         4.24        14.99        70.13        33.11        43.04 
TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 
       28.83        29.36        32.81        12.46        31.23        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6480 
       37.87        26.27        50.01        39.52        34.52        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7368 
       10.22        11.34         7.69        11.51        15.75        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 
       35.84         3.09         0.99        31.96        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
       47.01        27.06        29.82        30.02        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5439 
       30.58         5.13         5.95        48.39        17.16        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
      107.51        94.88        17.92        86.83        48.59        43.23 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6941 
       62.43         9.60         2.14         9.70         4.73        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
      126.08        19.79        15.09         6.08        53.95        10.98 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        2.50        64.83       111.16        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7183 TCGA-CV-7235 
        5.26         1.84        52.31        12.92       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
        4.73        47.47        18.97        95.34         4.96        11.87 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        57.47        35.54       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 
        0.46        22.85        25.94        34.09        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45V 
      153.86        22.19        27.98        24.99       169.38         1.05 
TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A468 
       45.96        88.87        60.43        67.86         0.76        15.25 
TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6K1 TCGA-CV-A6K2 
        5.98         6.38         6.48        22.03        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 
       10.42        10.55        34.36        13.25         9.60         2.53 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        24.95        17.72        12.36        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
        7.63        14.30        12.10        12.79        11.11        35.54 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       30.94        33.86        25.48        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
       11.18        37.18        21.63        20.25         3.02        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 
        0.46        17.85        11.80        12.43        13.38        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 
       13.61        21.11         6.77         0.07        25.74        14.66 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 
       12.66        22.85         0.36        13.84         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
       12.76        11.84        13.55        14.47        11.84        13.35 
TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF 
       10.75        12.62        16.08        29.92        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       36.82        47.01        75.55        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       21.07        17.65        16.70         9.34         5.62        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X0 
        9.73         9.76         8.32        12.72         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JC 
       32.45        13.68        43.59        54.67        43.36        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       24.16        21.86        20.75        22.36        32.65        17.03 
TCGA-WA-A7H4 
       14.56 

  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                         180.16                          210.97 
  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE 
                         18.955                          17.100 
[1] "0.1 - 180.2 (19.0)" "0.1 - 211.0 (17.1)"
[1] "hr=" "1.1"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 28(20Q11.22) MUTATED        15       32        37       104
  AMP PEAK 28(20Q11.22) WILD-TYPE      12       45        40       148
                                 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                              12
  STAGE II                             32                              45
  STAGE III                            37                              40
  STAGE IVA                           104                             148
  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 53 44 74
  AMP PEAK 28(20Q11.22) WILD-TYPE    24 80 55 98
D28V4, multiclass
       clus
vv      AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  T0+T1                            26                              24
  T2                               53                              80
  T3                               44                              55
  T4                               74                              98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 28(20Q11.22) MUTATED    78  29  70   4
  AMP PEAK 28(20Q11.22) WILD-TYPE 100  37  95   4
D28V5, multiclass
    clus
vv   AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  N0                            78                             100
  N1                            29                              37
  N2                            70                              95
  N3                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                                 cls
clus                               0  1
  AMP PEAK 28(20Q11.22) MUTATED   86  0
  AMP PEAK 28(20Q11.22) WILD-TYPE 97  1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     86    0
  AMP PEAK 28(20Q11.22) WILD-TYPE   97    1
   clus
vv  AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  0                            86                              97
  1                             0                               1
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.22) MUTATED    57 168
  AMP PEAK 28(20Q11.22) WILD-TYPE  82 209
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     57  168
  AMP PEAK 28(20Q11.22) WILD-TYPE   82  209
        clus
vv       AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  FEMALE                            57                              82
  MALE                             168                             209
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.22) MUTATED                                     222
  AMP PEAK 28(20Q11.22) WILD-TYPE                                   283
                                 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                                                 222
  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                                                   283
  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    40 185
  AMP PEAK 28(20Q11.22) WILD-TYPE  41 250
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     40  185
  AMP PEAK 28(20Q11.22) WILD-TYPE   41  250
     clus
vv    AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
  NO                             40                              41
  YES                           185                             250
[1] 2 2
[1] FALSE
D28V10, continuous
D28V11, continuous
D28V12, 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                          23   188
  AMP PEAK 28(20Q11.22) WILD-TYPE                        22   253
D28V13, multiclass
                                  clus
vv                                 AMP PEAK 28(20Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      188
                                  clus
vv                                 AMP PEAK 28(20Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                        253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.22) MUTATED    13 193
  AMP PEAK 28(20Q11.22) WILD-TYPE  12 261
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.22) MUTATED     13  193
  AMP PEAK 28(20Q11.22) WILD-TYPE   12  261
                        clus
vv                       AMP PEAK 28(20Q11.22) MUTATED
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           193
                        clus
vv                       AMP PEAK 28(20Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             261
[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    80  65
  AMP PEAK 29(XQ28) WILD-TYPE 233 135
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        145                         368 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         65                         135 
$`AMP PEAK 29(XQ28) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6872 TCGA-BA-7269 
        9.30        37.28        26.50        53.79        12.62         7.76 
TCGA-BA-A6DA TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
       11.54        20.48        16.41        94.62         4.60         4.41 
TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        25.71        10.55        27.19        12.92         8.81 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 
       38.04        37.84        12.99        20.55        14.33        13.05 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6023 TCGA-CN-6988 
       11.57        20.71        20.68        20.65        36.49        10.45 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63Y TCGA-CN-A6V6 TCGA-CQ-5327 
       20.09        17.42        29.72         5.75         7.69        54.58 
TCGA-CQ-5329 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 
       46.75        41.19        32.38         4.24        38.76        16.73 
TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6467 
       64.11        11.61        14.14        11.77        54.67        58.42 
TCGA-CR-6477 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7390 
       16.90         7.69         9.27        19.92        17.13        29.82 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        7.10         5.95       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 
       76.24        17.95        76.50        80.12        13.35        48.59 
TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 
       60.49        21.07        90.12         9.70         5.46        26.43 
TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 
       30.08         8.42        18.81         5.26         1.84        71.21 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 
       77.16         4.73        31.36        26.20        18.97        95.34 
TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7424 TCGA-CV-7425 
        2.10        35.54        17.85        22.85        14.89        56.48 
TCGA-CV-7432 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45X TCGA-CV-A465 
       84.49        16.64         6.38       169.38         6.51         7.07 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 
       35.34         6.38        21.24        18.84        25.41        23.05 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 
       18.67        24.95        15.88        35.54        30.94        18.02 
TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50G TCGA-H7-A6C5 TCGA-HD-7754 
       14.04         9.83        37.18        20.25        21.11        25.74 
TCGA-HD-7917 TCGA-HD-8635 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61K 
        1.22        22.85         6.90        15.95        11.84         5.29 
TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QE 
       18.15         7.96        15.42        16.08        15.78        51.25 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       18.97         2.04        29.00        12.99         5.62        11.57 
TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       15.91        13.55        13.25        54.67         2.83        43.36 
TCGA-UF-A71E TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ 
       42.02        24.16        21.86        20.75        22.36        20.55 
TCGA-WA-A7H4 
       14.56 

$`AMP PEAK 29(XQ28) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
        3.35        15.19        13.64         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
       57.93        17.10        23.84        20.48        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG 
       21.17        14.83         3.55         4.01        29.42        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        30.18        27.95         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4224 
        7.82         2.27        11.05        13.38         6.15         9.14 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.35        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
       66.28        24.66        38.40        20.52         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
       26.27        23.70         4.67        40.44        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       32.65        21.11        41.10        43.73        27.58        41.69 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       33.11        34.36         8.58        12.39        35.54         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.84        12.49         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       56.94        30.67        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 
        6.74         9.07         9.24        11.08        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       12.85        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5330 
        6.18        48.20        39.68        21.50         2.93        45.80 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 
       45.99        10.42        11.21         4.24        32.88        34.75 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58        13.25        14.99        70.13        51.29        33.11 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       43.04        41.88        28.83        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5249 
       32.81        25.81        12.46        31.23        84.23        37.87 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       26.27        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 
        6.02        11.90        10.22        11.34        11.64        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       11.51        15.75        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       35.84         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        34.06        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 
       30.58         5.13        35.41        29.95        48.39        19.20 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
      107.51        94.88        91.53        17.92        23.05        86.83 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        7.07        43.23        54.74        62.43         9.60         2.14 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        11.24       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       12.03        42.38        15.09         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
       10.98         7.13        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 
      126.15       111.16        12.66         7.99         9.01        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
       12.92        21.80        10.75       130.88        47.47        36.00 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       17.13         4.96        11.87        47.97        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 
       57.47       210.97        89.33         9.67         0.46        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7427 TCGA-CV-7428 
       25.94         0.07        34.09       100.57       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        3.52        16.27        19.76         7.17       153.86        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        24.99       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
       45.96        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       56.61        15.25         5.98        29.79         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       10.55        34.36        13.25         9.60         2.53        16.14 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO 
       11.44        25.32        17.72        12.36         7.63        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 
       13.94        12.10        12.79        11.11        58.45        33.86 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       18.90        25.48        20.45        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       11.18        16.11        21.63         3.02        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        15.06        13.61         6.77         0.07 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
        0.16        14.66        22.03        12.66         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        4.27         3.65        34.75        12.76        14.50        19.33 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
       13.55         0.07        14.47        11.54        11.84        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       12.43        10.75        14.37        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QF 
        3.68         7.13        17.98        29.92        56.75        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T7 TCGA-P3-A6T8 
       36.82        47.01        19.00        75.55        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8ZA 
       12.72        18.64        14.79        12.43         6.51        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        9.73         9.76         8.32        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7J9 
        7.10        32.45        13.68        43.59        41.16        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT 
       62.27        17.95        49.22        16.11        13.94        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW 
        2.96        17.03 

  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                       1.22                        0.07 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                     169.38                      210.97 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                     18.970                      17.685 
[1] "1.2 - 169.4 (19.0)" "0.1 - 211.0 (17.7)"
[1] "hr=" "1.1"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 29(XQ28) MUTATED         6       19        20        78         3
  AMP PEAK 29(XQ28) WILD-TYPE      21       58        57       174         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                          21
  STAGE II                         19                          58
  STAGE III                        20                          57
  STAGE IVA                        78                         174
  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      11  32  37  50
  AMP PEAK 29(XQ28) WILD-TYPE    39 101  62 122
D29V4, multiclass
       clus
vv      AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T0+T1                        11                          39
  T2                           32                         101
  T3                           37                          62
  T4                           50                         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 29(XQ28) MUTATED    44  18  57   2
  AMP PEAK 29(XQ28) WILD-TYPE 134  48 108   6
D29V5, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  N0                        44                         134
  N1                        18                          48
  N2                        57                         108
  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"
D29V6, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    43   1
  AMP PEAK 29(XQ28) WILD-TYPE 140   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     43    1
  AMP PEAK 29(XQ28) WILD-TYPE  140    0
   clus
vv  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  0                        43                         140
  1                         1                           0
[1] 2 2
[1] FALSE
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    35 111
  AMP PEAK 29(XQ28) WILD-TYPE 104 266
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     35  111
  AMP PEAK 29(XQ28) WILD-TYPE  104  266
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        35                         104
  MALE                         111                         266
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                     144
  AMP PEAK 29(XQ28) WILD-TYPE                                   361
                             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                                             144
  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                                               361
  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    29 117
  AMP PEAK 29(XQ28) WILD-TYPE  52 318
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     29  117
  AMP PEAK 29(XQ28) WILD-TYPE   52  318
     clus
vv    AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  NO                         29                          52
  YES                       117                         318
[1] 2 2
[1] FALSE
D29V10, continuous
D29V11, continuous
D29V12, 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   128
  AMP PEAK 29(XQ28) WILD-TYPE                        34   313
D29V13, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                  128
                                  clus
vv                                 AMP PEAK 29(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 34
  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"
D29V14, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED     8 128
  AMP PEAK 29(XQ28) WILD-TYPE  17 326
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      8  128
  AMP PEAK 29(XQ28) WILD-TYPE   17  326
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             8                          17
  NOT HISPANIC OR LATINO                       128                         326
[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  40
  DEL PEAK  1(1P36.21) WILD-TYPE 260 160
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            93                            420 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            40                            160 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
       15.19         9.30         9.07        15.52        14.83         3.55 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7871 
        7.76        27.95        20.48        18.35        36.72        24.66 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6012 
       20.52        10.55        33.11        34.36        35.54        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 
       19.07        14.20         9.07        11.08        20.09        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-6221 
       24.16         3.68        14.10         7.40        10.42        32.88 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6470 
       13.25        14.99        64.11        23.24        31.23        50.01 
TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       34.52        11.64        39.16         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7380 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.23         0.99        19.92       129.21       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6935 
       17.95       107.51         7.07        54.74        90.12         9.70 
TCGA-CV-6948 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7254 
       42.38         4.14        18.81        12.66         5.26        47.97 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7430 
       36.13        57.47        25.94        14.89        56.48        16.27 
TCGA-CV-7440 TCGA-CV-A6JE TCGA-D6-6516 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q 
       22.19        35.34        25.41         7.63        13.94        11.11 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-8489 TCGA-HD-8314 
       30.94        18.90        20.45         9.83        21.63        22.03 
TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W 
       12.66         3.65        11.84        11.54        13.35        14.37 
TCGA-QK-A8Z7 TCGA-T2-A6X0 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        6.51         7.10         2.83        41.16        42.02        44.65 
TCGA-UF-A7JD TCGA-UF-A7JO TCGA-WA-A7GZ 
       24.16        20.75        20.55 

$`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 
        3.35        13.64        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        53.79        57.44 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       21.17        12.62         4.01        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       30.18        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        16.41         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
        9.14         4.60         4.41        22.42        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HZ 
       44.98        66.28        38.40        71.05        25.71        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       12.92         8.81         6.28        12.69        26.27        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5359 
       43.73        27.58        41.69        13.05         8.58        12.39 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        8.52        22.45        56.94        20.71        30.67        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
       19.53        20.68         6.74         9.24        36.49        10.45 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.80        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
       41.19        32.38        34.75        56.58         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       28.83        44.48        11.61        29.36        32.81        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       26.27        58.42        39.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        6.02        11.90        10.22        11.34         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       11.51        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
       35.84        31.96         9.17        34.06        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       19.20        94.88        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       13.35        23.05        86.83        48.59        60.49        43.23 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 
       21.07        62.43         9.60         2.14         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       12.03        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 
       10.98         7.13         8.42        28.34         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
      126.15       111.16         7.99         9.01         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
       12.92        21.80        71.21        10.75       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        47.47        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 
       17.13        95.34         4.96        11.87         2.10        18.41 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       35.54        17.85       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7427 
       22.85        25.08         0.07        34.09       100.57       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94         3.52        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       16.64         6.38        27.98        24.99       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       48.20        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98         6.38        29.79         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 
       10.42        10.55        18.84        34.36        13.25         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ 
       25.32        17.72        12.36        15.88        14.30        12.10 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       12.79        58.45        35.54        33.86        18.02        14.04 
TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       25.48        12.13        12.10        10.65        11.18        37.18 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       16.11        20.25         3.02        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A4C1 
        0.16        25.74         1.22        14.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         6.90        34.75        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        19.33        13.55         0.07        14.47         5.29 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A 
       11.84        18.15        12.43        10.75         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         3.68        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       14.79        12.43         5.62        11.57        12.10         9.73 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
        9.76         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        13.68        43.59        54.67 
TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       43.36        62.27        17.95        49.22        21.86        16.11 
TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       13.94        22.36        32.65         2.96        17.03        14.56 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          0.99                           0.07 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        129.21                         210.97 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        19.070                         17.885 
[1] "1.0 - 129.2 (19.1)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.2"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.21) MUTATED         4       11        18        40         3
  DEL PEAK  1(1P36.21) WILD-TYPE      23       66        59       212         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                             23
  STAGE II                            11                             66
  STAGE III                           18                             59
  STAGE IVA                           40                            212
  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  19  21  31
  DEL PEAK  1(1P36.21) WILD-TYPE    42 114  78 141
D30V4, multiclass
       clus
vv      DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  T0+T1                            8                             42
  T2                              19                            114
  T3                              21                             78
  T4                              31                            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  1(1P36.21) MUTATED    31  12  25   2
  DEL PEAK  1(1P36.21) WILD-TYPE 147  54 140   6
D30V5, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  N0                           31                            147
  N1                           12                             54
  N2                           25                            140
  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"
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    29   0
  DEL PEAK  1(1P36.21) WILD-TYPE 154   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     29    0
  DEL PEAK  1(1P36.21) WILD-TYPE  154    1
   clus
vv  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  0                           29                            154
  1                            0                              1
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    22  71
  DEL PEAK  1(1P36.21) WILD-TYPE 117 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     22   71
  DEL PEAK  1(1P36.21) WILD-TYPE  117  306
        clus
vv       DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           22                            117
  MALE                             71                            306
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                      88
  DEL PEAK  1(1P36.21) WILD-TYPE                                   417
                                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                                                 88
  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                                                  417
  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    23  70
  DEL PEAK  1(1P36.21) WILD-TYPE  58 365
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     23   70
  DEL PEAK  1(1P36.21) WILD-TYPE   58  365
     clus
vv    DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  NO                            23                             58
  YES                           70                            365
[1] 2 2
[1] FALSE
D30V10, continuous
D30V11, continuous
D30V12, 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    77
  DEL PEAK  1(1P36.21) WILD-TYPE                        35   364
D30V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      77
                                  clus
vv                                 DEL PEAK  1(1P36.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       364
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED     4  80
  DEL PEAK  1(1P36.21) WILD-TYPE  21 374
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED      4   80
  DEL PEAK  1(1P36.21) WILD-TYPE   21  374
                        clus
vv                       DEL PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       DEL PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            374
[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    72  56
  DEL PEAK  2(1P13.2) WILD-TYPE 241 144
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          128                           385 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           56                           144 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-6870 TCGA-BA-6871 
        3.35         9.30        13.64        42.35        14.83         3.55 
TCGA-BA-7269 TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BB-7862 TCGA-BB-8601 TCGA-BB-A5HY 
        7.76        14.47        11.05        36.72        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4731 
       27.19         8.81         6.28        23.70        12.89        32.65 
TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6012 
       20.55        33.11        12.39        35.54        20.71        20.68 
TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 
       19.07         9.07         9.24        11.08        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A6V3 
        3.68        14.10        11.74         7.40        11.44         9.80 
TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CI 
       10.42        13.25        51.29        16.73        64.11        31.23 
TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        6.02        10.22        39.16         3.45         3.09        24.95 
TCGA-CR-7374 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        0.99         5.95       139.43       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 
       19.20        17.95       107.51        80.12        86.83        60.49 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        7.07        54.74        21.07         9.70         5.46        20.52 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 
       26.43        11.24        42.38         4.14       111.16        18.81 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7245 
        5.26         1.84        52.31        10.75        36.00        26.20 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 
       47.97        36.13        35.54         0.46        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A45W TCGA-CV-A461 TCGA-CV-A6JT 
        0.07        14.89       153.86        45.96        67.86        22.03 
TCGA-CX-7082 TCGA-D6-6516 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
       10.42        25.41        12.36         7.63        14.30        13.94 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 
       11.11        30.94        21.63         3.02        18.94        20.25 
TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-IQ-A61H TCGA-IQ-A61L 
        0.16        22.03        12.66        22.85        13.55        11.54 
TCGA-KU-A66T TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A6VC 
       18.15        15.78        51.25        29.00        13.15        12.43 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-T2-A6WZ TCGA-UF-A718 TCGA-UF-A719 
        5.62        11.57         9.73        15.91        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        41.16        42.02        44.65        17.95        24.16 
TCGA-UF-A7JK TCGA-WA-A7GZ 
       13.94        20.55 

$`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 
       15.19        37.28         9.07        26.50        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       17.10        23.84        20.48        53.79        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       21.17        12.62         4.01        29.42        28.11        20.45 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF 
       30.18        27.95        11.54         7.10         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        2.27        13.38        20.48        16.41         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        9.14         4.60         4.41        18.35        22.42        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        66.28        24.66        38.40        71.05 
TCGA-BB-A5HU TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 
       25.71        12.92        12.69        26.27        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       40.44        37.84        26.86        21.11        41.10        12.99 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       14.33        43.73        27.58        41.69        13.05        34.36 
TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        8.58         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 
       12.49         8.52        22.45        56.94        30.67        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6988 
       19.53        20.68        14.20         6.74        36.49        10.45 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       20.09        17.42        35.01        14.56        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21        17.29        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07         2.70        10.09         7.33         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.80        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       32.88        34.75        56.58         4.24        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       70.13        33.11        43.04        41.88        28.83        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        32.81        25.81        14.14 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       16.90        11.90        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       11.51        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       35.84        29.23        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
        7.10         5.13        35.41        29.95        48.39        17.16 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       94.88        76.50        91.53        17.92        13.35        23.05 
TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       48.59        43.23        62.43         9.60        90.12         2.14 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
        4.73        21.90       126.08        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 
        8.42        28.34         2.50        64.83       126.15        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 
        7.99         9.01        12.92        21.80        71.21       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 
       77.16         4.73        47.47        31.36        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 
       95.34         4.96        11.87         2.10        18.41        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7422 
       17.85       210.97        89.33         9.67        22.85        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
      100.57        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76         7.17        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        24.99       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 
        1.05         6.51        88.87        48.20        60.43         0.76 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       56.61         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       22.52        10.42        10.55        18.84        34.36        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EQ TCGA-D6-A6ES 
       24.95        25.32        17.72        15.88        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        35.54        33.86        18.02        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V 
       11.18        37.18        16.11        20.25        19.23        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       15.06        13.61        21.11         6.77         0.07        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
        1.22        14.66         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S 
       11.84         0.07        14.47         5.29        11.84        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         3.68        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       29.92        56.75        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z 
       75.55        18.97         2.04        12.99        16.01        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K 
       18.64        14.79         6.51        12.10         9.76         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       12.72        16.96         6.87         7.10        32.45        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH 
       13.25        13.68        43.36        62.27        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       16.11        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                        17.95                         18.35 
[1] "0.1 - 153.9 (17.9)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.2"
D31V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  2(1P13.2) MUTATED         6       18        21        69         2
  DEL PEAK  2(1P13.2) WILD-TYPE      21       59        56       183        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                            21
  STAGE II                           18                            59
  STAGE III                          21                            56
  STAGE IVA                          69                           183
  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  31  31  48
  DEL PEAK  2(1P13.2) WILD-TYPE    41 102  68 124
D31V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                           9                            41
  T2                             31                           102
  T3                             31                            68
  T4                             48                           124
[1] 4 2
[1] TRUE
[1] "dimension of 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    47  19  44   2
  DEL PEAK  2(1P13.2) WILD-TYPE 131  47 121   6
D31V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          47                           131
  N1                          19                            47
  N2                          44                           121
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    44   1
  DEL PEAK  2(1P13.2) WILD-TYPE 139   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     44    1
  DEL PEAK  2(1P13.2) WILD-TYPE  139    0
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          44                           139
  1                           1                             0
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    35  95
  DEL PEAK  2(1P13.2) WILD-TYPE 104 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     35   95
  DEL PEAK  2(1P13.2) WILD-TYPE  104  282
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          35                           104
  MALE                            95                           282
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED                                     126
  DEL PEAK  2(1P13.2) WILD-TYPE                                   379
                               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                                               126
  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                                                 379
  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    17 113
  DEL PEAK  2(1P13.2) WILD-TYPE  64 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     17  113
  DEL PEAK  2(1P13.2) WILD-TYPE   64  322
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                           17                            64
  YES                         113                           322
[1] 2 2
[1] FALSE
D31V10, continuous
D31V11, continuous
D31V12, 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                          15   107
  DEL PEAK  2(1P13.2) WILD-TYPE                        30   334
D31V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    107
                                  clus
vv                                 DEL PEAK  2(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   30
  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"
D31V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     7 111
  DEL PEAK  2(1P13.2) WILD-TYPE  18 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7  111
  DEL PEAK  2(1P13.2) WILD-TYPE   18  343
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         111
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           343
[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    25  22
  DEL PEAK  3(1Q44) WILD-TYPE 288 178
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         47                         466 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         22                         178 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-BA-4074 TCGA-BA-5152 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4736 
       15.19        42.35        20.52        27.19         6.28        12.99 
TCGA-CN-5355 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T TCGA-CN-A63W 
       33.11        19.07        24.16         3.68         7.40        11.44 
TCGA-CN-A640 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6227 
        4.41        45.80        11.21        41.19        32.38         4.24 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7372 TCGA-CV-5439 TCGA-CV-5441 
       11.61         6.02        39.16        24.95        17.95        94.88 
TCGA-CV-6003 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-7095 TCGA-CV-7416 TCGA-CV-A463 
       54.74        12.03        15.09        18.81        25.08         0.76 
TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JT TCGA-D6-6517 TCGA-D6-A4Z9 TCGA-DQ-7588 
        7.07        29.79        22.03         9.60        17.72        14.04 
TCGA-DQ-7589 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A61W TCGA-HD-8634 TCGA-IQ-A61L 
       18.90        21.63        18.94         0.46        12.66        11.54 
TCGA-KU-A6H7 TCGA-P3-A6T8 TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-WA-A7GZ 
       12.43        13.15        44.65        17.95        20.55 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
        3.35         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        57.93        17.10        23.84        20.48        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       57.44        15.52        21.17        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
        4.01         7.76        29.42        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
       94.62         9.14         4.60         4.41        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       36.72        33.70        50.20        44.98        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO 
       38.40        71.05        25.71        10.55        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        26.27        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       37.84        12.89        26.86        32.65        21.11        41.10 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       34.36         8.58        12.39        35.54         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        20.71        30.67        20.68        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       20.68        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
       11.08        10.45        20.09        12.95        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        14.56        17.59        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 
       21.21        17.29        15.91         5.75        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       39.68        21.50         2.93        54.58        46.75        45.99 
TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       10.42         4.24        32.88        34.75        56.58        13.25 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        51.29        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       43.04        41.88        28.83        64.11        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       50.01        39.52        34.52        36.99        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       11.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       11.51        15.75         9.27        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
       35.84         3.45         3.09        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
      108.95        76.24        19.20       107.51        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       80.12        17.92        13.35        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49         7.07        43.23        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
       21.90        26.43        11.24       126.08        19.79        42.38 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       18.97        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
        2.10        36.13        18.41        57.47        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.07        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        6.51        88.87        48.20        60.43        67.86        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JU 
       15.25         5.98        35.34         6.38         6.48         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 
       10.55        18.84        34.36        13.25        25.41        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        35.54        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       18.02        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        11.18        37.18        16.11        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       19.23        12.62        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        14.66        22.03 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
       34.75        15.95        12.76        14.50        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S 
       13.55         0.07        14.47         5.29        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       18.15        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         3.68        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        56.75        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        16.01        21.07        11.74        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       16.70         9.34        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
        6.51         5.62        11.57        12.10         9.73         9.76 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
        8.32        12.72        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
        2.83        43.36        41.16        42.02        62.27        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       49.22        21.86        16.11        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       32.65         2.96        17.03        14.56 

  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                       0.46                        0.07 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      94.88                      210.97 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                      17.95                       18.25 
[1] "0.5 - 94.9 (17.9)"  "0.1 - 211.0 (18.2)"
[1] "hr=" "1.5"
D32V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  3(1Q44) MUTATED         2        5         8        26         0
  DEL PEAK  3(1Q44) WILD-TYPE      25       72        69       226        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                          25
  STAGE II                          5                          72
  STAGE III                         8                          69
  STAGE IVA                        26                         226
  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  13  13  14
  DEL PEAK  3(1Q44) WILD-TYPE    47 120  86 158
D32V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         3                          47
  T2                           13                         120
  T3                           13                          86
  T4                           14                         158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  3(1Q44) MUTATED    18   5  17   0
  DEL PEAK  3(1Q44) WILD-TYPE 160  61 148   8
D32V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                        18                         160
  N1                         5                          61
  N2                        17                         148
  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"
D32V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    18   0
  DEL PEAK  3(1Q44) WILD-TYPE 165   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     18    0
  DEL PEAK  3(1Q44) WILD-TYPE  165    1
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        18                         165
  1                         0                           1
[1] 2 2
[1] FALSE
D32V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    15  32
  DEL PEAK  3(1Q44) WILD-TYPE 124 345
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     15   32
  DEL PEAK  3(1Q44) WILD-TYPE  124  345
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        15                         124
  MALE                          32                         345
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(1Q44) MUTATED                                      47
  DEL PEAK  3(1Q44) WILD-TYPE                                   458
                             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                                              47
  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                                               458
  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  40
  DEL PEAK  3(1Q44) WILD-TYPE  74 395
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      7   40
  DEL PEAK  3(1Q44) WILD-TYPE   74  395
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                          7                          74
  YES                        40                         395
[1] 2 2
[1] FALSE
D32V10, continuous
D32V11, continuous
D32V12, 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    42
  DEL PEAK  3(1Q44) WILD-TYPE                        43   399
D32V13, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                   42
                                  clus
vv                                 DEL PEAK  3(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 43
  WHITE                                                    399
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED     4  41
  DEL PEAK  3(1Q44) WILD-TYPE  21 413
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      4   41
  DEL PEAK  3(1Q44) WILD-TYPE   21  413
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             4                          21
  NOT HISPANIC OR LATINO                        41                         413
[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    50  26
  DEL PEAK  4(2Q21.2) WILD-TYPE 263 174
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           76                           437 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           26                           174 
$`DEL PEAK  4(2Q21.2) MUTATED`
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A6DF 
       13.64        23.74        42.35        15.52         4.01         7.82 
TCGA-BA-A8YP TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-C9-A47Z TCGA-CN-4723 
       16.41        22.42        36.72        33.70         6.28        23.70 
TCGA-CN-4736 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
       12.99        12.39         8.32        22.45        56.94        30.67 
TCGA-CN-6018 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A498 TCGA-CN-A499 
       19.07        11.08        24.16         3.68        14.56        17.59 
TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A6V3 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-7064 
       29.72        15.91         9.80        45.99         4.24        51.29 
TCGA-CQ-7069 TCGA-CQ-A4CB TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7395 TCGA-CR-7399 
       41.88        29.36        34.52        11.64        30.58         5.95 
TCGA-CR-7402 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-7091 TCGA-CV-7095 
       29.95        86.83        54.74        62.43       111.16        18.81 
TCGA-CV-7235 TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-A45R 
       77.16         4.96         2.10       100.57        56.48       180.16 
TCGA-CV-A465 TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-D6-6826 TCGA-D6-A6EM TCGA-D6-A6EP 
        7.07        21.24        10.42        11.44         7.63        13.94 
TCGA-DQ-7593 TCGA-F7-A50J TCGA-F7-A620 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ 
       12.13        19.23        17.85         0.16         1.22         3.65 
TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T TCGA-KU-A6H7 TCGA-P3-A5Q6 TCGA-P3-A6T4 
       19.33        11.54        18.15        12.43        15.78         2.04 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO 
        7.30        16.70         6.51        12.10         8.32        12.72 
TCGA-T2-A6WZ TCGA-UF-A71E TCGA-UF-A7JF TCGA-WA-A7GZ 
       15.91        42.02        49.22        20.55 

$`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 
        3.35        15.19         9.30        37.28         9.07        26.50 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        53.79        57.44 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83         3.55        12.62         7.76        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       28.11        20.45        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69        14.47         2.27        11.05        13.38        20.48 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15        94.62         9.14         4.60         4.41        18.35 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       50.20        44.98        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       20.52        25.71        10.55        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
       12.69        26.27        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
       12.89        26.86        32.65        21.11        41.10        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        43.73        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       34.36         8.58        35.54        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 
       11.57        12.49         8.52        20.71        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       19.53        20.68        14.20         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
       36.49        10.45        20.09        12.95        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       11.74        35.01        12.85        21.21         7.40        17.29 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       11.44         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        7.33         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        54.58        46.75        45.80        10.42        11.21 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       41.19        32.38        32.88        34.75        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        70.13        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       43.04        28.83        64.11        44.48        11.61        23.24 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       32.81        25.81        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        36.99        18.54        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 
       29.85        29.52         7.10         5.13        35.41        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
      139.43        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.95       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       17.92        13.35        23.05        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        21.07         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 
       28.34         2.50         4.14        64.83       126.15        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       21.80        71.21        10.75       130.88         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       11.87        47.97        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
       25.08        25.94         0.07        34.09        14.89       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       54.94         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      153.86        16.64         6.38        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      169.38       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 
       22.03         3.62        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
       23.05         2.53        16.14        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
       17.72        12.36        15.88        14.30        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       11.11        58.45        35.54        30.94        33.86        18.02 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       14.04        18.90        25.48        20.45         9.83        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       10.65        11.18        37.18        16.11        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 
        3.02        18.94        12.62         0.46        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
        6.77         0.07        25.74        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.85         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        12.76        14.50        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
       14.47         5.29        11.84        13.35        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
        7.13        16.08        17.98        29.92        56.75        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       10.85        36.82        47.01        19.00        75.55        18.97 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       17.65         9.34        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62        11.57         9.73         9.76        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        43.36        41.16        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.16        21.86        16.11        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       22.36        32.65         2.96        17.03        14.56 

  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                         0.16                          0.07 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                       16.555                        18.540 
[1] "0.2 - 180.2 (16.6)" "0.1 - 211.0 (18.5)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  4(2Q21.2) MUTATED         3        9        18        34         3
  DEL PEAK  4(2Q21.2) WILD-TYPE      24       68        59       218         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                            24
  STAGE II                            9                            68
  STAGE III                          18                            59
  STAGE IVA                          34                           218
  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  19  17  29
  DEL PEAK  4(2Q21.2) WILD-TYPE    44 114  82 143
D33V4, multiclass
       clus
vv      DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  T0+T1                           6                            44
  T2                             19                           114
  T3                             17                            82
  T4                             29                           143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  4(2Q21.2) MUTATED    31  13  20   2
  DEL PEAK  4(2Q21.2) WILD-TYPE 147  53 145   6
D33V5, multiclass
    clus
vv   DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  N0                          31                           147
  N1                          13                            53
  N2                          20                           145
  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"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED    31   0
  DEL PEAK  4(2Q21.2) WILD-TYPE 152   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     31    0
  DEL PEAK  4(2Q21.2) WILD-TYPE  152    1
   clus
vv  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  0                          31                           152
  1                           0                             1
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED    31  45
  DEL PEAK  4(2Q21.2) WILD-TYPE 108 332
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     31   45
  DEL PEAK  4(2Q21.2) WILD-TYPE  108  332
        clus
vv       DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  FEMALE                          31                           108
  MALE                            45                           332
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q21.2) MUTATED                                      74
  DEL PEAK  4(2Q21.2) WILD-TYPE                                   431
                               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                                                74
  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                                                 431
  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  69
  DEL PEAK  4(2Q21.2) WILD-TYPE  74 366
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED      7   69
  DEL PEAK  4(2Q21.2) WILD-TYPE   74  366
     clus
vv    DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  NO                            7                            74
  YES                          69                           366
[1] 2 2
[1] FALSE
D33V10, continuous
D33V11, continuous
D33V12, 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    64
  DEL PEAK  4(2Q21.2) WILD-TYPE                        37   377
D33V13, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     64
                                  clus
vv                                 DEL PEAK  4(2Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      377
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED     6  66
  DEL PEAK  4(2Q21.2) WILD-TYPE  19 388
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED      6   66
  DEL PEAK  4(2Q21.2) WILD-TYPE   19  388
                        clus
vv                       DEL PEAK  4(2Q21.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          66
                        clus
vv                       DEL PEAK  4(2Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           388
[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  49
  DEL PEAK  5(2Q22.1) WILD-TYPE 244 151
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          118                           395 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           49                           151 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5558 TCGA-BA-6871 TCGA-BA-6873 
       13.64        37.28        42.35        53.79         3.55         4.01 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DF TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-A5HU 
        7.76        20.45         7.82        22.42        36.72        25.71 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 
        6.28        23.70        12.99        34.36        12.39         8.32 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6020 
       12.49        56.94        20.71        30.67        19.07         6.74 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A499 TCGA-CN-A49A 
       36.49        24.16         3.68        14.10        17.59        12.85 
TCGA-CN-A49B TCGA-CN-A641 TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4CD 
       29.72        12.07        54.58        51.29        41.88        32.81 
TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7367 TCGA-CR-7371 
       11.77        34.52        18.54        11.64        47.34         3.09 
TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5436 
       47.01        29.82         5.95        29.95        76.24        19.20 
TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6953 
       94.88        86.83         7.07        12.03        42.38        53.95 
TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7252 TCGA-CV-7253 
        4.14       111.16        21.80        77.16         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 
        2.10        35.54        22.85       100.57        14.89       156.49 
TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45V 
        3.52        16.64       169.38       180.16        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K2 
       45.96         7.07        29.79         3.62        21.24        10.42 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM 
       25.41        11.44        24.95        17.72        12.36         7.63 
TCGA-D6-A6EP TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-F7-A50J TCGA-F7-A61V 
       13.94        58.45        30.94        12.13        19.23        12.62 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-A61E 
       17.85        20.25        13.38        14.66         3.65        19.33 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       13.55        11.54        18.15        12.43        17.98        15.78 
TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       13.15        16.70         6.51         5.62        12.10         9.73 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC 
        8.32        12.72         2.83        42.02        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JT 
       24.16        49.22        20.75        32.65 

$`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 
        3.35        15.19         9.30         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
       57.93        17.10        23.84        20.48        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II 
       21.17        14.83        12.62        29.42        28.11        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG 
       27.95        11.54         7.10         5.69        14.47         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 
        9.14         4.60         4.41        18.35        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       44.98        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       10.55        27.19        12.92         8.81        12.69        26.27 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       32.65        21.11        41.10        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       27.58        41.69        13.05        33.11         8.58        35.54 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.84        11.57         8.52        22.45 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 
       20.68        20.65        19.53        20.68        14.20         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
        9.24        11.08        10.45        20.09        12.95        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       11.74        35.01        14.56        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
       15.91        11.44         5.75         4.41         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        7.33         9.80         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        46.75        45.80        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       11.21         4.24        41.19        32.38        32.88        34.75 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       33.11        16.73        43.04        28.83        64.11        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       11.61        23.24        29.36        25.81        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       31.23        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       50.01        39.52        36.99        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34         7.69        12.46        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        9.27        47.18        39.16        40.93        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 
       19.92        26.17        17.13        32.78        27.06        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.13        35.41        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
      108.95        17.95       107.51        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       17.92        13.35        23.05        48.59        60.49        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        9.70         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       11.24       126.08        19.79        15.09        30.08         6.08 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       126.15        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 
        5.26         1.84        52.31        12.92        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
      130.88         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 
       18.97        17.13        95.34        47.97        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        17.85       210.97        89.33         9.67         0.46 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7428 
       25.08        25.94         0.07        34.09        56.48        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 
       16.27        84.49        19.76         7.17       153.86         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45T TCGA-CV-A45X TCGA-CV-A45Y 
       22.19        27.98        24.99       159.65         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       48.20        60.43        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ 
        5.98        35.34         6.38         6.48        22.03        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       19.92        22.52        10.42        10.55        18.84        34.36 
TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
       13.25         9.60        23.05         2.53        16.14        18.67 
TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       25.32        15.88        14.30        12.10        12.79        11.11 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       35.54        33.86        18.02        14.04        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45         9.83        12.10        10.65        11.18        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61W 
       16.11        21.63        20.25         3.02        18.94         0.46 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       11.80        12.43        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 
        6.77         0.07         0.16        25.74         1.22        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       12.66        22.85         0.36        13.84         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I 
       34.75        15.95        12.76        14.50        11.84         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
       14.47         5.29        11.84        13.35        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         3.68        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        29.92        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       29.00        12.99        16.01        21.07        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30         9.34        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       11.57         9.76        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        13.68        43.59        54.67 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       43.36        41.16        44.65        21.86        16.11        13.94 
TCGA-UF-A7JS TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36         2.96        17.03        20.55        14.56 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         1.05                          0.07 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       18.065                        18.020 
[1] "1.1 - 180.2 (18.1)" "0.1 - 211.0 (18.0)"
[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        65         6
  DEL PEAK  5(2Q22.1) WILD-TYPE      25       63        59       187         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                            25
  STAGE II                           14                            63
  STAGE III                          18                            59
  STAGE IVA                          65                           187
  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  53
  DEL PEAK  5(2Q22.1) WILD-TYPE    45 108  75 119
D34V4, multiclass
       clus
vv      DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T0+T1                           5                            45
  T2                             25                           108
  T3                             24                            75
  T4                             53                           119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  5(2Q22.1) MUTATED    41  16  40   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 137  50 125   5
D34V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          41                           137
  N1                          16                            50
  N2                          40                           125
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    53   1
  DEL PEAK  5(2Q22.1) WILD-TYPE 130   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     53    1
  DEL PEAK  5(2Q22.1) WILD-TYPE  130    0
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                          53                           130
  1                           1                             0
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    42  76
  DEL PEAK  5(2Q22.1) WILD-TYPE  97 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     42   76
  DEL PEAK  5(2Q22.1) WILD-TYPE   97  301
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          42                            97
  MALE                            76                           301
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                                     115
  DEL PEAK  5(2Q22.1) WILD-TYPE                                   390
                               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                                               115
  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                                                 390
  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    17 101
  DEL PEAK  5(2Q22.1) WILD-TYPE  64 334
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     17  101
  DEL PEAK  5(2Q22.1) WILD-TYPE   64  334
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           17                            64
  YES                         101                           334
[1] 2 2
[1] FALSE
D34V10, continuous
D34V11, continuous
D34V12, 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   100
  DEL PEAK  5(2Q22.1) WILD-TYPE                        34   341
D34V13, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    100
                                  clus
vv                                 DEL PEAK  5(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   34
  WHITE                                                      341
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     7 100
  DEL PEAK  5(2Q22.1) WILD-TYPE  18 354
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      7  100
  DEL PEAK  5(2Q22.1) WILD-TYPE   18  354
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                18
  NOT HISPANIC OR LATINO                           354
[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    91  63
  DEL PEAK  6(2Q36.2) WILD-TYPE 222 137
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          154                           359 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                           63                           137 
$`DEL PEAK  6(2Q36.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5558 
        9.30        13.64        37.28        42.35        17.10        53.79 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A6D8 
       57.44        15.52         3.55         4.01        28.11        27.95 
TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 
       14.47        13.38        16.41         4.41        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-C9-A480 
       33.70        50.20        20.52        10.55         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       23.70        40.44        12.99        27.58        41.69        13.05 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 
       34.36        35.54         8.32         8.52        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6995 
       20.68        19.07         9.07        11.08        24.16         3.68 
TCGA-CN-6997 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A6V3 
       14.10        17.59        12.85        29.72        11.44         9.80 
TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6225 
        7.69        48.20        54.58        10.42        41.19        13.25 
TCGA-CQ-7064 TCGA-CQ-A4CI TCGA-CR-6472 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6493 
       51.29        31.23        34.52        16.90        11.64         9.27 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
       47.18        47.34        35.84         3.45         3.09        29.23 
TCGA-CR-7374 TCGA-CR-7380 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
        0.99        19.92         5.95        29.95        48.39        17.16 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5978 
      108.95        19.20       107.51        17.92        86.83         7.07 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 
       54.74        21.07        90.12         9.70        11.24       126.08 
TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       12.03         2.50         4.14       111.16        18.81        12.66 
TCGA-CV-7103 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       52.31        17.13         4.96        11.87        47.97        36.13 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 
       57.47        35.54        17.85         9.67        25.08        25.94 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A465 
       34.09        14.89        22.19       180.16        45.96         7.07 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JY TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EM 
       35.34        29.79        21.24        11.44        12.36         7.63 
TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       13.94        30.94        18.90         9.83        12.13        12.10 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 
       20.25        19.23        17.85        20.25        21.11         0.16 
TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       14.66        13.84         3.65        19.33        11.84        13.55 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       11.54        18.15        12.43        16.08        17.98        15.78 
TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZB 
       12.99        13.15         7.30        12.72         6.51         9.73 
TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E 
        8.32        16.96        15.91         2.83        41.16        42.02 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UP-A6WW TCGA-WA-A7GZ 
       21.86        16.11        17.03        20.55 

$`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 
        3.35        15.19         9.07        26.50        23.74        57.93 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       23.84        20.48        21.17        14.83        12.62         7.76 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        30.18        11.54         7.10         5.69 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        11.05        20.48         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
        9.14         4.60        18.35        44.98        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       38.40        71.05        25.71        27.19        12.92         8.81 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       26.27        38.04         4.67        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       32.65        21.11        41.10        20.55        14.33        43.73 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       33.11         8.58        12.39        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 
       11.57        12.49        22.45        20.71        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
       20.68        14.20         6.74         9.24        36.49        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       20.09        12.95        17.42        11.74        35.01        14.56 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        17.29        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        10.09         7.33         6.18        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50         2.93        46.75        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
        4.24        32.38        32.88        34.75        56.58         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       14.99        38.76        70.13        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       41.88        28.83        64.11        44.48        11.61        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        32.81        25.81        14.14        12.46        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7365 
       11.34         7.69        12.46        11.51        15.75        39.16 
TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
       40.93        24.95        31.96         9.17        34.06        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        29.82 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5439 
        5.13        35.41       139.43       129.21        76.24        17.95 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
       94.88        76.50        91.53        80.12        13.35        23.05 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       48.59        60.49        43.23        62.43         9.60         2.14 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 
        5.46        20.52         4.73        21.90        26.43        19.79 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7089 TCGA-CV-7090 
       10.98         7.13         8.42        28.34        64.83       126.15 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         5.26         1.84        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7255 
       36.00        31.36        26.20        18.97        95.34         2.10 
TCGA-CV-7263 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 
       18.41       210.97        89.33         0.46        22.85         0.07 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
      100.57        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        24.99       169.38       159.65        35.47         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT 
       56.61        15.25         5.98         6.38         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
       23.05         2.53        16.14        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       17.72        15.88        14.30        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
       58.45        35.54        33.86        18.02        14.04        25.48 
TCGA-DQ-7591 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45        10.65        11.18        37.18        16.11        21.63 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 
        3.02        18.94        12.62         0.46        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        15.06        13.61         6.77         0.07 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       25.74         1.22        22.03        12.66        22.85         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         6.90        34.75        15.95        12.76        14.50 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 
        0.07        14.47         5.29        11.84        13.35        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         3.68 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       15.42         7.13        29.92        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       29.00        16.01        21.07        11.74        17.65        16.70 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        9.34        18.64        14.79        12.43         5.62        11.57 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.10         9.76        12.72         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       13.55        13.25        13.68        43.59        54.67        43.36 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JK 
       44.65        62.27        17.95        24.16        49.22        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7H4 
       20.75        22.36        32.65         2.96        14.56 

  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                         0.16                          0.07 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                       17.375                        18.670 
[1] "0.2 - 180.2 (17.4)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.1"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  6(2Q36.2) MUTATED         3       18        30        72         6
  DEL PEAK  6(2Q36.2) WILD-TYPE      24       59        47       180         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                            24
  STAGE II                           18                            59
  STAGE III                          30                            47
  STAGE IVA                          72                           180
  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  31  40  55
  DEL PEAK  6(2Q36.2) WILD-TYPE    43 102  59 117
D35V4, multiclass
       clus
vv      DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  T0+T1                           7                            43
  T2                             31                           102
  T3                             40                            59
  T4                             55                           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  6(2Q36.2) MUTATED    51  22  45   4
  DEL PEAK  6(2Q36.2) WILD-TYPE 127  44 120   4
D35V5, multiclass
    clus
vv   DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  N0                          51                           127
  N1                          22                            44
  N2                          45                           120
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    53   0
  DEL PEAK  6(2Q36.2) WILD-TYPE 130   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     53    0
  DEL PEAK  6(2Q36.2) WILD-TYPE  130    1
   clus
vv  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  0                          53                           130
  1                           0                             1
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    43 111
  DEL PEAK  6(2Q36.2) WILD-TYPE  96 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     43  111
  DEL PEAK  6(2Q36.2) WILD-TYPE   96  266
        clus
vv       DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  FEMALE                          43                            96
  MALE                           111                           266
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(2Q36.2) MUTATED                                     151
  DEL PEAK  6(2Q36.2) WILD-TYPE                                   354
                               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                                               151
  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                                                 354
  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    22 132
  DEL PEAK  6(2Q36.2) WILD-TYPE  59 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     22  132
  DEL PEAK  6(2Q36.2) WILD-TYPE   59  303
     clus
vv    DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  NO                           22                            59
  YES                         132                           303
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, continuous
D35V12, 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   123
  DEL PEAK  6(2Q36.2) WILD-TYPE                        25   318
D35V13, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q36.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                    123
                                  clus
vv                                 DEL PEAK  6(2Q36.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    13 132
  DEL PEAK  6(2Q36.2) WILD-TYPE  12 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     13  132
  DEL PEAK  6(2Q36.2) WILD-TYPE   12  322
                        clus
vv                       DEL PEAK  6(2Q36.2) MUTATED
  HISPANIC OR LATINO                              13
  NOT HISPANIC OR LATINO                         132
                        clus
vv                       DEL PEAK  6(2Q36.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           322
[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   198 142
  DEL PEAK  7(3P26.2) WILD-TYPE 115  58
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          340                           173 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          142                            58 
$`DEL PEAK  7(3P26.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
        3.35        15.19         9.30        13.64         9.07        26.50 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        53.79        57.44        15.52        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
        3.55        12.62        29.42        30.18        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 
        7.10        14.47        11.05        20.48        16.41         9.14 
TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
        4.41        36.72        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 
       20.52        25.71        27.19         8.81         6.28        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        37.84        12.89        26.86        32.65 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       41.10        12.99        20.55        14.33        43.73        27.58 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        8.32        16.21        11.54        11.84        11.57         8.52 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       22.45        20.71        30.67        20.68        20.65        19.53 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 
       19.07        14.20         6.74         9.07        11.08        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       12.95        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        14.56        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5325 
       17.29        11.44         4.41        12.07         9.80        21.50 
TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
        2.93        45.80        10.42        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       34.75        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
       51.29        33.11        16.73        41.88        64.11        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        29.36        32.81        25.81        31.23        84.23 
TCGA-CR-5247 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 
       11.77        36.99        18.54        16.90         6.02        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.64         7.69        12.46        11.51        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       47.18        39.16        47.34        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 
       24.95        29.23         9.17        34.06        19.92        17.13 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
       47.01        12.89        29.82         7.10         5.13        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.95       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 
       19.20        17.95       107.51        94.88        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       13.35        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       54.74         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       20.52        26.43        11.24        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       30.08         6.08        65.82         7.13         8.42        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        2.50         4.14        64.83       126.15       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7236 TCGA-CV-7238 
       12.92        21.80        71.21        10.75         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 
       36.00        31.36        26.20        18.97        17.13         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7409 
       11.87        47.97         2.10        36.13        18.41        17.85 
TCGA-CV-7410 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
      210.97         9.67         0.46        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 
        0.07       100.57        14.89        54.94         3.52        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W 
       19.76         7.17       153.86       180.16        35.47        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        6.51        88.87        48.20        60.43        67.86        56.61 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
        7.07        35.34        29.79        22.03         3.62        23.47 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
       22.52        10.42        18.84        34.36        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB 
       23.05        16.14        11.44        24.95        25.32        12.36 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       20.45         9.83        10.65        37.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        19.23        18.94        12.62         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       17.85        11.80        20.25        15.06        13.61        21.11 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ 
        0.07         0.16        12.66        22.85        13.84         3.65 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
        5.29        11.54        11.84        18.15        14.37         7.96 
TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 
        1.84        17.98        15.78        56.75        47.01        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        16.01        13.15        21.07        11.74 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       16.70        12.72        18.64        14.79        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        11.57        12.10         9.73         9.76         8.32 
TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       15.91        13.25        43.59        54.67         2.83        43.36 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       42.02        44.65        17.95        24.16        49.22        21.86 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7H4 
       13.94        20.75        22.36        14.56 

$`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 
       37.28        23.74        42.35        57.93        23.84        20.48 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DD TCGA-BA-A6DF 
        4.01         7.76        28.11        20.45         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 
        2.27        13.38         6.15        94.62         4.60        18.35 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-A5HY TCGA-BB-A6UM 
       22.42        33.70        50.20        44.98        10.55        12.92 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-5369 
       12.69        26.27        40.44        21.11        41.69        12.49 
TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-A499 
       56.94        20.68         9.24        36.49        10.45        17.59 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 
       15.91         5.75         2.70        10.09         7.33         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
        6.18        48.20        39.68        54.58        46.75        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
       11.21         4.24        70.13        43.04        28.83        44.48 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       14.14        12.46        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-7370 
       50.01        39.52        34.52        11.90        10.22         3.45 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7391 
        0.99        31.96        26.17        32.78        27.06        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 
       31.10        29.85        29.52        30.58         5.95        48.39 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 
       76.50        91.53        23.05        21.07        62.43         4.73 
TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7183 
       21.90       126.08        19.79        53.95        10.98       130.88 
TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7411 TCGA-CV-7422 
       77.16        95.34        57.47        35.54        89.33        34.09 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       56.48       156.49        16.27        16.64         6.38        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A463 
       27.98        24.99       169.38       159.65         1.05         0.76 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 
       15.25         5.98         6.38         6.48        21.24        19.92 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 
       10.42        10.55        13.25         2.53        18.67        17.72 
TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
       15.88        35.54        25.48        12.13        12.10        11.18 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 
       12.43        13.38        15.16         6.77        25.74         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       14.66        22.03         0.36         4.27         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A 
       12.76        14.50        13.35        12.43        10.75        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       12.62         3.68        15.42         7.13        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 
       51.25        10.85        36.82        19.00        75.55        12.99 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       17.65         7.30         9.34        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71D TCGA-UF-A7JA 
        7.10        32.45        13.55        13.68        41.16        62.27 
TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       16.11        32.65         2.96        17.03        20.55 

  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                         0.07                          0.36 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                       210.97                        169.38 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                        17.95                         19.00 
[1] "0.1 - 211.0 (17.9)" "0.4 - 169.4 (19.0)"
[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       48        54       176        10
  DEL PEAK  7(3P26.2) WILD-TYPE       9       29        23        76         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                             9
  STAGE II                           48                            29
  STAGE III                          54                            23
  STAGE IVA                         176                            76
  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      30  81  75 125
  DEL PEAK  7(3P26.2) WILD-TYPE    20  52  24  47
D36V4, multiclass
       clus
vv      DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  T0+T1                          30                            20
  T2                             81                            52
  T3                             75                            24
  T4                            125                            47
[1] 4 2
[1] TRUE
[1] "dimension of 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   117  46 122   6
  DEL PEAK  7(3P26.2) WILD-TYPE  61  20  43   2
D36V5, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  N0                         117                            61
  N1                          46                            20
  N2                         122                            43
  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"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED   123   1
  DEL PEAK  7(3P26.2) WILD-TYPE  60   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED    123    1
  DEL PEAK  7(3P26.2) WILD-TYPE   60    0
   clus
vv  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  0                         123                            60
  1                           1                             0
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    78 265
  DEL PEAK  7(3P26.2) WILD-TYPE  61 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     78  265
  DEL PEAK  7(3P26.2) WILD-TYPE   61  112
        clus
vv       DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  FEMALE                          78                            61
  MALE                           265                           112
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P26.2) MUTATED                                     338
  DEL PEAK  7(3P26.2) WILD-TYPE                                   167
                               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                                               338
  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                                                 167
  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    59 284
  DEL PEAK  7(3P26.2) WILD-TYPE  22 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     59  284
  DEL PEAK  7(3P26.2) WILD-TYPE   22  151
     clus
vv    DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  NO                           59                            22
  YES                         284                           151
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, continuous
D36V12, 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                          41   282
  DEL PEAK  7(3P26.2) WILD-TYPE                         4   159
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 41
  WHITE                                                    282
                                  clus
vv                                 DEL PEAK  7(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                      159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    17 299
  DEL PEAK  7(3P26.2) WILD-TYPE   8 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     17  299
  DEL PEAK  7(3P26.2) WILD-TYPE    8  155
                        clus
vv                       DEL PEAK  7(3P26.2) MUTATED
  HISPANIC OR LATINO                              17
  NOT HISPANIC OR LATINO                         299
                        clus
vv                       DEL PEAK  7(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           155
[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   209 151
  DEL PEAK  8(3P24.1) WILD-TYPE 104  49
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          360                           153 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          151                            49 
$`DEL PEAK  8(3P24.1) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
       26.50        17.10        53.79        57.44        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4II 
       14.83         3.55        12.62         7.76        29.42        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI 
       27.95        11.54         7.10         5.69        14.47        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
       20.48        16.41         9.14         4.41        18.35        36.72 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
       50.20        66.28        24.66        38.40        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 
       25.71        27.19         8.81         6.28        23.70        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 
        4.67        37.84        12.89        26.86        32.65        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
       12.99        20.55        14.33        43.73        27.58        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       33.11        34.36         8.58        12.39        35.54         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.84        11.57         8.52        22.45 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
       20.71        30.67        20.68        20.65        19.53        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
       14.20         6.74         9.07         9.24        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 
       20.09        12.95        24.16         3.68        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        35.01        14.56        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY 
        7.40        17.29        11.44         4.41        12.07        10.09 
TCGA-CN-A6V3 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
        9.80         2.93        45.80        10.42        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        34.75        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
       38.76        51.29        33.11        16.73        41.88        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        32.81        25.81 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6473 
       31.23        84.23        11.77        54.67        26.27        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90         6.02        11.90        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        11.51        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 
       24.95        29.23         9.17        34.06        19.92        17.13 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
       47.01        27.06        12.89        29.82         7.10         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       35.41        29.95       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 
       76.24        19.20        17.95       107.51        94.88        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       17.92        13.35        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        54.74         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 
        5.46        20.52        21.90        26.43        11.24        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6956 
       42.38        15.09        30.08         6.08        65.82         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        8.42        28.34         2.50         4.14        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        47.47        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       17.13         4.96        11.87        47.97         2.10        36.13 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7413 TCGA-CV-7414 
       18.41        35.54        17.85       210.97         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       14.89        54.94         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X 
        7.17       153.86       180.16        35.47        45.96         6.51 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JE 
       48.20        60.43        67.86        56.61         7.07        35.34 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 
       29.79        22.03         3.62        23.47        22.52        10.42 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 
       18.84        34.36        25.41         9.60        23.05        16.14 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO 
       11.44        24.95        25.32        12.36         7.63        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
       13.94        12.10        12.79        11.11        58.45        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        14.04        18.90        20.45         9.83 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       10.65        11.18        37.18        16.11        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        19.23        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
       11.80        15.06        13.61        21.11         0.07         0.16 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ 
        1.22        14.66        12.66        22.85        13.84         3.65 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W 
        5.29        11.54        11.84        18.15        12.43        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.96         1.84         7.13        17.98        15.78        56.75 
TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 
       47.01        18.97         2.04        29.00        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       21.07        11.74        16.70        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       12.43         6.51         5.62        11.57        12.10         9.73 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
        9.76         8.32        15.91        13.25        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        43.36        42.02        44.65        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ 
       49.22        21.86        13.94        20.75        22.36        20.55 

$`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 
       23.74        42.35        57.93        23.84        20.48         4.01 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
       28.11        20.45         7.82         2.27        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-A5HY 
       94.62         4.60        22.42        33.70        44.98        10.55 
TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4733 TCGA-CN-4741 
       12.92        12.69        26.27        40.44        21.11        41.69 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-6023 TCGA-CN-A499 TCGA-CN-A63V 
       12.49        56.94        20.68        36.49        17.59        15.91 
TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
        5.75         2.70         7.33         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 
       39.68        21.50        54.58        46.75        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH 
        4.24        70.13        43.04        28.83        14.14        12.46 
TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6481 
       37.87        58.42        50.01        39.52        34.52        10.22 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 
        0.99        31.96        26.17        32.78        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5442 
       29.85        29.52        30.58         5.95        48.39        76.50 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6942 
       91.53        23.05        21.07        62.43         4.73       126.08 
TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7250 
       19.79        53.95        10.98       130.88        77.16        95.34 
TCGA-CV-7406 TCGA-CV-7411 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7437 TCGA-CV-7438 
       57.47        89.33        56.48       156.49        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
       22.19        27.98        24.99       169.38       159.65         1.05 
TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO 
       88.87         0.76        15.25         5.98         6.38         6.48 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 
       21.24        19.92        10.42        10.55        13.25         2.53 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 
       18.67        17.72        15.88        35.54        25.48        12.13 
TCGA-DQ-7594 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       12.10        20.25        12.43        13.38        15.16         6.77 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       25.74        22.03         0.36         4.27         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
       12.76        14.50        13.35        10.75        30.05        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF 
        3.68        15.42        16.08        29.92        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6IG 
       36.82        19.00        75.55        12.99        17.65         7.30 
TCGA-QK-A6II TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        9.34        12.72        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JT 
       13.55        13.68        41.16        62.27        16.11        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                         0.07                          0.36 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                       210.97                        169.38 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                       17.885                        20.250 
[1] "0.1 - 211.0 (17.9)" "0.4 - 169.4 (20.2)"
[1] "hr=" "1.5"
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  8(3P24.1) MUTATED        17       50        56       185        10
  DEL PEAK  8(3P24.1) WILD-TYPE      10       27        21        67         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                            10
  STAGE II                           50                            27
  STAGE III                          56                            21
  STAGE IVA                         185                            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  8(3P24.1) MUTATED      28  87  78 131
  DEL PEAK  8(3P24.1) WILD-TYPE    22  46  21  41
D37V4, multiclass
       clus
vv      DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  T0+T1                          28                            22
  T2                             87                            46
  T3                             78                            21
  T4                            131                            41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  8(3P24.1) MUTATED   119  49 128   6
  DEL PEAK  8(3P24.1) WILD-TYPE  59  17  37   2
D37V5, multiclass
    clus
vv   DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  N0                         119                            59
  N1                          49                            17
  N2                         128                            37
  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"
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED   127   1
  DEL PEAK  8(3P24.1) WILD-TYPE  56   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED    127    1
  DEL PEAK  8(3P24.1) WILD-TYPE   56    0
   clus
vv  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  0                         127                            56
  1                           1                             0
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED    84 279
  DEL PEAK  8(3P24.1) WILD-TYPE  55  98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     84  279
  DEL PEAK  8(3P24.1) WILD-TYPE   55   98
        clus
vv       DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  FEMALE                          84                            55
  MALE                           279                            98
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P24.1) MUTATED                                     358
  DEL PEAK  8(3P24.1) WILD-TYPE                                   147
                               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                                               358
  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                                                 147
  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    60 303
  DEL PEAK  8(3P24.1) WILD-TYPE  21 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     60  303
  DEL PEAK  8(3P24.1) WILD-TYPE   21  132
     clus
vv    DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  NO                           60                            21
  YES                         303                           132
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, continuous
D37V12, 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                          42   301
  DEL PEAK  8(3P24.1) WILD-TYPE                         3   140
D37V13, multiclass
                                  clus
vv                                 DEL PEAK  8(3P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 42
  WHITE                                                    301
                                  clus
vv                                 DEL PEAK  8(3P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                      140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED    17 318
  DEL PEAK  8(3P24.1) WILD-TYPE   8 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     17  318
  DEL PEAK  8(3P24.1) WILD-TYPE    8  136
                        clus
vv                       DEL PEAK  8(3P24.1) MUTATED
  HISPANIC OR LATINO                              17
  NOT HISPANIC OR LATINO                         318
                        clus
vv                       DEL PEAK  8(3P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           136
[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   211 153
  DEL PEAK  9(3P14.2) WILD-TYPE 102  47
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          364                           149 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          153                            47 
$`DEL PEAK  9(3P14.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       26.50        57.93        17.10        20.48        53.79        57.44 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       15.52        21.17        14.83         3.55        12.62         7.76 
TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        30.18        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 
       14.47        11.05        20.48        16.41         9.14         4.41 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       36.72        50.20        44.98        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO 
       71.05        20.52        25.71        10.55        27.19         8.81 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        6.28        23.70        38.04         4.67        40.44        37.84 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       12.89        26.86        32.65        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       43.73        27.58        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        35.54         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       11.57         8.52        22.45        20.71        30.67        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       20.65        19.53        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        9.24        11.08        10.45        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CN-A6V7 
       11.44         4.41        12.07        10.09         9.80         6.18 
TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       48.20         2.93        45.80        10.42        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        34.75        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
       38.76        51.29        33.11        16.73        41.88        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CI 
       44.48        11.61        23.24        29.36        25.81        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6473 
       84.23        11.77        54.67        26.27        58.42        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90         6.02        11.90        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        11.51        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95        29.23         0.99         9.17        34.06        19.92 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 
       17.13        47.01        27.06        12.89        29.82         7.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
        5.13         5.95        35.41        29.95       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 
       94.88        80.12        17.92        13.35        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 
       60.49         7.07        43.23        54.74         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 
        2.14         9.70         5.46        20.52        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       11.24        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       10.75         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7413 
       36.13        18.41        35.54        17.85       210.97         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
      100.57        14.89        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U 
       19.76         7.17       153.86        22.19       180.16        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 
       45.96         6.51        48.20        60.43        67.86         7.07 
TCGA-CV-A6JE TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 
       35.34        22.03         3.62        23.47        22.52        10.42 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 
       18.84        34.36        25.41         9.60        23.05        16.14 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO 
       24.95        25.32        17.72        12.36         7.63        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
       13.94        12.10        12.79        11.11        58.45        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        18.02        14.04        18.90        20.45         9.83 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        37.18        16.11        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       19.23        18.94         0.46        17.85        11.80        20.25 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 
       15.06        13.61        21.11         0.07         0.16         1.22 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E 
       12.66        22.85        13.84         3.65        15.95        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       11.84        18.15        12.43        14.37         7.96         1.84 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX 
        7.13        17.98        15.78        56.75        10.85        47.01 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        29.00        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 
       11.74        16.70        12.72        18.64        14.79         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        11.57        12.10         9.73         9.76         8.32 
TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       15.91        13.25        43.59        54.67         2.83        43.36 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       42.02        44.65        17.95        24.16        49.22        21.86 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ 
       13.94        20.75        22.36        20.55 

$`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 
       23.74        42.35        23.84         4.01        28.11        20.45 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
        7.82         2.27        13.38         6.15        94.62         4.60 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 
       18.35        22.42        33.70        12.92        12.69        26.27 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6017 
       21.11        41.10        41.69        12.49        56.94        20.68 
TCGA-CN-6023 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V6 
       36.49        15.91         5.75         2.70         7.33         7.69 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 
       39.68        21.50        54.58        46.75        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CD TCGA-CQ-A4CG 
        4.24        70.13        43.04        28.83        32.81        14.14 
TCGA-CQ-A4CH TCGA-CR-5249 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6481 
       12.46        37.87        50.01        39.52        34.52        10.22 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       31.96        26.17        32.78        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
       29.52        30.58        48.39        76.50        91.53        23.05 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6953 
       21.07        62.43         4.73       126.08        19.79        53.95 
TCGA-CV-6955 TCGA-CV-7090 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 
       10.98       126.15       130.88        77.16        95.34        57.47 
TCGA-CV-7411 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O 
       89.33        56.48       156.49        16.64         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A463 
       24.99       169.38       159.65         1.05        88.87         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61        15.25         5.98         6.38        29.79         6.48 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 
       21.24        19.92        10.42        10.55        13.25         2.53 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 
       11.44        18.67        15.88        35.54        25.48        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A61V TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       12.10        11.18        12.62        12.43        13.38        15.16 
TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 
        6.77        25.74        14.66        22.03         0.36         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A66S TCGA-KU-A6H8 
        6.90        34.75        12.76        14.50        13.35        10.75 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05        12.62         3.68        15.42        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A6IF 
       51.25        36.82        19.00        75.55        12.99        17.65 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        7.30         9.34        12.43        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71D TCGA-UF-A7JA 
        7.10        32.45        13.55        13.68        41.16        62.27 
TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       16.11        32.65         2.96        17.03        14.56 

  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                         0.07                          0.36 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                       210.97                        169.38 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                       17.885                        19.920 
[1] "0.1 - 211.0 (17.9)" "0.4 - 169.4 (19.9)"
[1] "hr=" "1.5"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  9(3P14.2) MUTATED        18       50        56       187        10
  DEL PEAK  9(3P14.2) WILD-TYPE       9       27        21        65         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                             9
  STAGE II                           50                            27
  STAGE III                          56                            21
  STAGE IVA                         187                            65
  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      31  91  76 130
  DEL PEAK  9(3P14.2) WILD-TYPE    19  42  23  42
D38V4, multiclass
       clus
vv      DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  T0+T1                          31                            19
  T2                             91                            42
  T3                             76                            23
  T4                            130                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  9(3P14.2) MUTATED   119  50 131   6
  DEL PEAK  9(3P14.2) WILD-TYPE  59  16  34   2
D38V5, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  N0                         119                            59
  N1                          50                            16
  N2                         131                            34
  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"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED   127   1
  DEL PEAK  9(3P14.2) WILD-TYPE  56   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED    127    1
  DEL PEAK  9(3P14.2) WILD-TYPE   56    0
   clus
vv  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  0                         127                            56
  1                           1                             0
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    86 281
  DEL PEAK  9(3P14.2) WILD-TYPE  53  96
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     86  281
  DEL PEAK  9(3P14.2) WILD-TYPE   53   96
        clus
vv       DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  FEMALE                          86                            53
  MALE                           281                            96
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P14.2) MUTATED                                     362
  DEL PEAK  9(3P14.2) WILD-TYPE                                   143
                               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                                               362
  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                                                 143
  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    64 303
  DEL PEAK  9(3P14.2) WILD-TYPE  17 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     64  303
  DEL PEAK  9(3P14.2) WILD-TYPE   17  132
     clus
vv    DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  NO                           64                            17
  YES                         303                           132
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, continuous
D38V12, 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   305
  DEL PEAK  9(3P14.2) WILD-TYPE                         4   136
D38V13, multiclass
                                  clus
vv                                 DEL PEAK  9(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 41
  WHITE                                                    305
                                  clus
vv                                 DEL PEAK  9(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                      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"
D38V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    18 321
  DEL PEAK  9(3P14.2) WILD-TYPE   7 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     18  321
  DEL PEAK  9(3P14.2) WILD-TYPE    7  133
                        clus
vv                       DEL PEAK  9(3P14.2) MUTATED
  HISPANIC OR LATINO                              18
  NOT HISPANIC OR LATINO                         321
                        clus
vv                       DEL PEAK  9(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           133
[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   192 143
  DEL PEAK 10(3P12.1) WILD-TYPE 121  57
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          335                           178 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          143                            57 
$`DEL PEAK 10(3P12.1) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       26.50        57.93        17.10        20.48        53.79        57.44 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       15.52        21.17        14.83         3.55        12.62         7.76 
TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI 
       29.42        30.18        27.95         5.69        14.47        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
       20.48        16.41         9.14        50.20        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       38.40        71.05        20.52        25.71        10.55        27.19 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
        8.81         6.28        23.70        38.04         4.67        40.44 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        26.86        32.65        41.10        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       14.33        43.73        27.58        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        35.54         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       11.57        22.45        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
       19.53        19.07        14.20         6.74         9.07        36.49 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       11.08        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       14.10        11.74        35.01        14.56        17.59        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 
       21.21         7.40        17.29        11.44         4.41        12.07 
TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 
        9.80         6.18        48.20         2.93        45.80        10.42 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       41.19        32.38        32.88        34.75        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        51.29        33.11        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        64.11        44.48        11.61        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 
       32.81        25.81        31.23        84.23        11.77        58.42 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90         6.02        11.90        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        11.51        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95        29.23         0.99         9.17        34.06        19.92 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
       17.13        27.06        12.89        29.82         7.10         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       35.41        29.95       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 
       76.24        19.20        17.95       107.51        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
       13.35        86.83        48.59        60.49        43.23        54.74 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       26.43        11.24        12.03        42.38        15.09        30.08 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       10.75         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7413 
       36.13        18.41        35.54        17.85       210.97         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        0.46        22.85        25.08        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
      100.57        14.89        54.94         3.52        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z 
        7.17       153.86        22.19        35.47         6.51        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT 
       60.43        67.86         7.07        35.34        29.79        22.03 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        3.62        23.47        22.52        10.42        18.84        34.36 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       25.41         9.60        11.44        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q 
       12.36         7.63        14.30        13.94        12.10        11.11 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 
       58.45        30.94        33.86        14.04        18.90         9.83 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        37.18        16.11        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 
       19.23        18.94         0.46        17.85        20.25        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 
       13.61        21.11         1.22        14.66        22.85        13.84 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
        3.65        15.95        19.33        11.84        13.55         0.07 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
       14.47        11.54        11.84        13.35        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
        7.96         1.84        17.98        15.78        56.75        10.85 
TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 
       47.01        18.97         2.04        29.00        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 
       21.07        11.74        12.72        18.64        14.79         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        11.57        12.10         9.73         9.76         8.32 
TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       15.91        13.25        43.59        54.67         2.83        43.36 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ 
       21.86        13.94        20.75        22.36        20.55 

$`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 
       23.74        42.35        23.84         4.01        28.11        20.45 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
       11.54         7.10         7.82         2.27        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
       94.62         4.60         4.41        18.35        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4728 
       33.70        44.98        12.92        12.69        26.27        37.84 
TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5374 
       21.11        41.69        13.05        12.49         8.52        56.94 
TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-A49A TCGA-CN-A63V TCGA-CN-A63Y 
       20.68         9.24        10.45        12.85        15.91         5.75 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        10.09         7.33         7.69        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 
       54.58        46.75        45.99        11.21         4.24        70.13 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
       43.04        28.83        14.14        12.46        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6481 
       26.27        50.01        39.52        34.52        36.99        10.22 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
       31.96        26.17        32.78        47.01        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5441 
       29.85        29.52        30.58         5.95        48.39        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
       76.50        91.53        23.05         7.07        21.07        62.43 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6953 
        4.73        21.90       126.08        19.79         6.08        53.95 
TCGA-CV-6955 TCGA-CV-7090 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 
       10.98       126.15       130.88        77.16        95.34        57.47 
TCGA-CV-7411 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-7438 
       89.33        56.48       156.49        19.76        16.64         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        24.99       169.38       180.16       159.65         1.05 
TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       45.96        88.87         0.76        56.61        15.25         5.98 
TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
        6.38         6.48        21.24        19.92        10.42        10.55 
TCGA-D6-6515 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK 
       13.25        23.05         2.53        16.14        18.67        15.88 
TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
       12.79        35.54        18.02        25.48        20.45        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       12.10        11.18        12.62        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 
       15.16         6.77         0.07         0.16        25.74        22.03 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
       12.66         0.36         4.27         6.90        34.75        12.76 
TCGA-IQ-7632 TCGA-IQ-A61K TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
       14.50         5.29        12.43        10.75        30.05        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
        3.68        15.42         7.13        16.08        29.92        51.25 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6IG 
       36.82        19.00        75.55        12.99        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6VC TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       16.70         9.34        12.43        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71D TCGA-UF-A7JJ 
        7.10        32.45        13.55        13.68        41.16        16.11 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       32.65         2.96        17.03        14.56 

  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                       210.97                        180.16 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                       18.150                        17.835 
[1] "0.1 - 211.0 (18.1)" "0.1 - 180.2 (17.8)"
[1] "hr=" "1.5"
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 10(3P12.1) MUTATED        14       48        54       175         7
  DEL PEAK 10(3P12.1) WILD-TYPE      13       29        23        77         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                            13
  STAGE II                           48                            29
  STAGE III                          54                            23
  STAGE IVA                         175                            77
  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      28  87  71 119
  DEL PEAK 10(3P12.1) WILD-TYPE    22  46  28  53
D39V4, multiclass
       clus
vv      DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  T0+T1                          28                            22
  T2                             87                            46
  T3                             71                            28
  T4                            119                            53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 10(3P12.1) MUTATED   111  49 119   5
  DEL PEAK 10(3P12.1) WILD-TYPE  67  17  46   3
D39V5, multiclass
    clus
vv   DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  N0                         111                            67
  N1                          49                            17
  N2                         119                            46
  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"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED   117   1
  DEL PEAK 10(3P12.1) WILD-TYPE  66   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED    117    1
  DEL PEAK 10(3P12.1) WILD-TYPE   66    0
   clus
vv  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  0                         117                            66
  1                           1                             0
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED    79 259
  DEL PEAK 10(3P12.1) WILD-TYPE  60 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     79  259
  DEL PEAK 10(3P12.1) WILD-TYPE   60  118
        clus
vv       DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  FEMALE                          79                            60
  MALE                           259                           118
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3P12.1) MUTATED                                     332
  DEL PEAK 10(3P12.1) WILD-TYPE                                   173
                               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                                               332
  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                                                 173
  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    59 279
  DEL PEAK 10(3P12.1) WILD-TYPE  22 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     59  279
  DEL PEAK 10(3P12.1) WILD-TYPE   22  156
     clus
vv    DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  NO                           59                            22
  YES                         279                           156
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, continuous
D39V12, 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   278
  DEL PEAK 10(3P12.1) WILD-TYPE                         6   163
D39V13, multiclass
                                  clus
vv                                 DEL PEAK 10(3P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 39
  WHITE                                                    278
                                  clus
vv                                 DEL PEAK 10(3P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                      163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED    16 294
  DEL PEAK 10(3P12.1) WILD-TYPE   9 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     16  294
  DEL PEAK 10(3P12.1) WILD-TYPE    9  160
                        clus
vv                       DEL PEAK 10(3P12.1) MUTATED
  HISPANIC OR LATINO                              16
  NOT HISPANIC OR LATINO                         294
                        clus
vv                       DEL PEAK 10(3P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           160
[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   124  83
  DEL PEAK 11(4P15.2) WILD-TYPE 189 117
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          207                           306 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                           83                           117 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
       23.74        17.10        20.48        53.79        15.52        14.83 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DL 
        3.55        29.42        28.11        27.95         7.10        20.48 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7871 
       16.41        94.62         9.14         4.41        22.42        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       71.05        20.52        27.19         6.28        12.69        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 
       38.04         4.67        37.84        26.86        41.10        43.73 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       13.05        33.11         8.58        35.54         8.32        16.21 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
       56.94        20.71        30.67        20.68        19.07        14.20 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        9.07        36.49        11.08        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 
        3.68        17.42        14.10        11.74        35.01        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
       12.85        29.72         7.40        17.29        11.44        12.07 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6223 
        9.80        48.20         2.93        10.42        32.38        34.75 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 
       13.25        14.99        51.29        16.73        64.11        23.24 
TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6474 
       32.81        31.23        11.77        54.67        34.52        18.54 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
        7.69        12.46        11.51        39.16        47.34        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 
        3.45         3.09        24.95        29.23         0.99        17.13 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
       27.06        29.82         5.13        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5978 
      108.95        76.24        19.20       107.51        80.12         7.07 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 
       90.12         2.14         9.70        20.52        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6956 
       11.24       126.08        42.38        15.09        30.08         7.13 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7235 
        2.50         4.14       111.16        12.66         5.26        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        4.73        47.47        36.00        26.20        18.97        17.13 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7415 
       47.97        36.13        57.47        35.54         9.67        22.85 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       25.94        34.09       100.57        16.27        84.49        19.76 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A465 
      153.86         6.38        22.19        45.96         6.51         7.07 
TCGA-CX-7082 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM 
       10.42        25.41        23.05        17.72        12.36         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       14.30        13.94        11.11        30.94        14.04        18.90 
TCGA-DQ-7595 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-8502 
       10.65        16.11        20.25        12.62         0.46        15.06 
TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 
       21.11         0.16         1.22        14.66        22.03        13.84 
TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G 
        3.65        19.33        11.84        13.55        14.47         3.68 
TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW 
       15.42        16.08        17.98        15.78        56.75        36.82 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       47.01         2.04        13.15        14.79        12.43         6.51 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T2-A6X0 
       11.57        12.10         9.76         8.32        15.91         7.10 
TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF 
       13.25         2.83        43.36        44.65        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JS TCGA-WA-A7GZ 
       21.86        22.36        20.55 

$`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 
        3.35        42.35        57.93        23.84        57.44        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
       12.62         4.01         7.76        20.45        30.18        11.54 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        6.15         4.60        18.35        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UM 
       44.98        66.28        38.40        25.71        10.55        12.92 
TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
        8.81        26.27        40.44        12.89        32.65        21.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 
       12.99        20.55        14.33        27.58        41.69        34.36 
TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       12.39        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 
       22.45        20.65        19.53        20.68         6.74         9.24 
TCGA-CN-6988 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       10.45        14.56        21.21        15.91         5.75         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
        2.70        10.09         7.33         7.69         6.18        39.68 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50        54.58        46.75        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
        4.24        41.19        32.88        56.58         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       70.13        33.11        43.04        41.88        28.83        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       11.61        29.36        25.81        14.14        12.46        84.23 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        11.90        10.22        11.34        11.64 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7376 TCGA-CR-7377 
       15.75         9.27        47.18        40.93        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
       34.06        19.92        26.17        32.78        47.01        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5441 
        5.95        35.41        29.95       139.43        17.95        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        17.92        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49        43.23        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        9.60         5.46         4.73        19.79        12.03         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7089 
       53.95        65.82        10.98         8.42        28.34        64.83 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 
      126.15        18.81         7.99         9.01         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 
       12.92        21.80        71.21        10.75       130.88        31.36 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7409 
       95.34         4.96        11.87         2.10        18.41        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7424 
      210.97        89.33         0.46        25.08         0.07        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-7437 
       56.48       156.49        54.94         3.52         7.17        16.64 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        24.99       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        1.05        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       22.52        10.42        10.55        18.84        34.36        13.25 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
        9.60         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       25.32        15.88        12.10        12.79        58.45        35.54 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       33.86        18.02        25.48        20.45         9.83        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       12.10        11.18        37.18        21.63         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       18.94        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8634 
       15.16        13.61         6.77         0.07        25.74        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       22.85         0.36         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       12.76        14.50         0.07         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5QE 
       30.05         1.84        12.62         7.13        29.92        51.25 
TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       10.85        19.00        75.55        18.97        29.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        21.07        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO 
        9.34        12.72        18.64         5.62         9.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
       16.96         6.87        32.45        13.55        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JJ 
       54.67        41.16        42.02        62.27        17.95        16.11 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       13.94        20.75        32.65         2.96        17.03        14.56 

  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         0.16                          0.07 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                        17.72                         18.25 
[1] "0.2 - 153.9 (17.7)" "0.1 - 211.0 (18.2)"
[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        29       105         6
  DEL PEAK 11(4P15.2) WILD-TYPE      14       48        48       147         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                            14
  STAGE II                           29                            48
  STAGE III                          29                            48
  STAGE IVA                         105                           147
  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      21  47  46  71
  DEL PEAK 11(4P15.2) WILD-TYPE    29  86  53 101
D40V4, multiclass
       clus
vv      DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T0+T1                          21                            29
  T2                             47                            86
  T3                             46                            53
  T4                             71                           101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 11(4P15.2) MUTATED    70  26  72   5
  DEL PEAK 11(4P15.2) WILD-TYPE 108  40  93   3
D40V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                          70                           108
  N1                          26                            40
  N2                          72                            93
  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"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    64   0
  DEL PEAK 11(4P15.2) WILD-TYPE 119   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     64    0
  DEL PEAK 11(4P15.2) WILD-TYPE  119    1
   clus
vv  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  0                          64                           119
  1                           0                             1
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    44 163
  DEL PEAK 11(4P15.2) WILD-TYPE  95 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     44  163
  DEL PEAK 11(4P15.2) WILD-TYPE   95  214
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          44                            95
  MALE                           163                           214
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P15.2) MUTATED                                     202
  DEL PEAK 11(4P15.2) WILD-TYPE                                   303
                               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                                               202
  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                                                 303
  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    37 170
  DEL PEAK 11(4P15.2) WILD-TYPE  44 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     37  170
  DEL PEAK 11(4P15.2) WILD-TYPE   44  265
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  NO                           37                            44
  YES                         170                           265
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, continuous
D40V12, 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                          24   172
  DEL PEAK 11(4P15.2) WILD-TYPE                        21   269
D40V13, multiclass
                                  clus
vv                                 DEL PEAK 11(4P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                    172
                                  clus
vv                                 DEL PEAK 11(4P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    10 184
  DEL PEAK 11(4P15.2) WILD-TYPE  15 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     10  184
  DEL PEAK 11(4P15.2) WILD-TYPE   15  270
                        clus
vv                       DEL PEAK 11(4P15.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         184
                        clus
vv                       DEL PEAK 11(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           270
[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    92  60
  DEL PEAK 12(4Q21.3) WILD-TYPE 221 140
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                          152                           361 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                           60                           140 
$`DEL PEAK 12(4Q21.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 
        3.35         9.30         9.07        17.10        14.83         4.01 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DI TCGA-BA-A6DL 
       29.42        28.11        27.95         7.10        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       16.41         4.41        24.66        71.05        20.52        10.55 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4737 
        6.28        12.69        38.04        12.89        41.10        20.55 
TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       43.73        35.54        20.71        30.67        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       14.20         9.07        11.08        20.09        24.16         3.68 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       14.10        11.74        35.01        14.56        17.59        29.72 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5334 TCGA-CQ-6220 
        7.40        11.44         6.18        48.20         4.24        32.38 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 
       56.58        14.99        51.29        16.73        64.11        23.24 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6487 
       12.46        31.23        54.67        34.52        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       12.46         9.27        39.16         3.45         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7404 
       29.23         0.99        17.13        31.10         5.13        48.39 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21       108.95        76.24        17.95       107.51 
TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6942 
       80.12        54.74         9.60        20.52        11.24       126.08 
TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 
       42.38        65.82         7.13         4.14       111.16        12.66 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7247 TCGA-CV-7261 
        5.26        52.31        12.92        10.75        18.97        36.13 
TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
       35.54         9.67        25.08        25.94        34.09        14.89 
TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45R 
       56.48         3.52       153.86        22.19       169.38       180.16 
TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A465 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       45.96        60.43         7.07        23.05        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
        7.63        13.94        11.11        30.94        14.04        18.90 
TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-8634 
        9.83        20.25        19.23        18.94        21.11        12.66 
TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-MT-A67G TCGA-MT-A7BN 
        3.65        13.55        14.47        11.54         3.68        15.42 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       56.75        47.01         2.04        11.74        17.65         7.30 
TCGA-QK-A6II TCGA-QK-A6VB TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T2-A6X0 
        9.34        14.79        12.10         8.32        15.91         7.10 
TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JO 
       54.67        41.16        17.95        24.16        49.22        20.75 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

$`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 
       15.19        13.64        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       57.93        23.84        20.48        53.79        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II 
       21.17         3.55        12.62         7.76        20.45        30.18 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       11.54         5.69        14.47         7.82         2.27        13.38 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
        6.15        94.62         9.14         4.60        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
       36.72        33.70        50.20        44.98        66.28        38.40 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 
       25.71        27.19        12.92         8.81        26.27        23.70 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        40.44        37.84        26.86        32.65        21.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       12.99        14.33        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       34.36         8.58        12.39         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.84        11.57        12.49         8.52        22.45        56.94 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 
       20.65        19.53        20.68         6.74         9.24        36.49 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U 
       10.45        12.95        17.42        12.85        21.21        17.29 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       15.91         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.33         9.80         7.69        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        46.75        45.80        45.99        10.42        11.21 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 
       41.19        32.88        34.75        13.25         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       70.13        33.11        43.04        41.88        28.83        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 
       11.61        29.36        32.81        25.81        14.14        84.23 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       11.77        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       11.34        11.51        15.75        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       35.84        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        29.82        30.02 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       29.85        29.52        30.58         7.10         5.95        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       29.95       139.43        19.20        94.88        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 
        7.07        43.23        21.07        62.43        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 
        9.70         5.46         4.73        21.90        26.43        19.79 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       12.03        15.09        30.08         6.08        53.95        10.98 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 
        8.42        28.34         2.50        64.83       126.15        18.81 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 
        7.99         9.01         1.84        21.80        71.21       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 
       18.41        57.47        17.85       210.97        89.33         0.46 
TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
       22.85         0.07       100.57       156.49        54.94        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O 
       84.49        19.76         7.17        16.64         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
       24.99       159.65        35.47         1.05         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       48.20        67.86         0.76        56.61        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        22.03         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        2.53        16.14        11.44        18.67        24.95        25.32 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       15.88        14.30        12.10        12.79        58.45        35.54 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
       33.86        18.02        25.48        20.45        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       10.65        11.18        37.18        16.11        21.63         3.02 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        15.06        13.61         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
        0.16        25.74         1.22        14.66        22.03        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K 
       12.76        14.50        19.33        11.84         0.07         5.29 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.84        13.35        18.15        12.43        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 
        7.96        30.05         1.84        12.62         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        15.78        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55        18.97        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
       13.15        21.07        16.70        12.72        18.64        12.43 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO 
        6.51         5.62        11.57         9.73         9.76        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       16.96         6.87        32.45        13.55        13.25        13.68 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       43.59         2.83        43.36        42.02        44.65        62.27 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       21.86        16.11        13.94        22.36        32.65         2.96 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE 
                       17.835                        18.350 
[1] "1.0 - 180.2 (17.8)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1"  
D41V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 12(4Q21.3) MUTATED         9       22        31        67         2
  DEL PEAK 12(4Q21.3) WILD-TYPE      18       55        46       185        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                            18
  STAGE II                           22                            55
  STAGE III                          31                            46
  STAGE IVA                          67                           185
  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      16  41  38  39
  DEL PEAK 12(4Q21.3) WILD-TYPE    34  92  61 133
D41V4, multiclass
       clus
vv      DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  T0+T1                          16                            34
  T2                             41                            92
  T3                             38                            61
  T4                             39                           133
[1] 4 2
[1] TRUE
[1] "dimension of 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    49  22  48   2
  DEL PEAK 12(4Q21.3) WILD-TYPE 129  44 117   6
D41V5, multiclass
    clus
vv   DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  N0                          49                           129
  N1                          22                            44
  N2                          48                           117
  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"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q21.3) MUTATED    49   0
  DEL PEAK 12(4Q21.3) WILD-TYPE 134   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q21.3) MUTATED     49    0
  DEL PEAK 12(4Q21.3) WILD-TYPE  134    1
   clus
vv  DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  0                          49                           134
  1                           0                             1
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q21.3) MUTATED    41 112
  DEL PEAK 12(4Q21.3) WILD-TYPE  98 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q21.3) MUTATED     41  112
  DEL PEAK 12(4Q21.3) WILD-TYPE   98  265
        clus
vv       DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  FEMALE                          41                            98
  MALE                           112                           265
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4Q21.3) MUTATED                                     152
  DEL PEAK 12(4Q21.3) WILD-TYPE                                   353
                               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                                               152
  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                                                 353
  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    25 128
  DEL PEAK 12(4Q21.3) WILD-TYPE  56 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q21.3) MUTATED     25  128
  DEL PEAK 12(4Q21.3) WILD-TYPE   56  307
     clus
vv    DEL PEAK 12(4Q21.3) MUTATED DEL PEAK 12(4Q21.3) WILD-TYPE
  NO                           25                            56
  YES                         128                           307
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, continuous
D41V12, 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   125
  DEL PEAK 12(4Q21.3) WILD-TYPE                        30   316
D41V13, multiclass
                                  clus
vv                                 DEL PEAK 12(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    125
                                  clus
vv                                 DEL PEAK 12(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   30
  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"
D41V14, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q21.3) MUTATED    11 131
  DEL PEAK 12(4Q21.3) WILD-TYPE  14 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q21.3) MUTATED     11  131
  DEL PEAK 12(4Q21.3) WILD-TYPE   14  323
                        clus
vv                       DEL PEAK 12(4Q21.3) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         131
                        clus
vv                       DEL PEAK 12(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           323
[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    96  68
  DEL PEAK 13(4Q22.1) WILD-TYPE 217 132
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                          164                           349 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                           68                           132 
$`DEL PEAK 13(4Q22.1) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF 
        9.30         9.07        17.10        14.83         4.01        29.42 
TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       28.11        27.95         7.10        11.05        20.48        16.41 
TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
        4.41        66.28        24.66        71.05        20.52        10.55 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4737 
        6.28        12.69        38.04        12.89        41.10        20.55 
TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       43.73        35.54        11.57        20.71        30.67        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 
       19.07        14.20         6.74         9.07        11.08        20.09 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       24.16         3.68        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-5323 
       17.59        29.72         7.40        11.44         6.18        48.20 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 
       32.38        32.88        56.58        14.99        51.29        16.73 
TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 
       64.11        11.61        23.24        12.46        31.23        54.67 
TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 
       34.52        11.64         7.69        12.46         9.27        39.16 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       47.34         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7383 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
       17.13        31.10         5.13        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5976 
      108.95        76.24        17.95       107.51        80.12        48.59 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6942 
       54.74         9.60         9.70        20.52        11.24       126.08 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7091 
       12.03        42.38        65.82         7.13         4.14       111.16 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7245 
       12.66         5.26        52.31        12.92        10.75        26.20 
TCGA-CV-7247 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7416 
       18.97        36.13        57.47        35.54         9.67        25.08 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7435 
       25.94        34.09        14.89         3.52        16.27       153.86 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       16.64        22.19       169.38        35.47         1.05        45.96 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 
       60.43         7.07        18.84        25.41        23.05        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 
       12.36         7.63        13.94        11.11        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-8634 
       18.90         9.83        19.23        18.94        21.11        12.66 
TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G 
        3.65        19.33        11.84        13.55        14.47         3.68 
TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
       15.42        17.98        15.78        56.75        47.01         2.04 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-T2-A6WZ 
       17.65         7.30        14.79        11.57        12.10        15.91 
TCGA-T2-A6X0 TCGA-UF-A719 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JO 
        7.10        54.67        17.95        24.16        49.22        20.75 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

$`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 
        3.35        15.19        13.64        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        57.93        23.84        20.48        53.79        57.44 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH 
       15.52        21.17         3.55        12.62         7.76        20.45 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18        11.54         5.69        14.47         7.82         2.27 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
       13.38         6.15        94.62         9.14         4.60        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 
       22.42        36.72        33.70        50.20        44.98        38.40 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 
       25.71        27.19        12.92         8.81        26.27        23.70 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        40.44        37.84        26.86        32.65        21.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       12.99        14.33        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       34.36         8.58        12.39         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 
       11.84        12.49         8.52        22.45        56.94        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 
       19.53        20.68         9.24        36.49        10.45        12.95 
TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       17.42        12.85        21.21        17.29        15.91         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
        7.69        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
       34.75        13.25         4.24        38.76        70.13        33.11 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.04        41.88        28.83        44.48        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 
       25.81        14.14        84.23        11.77        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6492 
        6.02        11.90        10.22        11.34        11.51        15.75 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       47.18        40.93        35.84        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       19.92        26.17        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       29.82        30.02        29.85        29.52        30.58         7.10 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5441 
        5.95        35.41        29.95       139.43        19.20        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        17.92        13.35        23.05        86.83 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 
       60.49         7.07        43.23        21.07        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 
        2.14         5.46         4.73        21.90        26.43        19.79 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6959 
       15.09        30.08         6.08        53.95        10.98         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 
       28.34         2.50        64.83       126.15        18.81         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 
        9.01         1.84        21.80        71.21       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        4.73        47.47        36.00        31.36        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7409 
        4.96        11.87        47.97         2.10        18.41        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7423 
      210.97        89.33         0.46        22.85         0.07       100.57 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       56.48       156.49        54.94        84.49        19.76         7.17 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45X 
        6.38        27.98        24.99       180.16       159.65         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       88.87        48.20        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 
       10.42        10.55        34.36        13.25         9.60         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK 
       16.14        11.44        18.67        24.95        25.32        15.88 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       14.30        12.10        12.79        58.45        35.54        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        25.48        20.45        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       11.18        37.18        16.11        21.63        20.25         3.02 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        15.06        13.61         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 
        0.16        25.74         1.22        14.66        22.03        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       12.76        14.50         0.07         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05         1.84        12.62         7.13        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        10.85        36.82        19.00        75.55        18.97 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        11.74 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 
       16.70         9.34        12.72        18.64        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
        5.62         9.73         9.76         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        6.87        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       21.86        16.11        13.94        22.36        32.65         2.96 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE 
                        17.95                         18.35 
[1] "1.0 - 169.4 (17.9)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 13(4Q22.1) MUTATED        10       23        31        76         2
  DEL PEAK 13(4Q22.1) WILD-TYPE      17       54        46       176        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                            17
  STAGE II                           23                            54
  STAGE III                          31                            46
  STAGE IVA                          76                           176
  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      16  42  39  49
  DEL PEAK 13(4Q22.1) WILD-TYPE    34  91  60 123
D42V4, multiclass
       clus
vv      DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  T0+T1                          16                            34
  T2                             42                            91
  T3                             39                            60
  T4                             49                           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 13(4Q22.1) MUTATED    54  23  53   2
  DEL PEAK 13(4Q22.1) WILD-TYPE 124  43 112   6
D42V5, multiclass
    clus
vv   DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  N0                          54                           124
  N1                          23                            43
  N2                          53                           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"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q22.1) MUTATED    50   0
  DEL PEAK 13(4Q22.1) WILD-TYPE 133   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     50    0
  DEL PEAK 13(4Q22.1) WILD-TYPE  133    1
   clus
vv  DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  0                          50                           133
  1                           0                             1
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q22.1) MUTATED    41 124
  DEL PEAK 13(4Q22.1) WILD-TYPE  98 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     41  124
  DEL PEAK 13(4Q22.1) WILD-TYPE   98  253
        clus
vv       DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  FEMALE                          41                            98
  MALE                           124                           253
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q22.1) MUTATED                                     164
  DEL PEAK 13(4Q22.1) WILD-TYPE                                   341
                               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                                               164
  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                                                 341
  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    28 137
  DEL PEAK 13(4Q22.1) WILD-TYPE  53 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     28  137
  DEL PEAK 13(4Q22.1) WILD-TYPE   53  298
     clus
vv    DEL PEAK 13(4Q22.1) MUTATED DEL PEAK 13(4Q22.1) WILD-TYPE
  NO                           28                            53
  YES                         137                           298
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, continuous
D42V12, 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   135
  DEL PEAK 13(4Q22.1) WILD-TYPE                        29   306
D42V13, multiclass
                                  clus
vv                                 DEL PEAK 13(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    135
                                  clus
vv                                 DEL PEAK 13(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q22.1) MUTATED    11 143
  DEL PEAK 13(4Q22.1) WILD-TYPE  14 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q22.1) MUTATED     11  143
  DEL PEAK 13(4Q22.1) WILD-TYPE   14  311
                        clus
vv                       DEL PEAK 13(4Q22.1) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         143
                        clus
vv                       DEL PEAK 13(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           311
[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   125  85
  DEL PEAK 14(4Q35.2) WILD-TYPE 188 115
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          210                           303 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                           85                           115 
$`DEL PEAK 14(4Q35.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 
        9.30         9.07        17.10        20.48        53.79        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB 
       12.62         4.01        29.42        28.11        27.95         7.10 
TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       11.05        16.41        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       20.52        10.55        27.19         6.28        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 
       23.70        38.04        12.89        12.99        20.55        43.73 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 
       13.05        33.11        12.39        35.54        11.57         8.52 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 
       20.71        30.67        20.68        19.07        14.20         9.24 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       12.95        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
       35.01        14.56        17.59        29.72         7.40        17.29 
TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6220 
       11.44         6.18         2.93        46.75        45.80        32.38 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C7 
       13.25        14.99        51.29        16.73        64.11        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6484 
       23.24        31.23        54.67        34.52        18.54        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 
        7.69        12.46        47.18        39.16         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7380 TCGA-CR-7389 TCGA-CR-7392 
       24.95        29.23         0.99        19.92        12.89        31.10 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
        5.13         5.95        35.41        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
      108.95        76.24        17.95       107.51        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 
       80.12        17.92        86.83        48.59         7.07        54.74 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
        9.60        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 
       11.24       126.08        42.38        65.82         7.13         8.42 
TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 
        4.14       111.16        12.66         5.26        52.31        12.92 
TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 
       10.75        36.00        31.36        18.97        17.13        47.97 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7422 
       36.13        35.54         9.67         0.46        25.08        34.09 
TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 
       56.48         3.52        16.27        19.76       153.86        16.64 
TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A465 
        6.38       169.38        35.47        45.96        60.43         7.07 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-A4Z9 
        3.62        23.47        18.84        34.36        23.05        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        15.88         7.63        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       12.79        11.11        30.94        18.02        14.04        18.90 
TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
        9.83        16.11        21.63        20.25         3.02        19.23 
TCGA-F7-A61S TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-8634 TCGA-HD-8635 
       18.94        13.61        21.11         0.07        12.66        22.85 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
       13.84         4.27         3.65        19.33        13.55        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q6 
        5.29        11.54        12.43         3.68        16.08        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG 
       56.75        47.01        13.15        21.07        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       16.70        14.79         6.51         5.62        12.10         9.73 
TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC 
       15.91        13.25        43.59        41.16        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-WA-A7GZ 
       24.16        49.22        21.86        13.94        20.75        20.55 

$`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 
        3.35        15.19        13.64        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
       42.35        57.93        23.84        57.44        15.52        21.17 
TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DD 
        3.55         7.76        20.45        30.18        11.54         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
       14.47         7.82         2.27        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
       94.62         9.14         4.60         4.41        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-A5HU TCGA-BB-A6UM 
       36.72        33.70        50.20        44.98        25.71        12.92 
TCGA-BB-A6UO TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
        8.81         4.67        40.44        37.84        26.86        32.65 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 
       21.11        41.10        14.33        27.58        41.69        34.36 
TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 
        8.58         8.32        16.21        11.54        11.84        12.49 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 
       22.45        56.94        20.65        19.53        20.68         6.74 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A49A 
        9.07        36.49        11.08        10.45        20.09        12.85 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       21.21        15.91         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         9.80         7.69        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       21.50        54.58        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
       41.19        32.88        34.75        56.58         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       70.13        33.11        43.04        41.88        28.83        44.48 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        32.81        25.81        14.14        12.46        84.23 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       11.77        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       11.51        15.75         9.27        47.34        40.93        35.84 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
       31.96         9.17        34.06        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
       47.01        27.06        29.82        30.02        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5441 
       30.58         7.10        29.95       139.43        19.20        94.88 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       13.35        23.05        60.49        43.23        21.07        62.43 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
        4.73        21.90        26.43        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6961 
       30.08         6.08        53.95        10.98        28.34         2.50 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
       64.83       126.15        18.81         7.99         9.01         1.84 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       21.80        71.21       130.88        77.16         4.73        47.47 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 
       26.20        95.34         4.96        11.87         2.10        18.41 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7418 
       57.47        17.85       210.97        89.33        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
        0.07       100.57        14.89       156.49        54.94        84.49 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T 
        7.17        22.19        27.98        24.99       180.16       159.65 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 
        1.05         6.51        88.87        48.20        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        6.48        22.03        21.24        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       10.42        10.55        13.25        25.41         9.60         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5624 
       16.14        11.44        18.67        24.95        25.32        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
       35.54        33.86        25.48        20.45        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       10.65        11.18        37.18        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        6.77         0.16        25.74         1.22        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        0.36         6.90        34.75        15.95        12.76        14.50 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 
       11.84         0.07        11.84        13.35        18.15        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN 
       14.37         7.96        30.05         1.84        12.62        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
        7.13        17.98        29.92        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       19.00        75.55        18.97         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
       16.01        11.74         9.34        12.72        18.64        12.43 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       11.57         9.76         8.32        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71A 
        7.10        32.45        13.55        13.68        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT 
       43.36        42.02        44.65        16.11        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                        17.62                         18.81 
[1] "0.1 - 169.4 (17.6)" "0.1 - 211.0 (18.8)"
[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        42       101         6
  DEL PEAK 14(4Q35.2) WILD-TYPE      16       51        35       151         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                            16
  STAGE II                           26                            51
  STAGE III                          42                            35
  STAGE IVA                         101                           151
  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      19 47 52 73
  DEL PEAK 14(4Q35.2) WILD-TYPE    31 86 47 99
D43V4, multiclass
       clus
vv      DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  T0+T1                          19                            31
  T2                             47                            86
  T3                             52                            47
  T4                             73                            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 14(4Q35.2) MUTATED    71  34  66   3
  DEL PEAK 14(4Q35.2) WILD-TYPE 107  32  99   5
D43V5, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  N0                          71                           107
  N1                          34                            32
  N2                          66                            99
  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"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    74   1
  DEL PEAK 14(4Q35.2) WILD-TYPE 109   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     74    1
  DEL PEAK 14(4Q35.2) WILD-TYPE  109    0
   clus
vv  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  0                          74                           109
  1                           1                             0
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    66 145
  DEL PEAK 14(4Q35.2) WILD-TYPE  73 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     66  145
  DEL PEAK 14(4Q35.2) WILD-TYPE   73  232
        clus
vv       DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  FEMALE                          66                            73
  MALE                           145                           232
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q35.2) MUTATED                                     209
  DEL PEAK 14(4Q35.2) WILD-TYPE                                   296
                               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                                               209
  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                                                 296
  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    33 178
  DEL PEAK 14(4Q35.2) WILD-TYPE  48 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     33  178
  DEL PEAK 14(4Q35.2) WILD-TYPE   48  257
     clus
vv    DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  NO                           33                            48
  YES                         178                           257
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, continuous
D43V12, 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   175
  DEL PEAK 14(4Q35.2) WILD-TYPE                        23   266
D43V13, multiclass
                                  clus
vv                                 DEL PEAK 14(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    175
                                  clus
vv                                 DEL PEAK 14(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      266
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    10 186
  DEL PEAK 14(4Q35.2) WILD-TYPE  15 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     10  186
  DEL PEAK 14(4Q35.2) WILD-TYPE   15  268
                        clus
vv                       DEL PEAK 14(4Q35.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         186
                        clus
vv                       DEL PEAK 14(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           268
[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  82
  DEL PEAK 15(5Q12.1) WILD-TYPE 183 118
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          212                           301 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                           82                           118 
$`DEL PEAK 15(5Q12.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 
       15.19         9.30         9.07        17.10        15.52        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH 
        3.55        12.62         4.01         7.76        28.11        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL 
       27.95        11.54         7.10        14.47        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7871 
       16.41         6.15         9.14         4.41        36.72        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 
       71.05        20.52        10.55         6.28        38.04        40.44 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 
       12.89        26.86        32.65        20.55        43.73        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 
       33.11        34.36        35.54        11.84        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6997 
       20.68        14.20        11.08        10.45        12.95        14.10 
TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5330 
       17.59        17.29        11.44        12.07         2.93        45.80 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 
       10.42        56.58        13.25         4.24        38.76        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       33.11        16.73        41.88        64.11        23.24        25.81 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6488 
       31.23        11.77        18.54        16.90         6.02        12.46 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
       11.51         9.27        47.18        39.16        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7390 
        3.45         3.09        24.95         9.17        34.06        29.82 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        5.13         5.95       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 
       76.24       107.51        94.88        80.12        13.35        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 
       48.59        60.49         7.07        43.23        54.74        90.12 
TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 
       26.43        42.38        15.09        65.82         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       28.34         4.14       126.15       111.16        18.81        12.66 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 
        5.26        52.31        12.92        21.80        10.75        77.16 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7255 
       36.00        31.36        26.20        17.13        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7416 
       36.13        18.41        57.47        35.54         0.46        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 
       25.94         0.07       100.57        14.89         3.52        16.27 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45Z 
      153.86         6.38       180.16        35.47        45.96        48.20 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-CX-7082 
       60.43         7.07        35.34        29.79        22.52        10.42 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5629 
       18.84        23.05        16.14        12.10        11.11        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        14.04        18.90         9.83        12.10 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-A6C5 TCGA-HD-7753 
       10.65        37.18        20.25        12.62        21.11         0.16 
TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
        1.22         6.90        11.84        13.55        14.47        11.84 
TCGA-KU-A66T TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       18.15         1.84        15.42        17.98        15.78        56.75 
TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 
       10.85        47.01        18.97         2.04        29.00        13.15 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
       11.74         7.30        16.70        12.72        14.79        12.43 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-UF-A719 
       11.57        12.10         9.73         9.76        15.91        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.16        49.22        21.86        13.94        20.75 
TCGA-UF-A7JS TCGA-WA-A7GZ 
       22.36        20.55 

$`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 
        3.35        13.64        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
       57.93        23.84        20.48        53.79        57.44        21.17 
TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       29.42        30.18         5.69         7.82         2.27        13.38 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
       94.62         4.60        18.35        22.42        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM 
       44.98        66.28        38.40        25.71        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
        8.81        12.69        26.27        23.70         4.67        37.84 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
       21.11        41.10        12.99        14.33        27.58        41.69 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
        8.58        12.39         8.32        16.21        11.54        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 
       12.49         8.52        22.45        56.94        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       20.68        19.07         6.74         9.07         9.24        36.49 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       20.09        24.16         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       14.56        12.85        29.72        21.21         7.40        15.91 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        5.75         4.41         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
        7.69         6.18        48.20        39.68        21.50        54.58 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       46.75        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 
       32.88        34.75        14.99        70.13        43.04        28.83 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
       44.48        11.61        29.36        32.81        14.14        12.46 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       39.52        34.52        36.99        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 
       11.64         7.69        15.75        47.34        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 
       30.58         7.10        35.41        29.95        48.39        19.20 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-6433 
       17.95        76.50        91.53        17.92        23.05        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        4.73        21.90        11.24       126.08        19.79        12.03 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7089 
       30.08         6.08        53.95        10.98         2.50        64.83 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 
        7.99         9.01         1.84        71.21       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7409 
       47.47        18.97        95.34         4.96        11.87        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7422 TCGA-CV-7425 
      210.97        89.33         9.67        22.85        34.09        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
      156.49        54.94        84.49        19.76         7.17        16.64 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
       22.19        27.98        24.99       169.38       159.65         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
        6.51        88.87        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        5.98         6.38         6.48        22.03         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 
       23.47        19.92        10.42        10.55        34.36        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       25.41         9.60         2.53        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       25.32        17.72        12.36        15.88         7.63        14.30 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 
       13.94        12.79        58.45        35.54        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       12.13        11.18        16.11        21.63         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 
       13.38        15.16        15.06        13.61         6.77         0.07 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
       25.74        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         4.27         3.65        34.75        15.95        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66S 
       14.50        19.33         0.07         5.29        11.54        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
       12.43        10.75        14.37         7.96        30.05        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
        3.68         7.13        16.08        29.92        51.25        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IF 
       19.00        75.55        12.99        16.01        21.07        17.65 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3K TCGA-RS-A6TO 
        9.34        18.64         6.51         5.62         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.68        43.59        16.11        32.65         2.96        17.03 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                       18.085                        17.950 
[1] "0.1 - 180.2 (18.1)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 15(5Q12.1) MUTATED         9       33        30       112         4
  DEL PEAK 15(5Q12.1) WILD-TYPE      18       44        47       140         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                            18
  STAGE II                           33                            44
  STAGE III                          30                            47
  STAGE IVA                         112                           140
  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 57 37 83
  DEL PEAK 15(5Q12.1) WILD-TYPE    36 76 62 89
D44V4, multiclass
       clus
vv      DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  T0+T1                          14                            36
  T2                             57                            76
  T3                             37                            62
  T4                             83                            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
  DEL PEAK 15(5Q12.1) MUTATED    65  31  75   3
  DEL PEAK 15(5Q12.1) WILD-TYPE 113  35  90   5
D44V5, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  N0                          65                           113
  N1                          31                            35
  N2                          75                            90
  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"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    71   0
  DEL PEAK 15(5Q12.1) WILD-TYPE 112   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     71    0
  DEL PEAK 15(5Q12.1) WILD-TYPE  112    1
   clus
vv  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  0                          71                           112
  1                           0                             1
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    46 166
  DEL PEAK 15(5Q12.1) WILD-TYPE  93 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     46  166
  DEL PEAK 15(5Q12.1) WILD-TYPE   93  211
        clus
vv       DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  FEMALE                          46                            93
  MALE                           166                           211
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(5Q12.1) MUTATED                                     207
  DEL PEAK 15(5Q12.1) WILD-TYPE                                   298
                               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                                               207
  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                                                 298
  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    37 175
  DEL PEAK 15(5Q12.1) WILD-TYPE  44 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     37  175
  DEL PEAK 15(5Q12.1) WILD-TYPE   44  260
     clus
vv    DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  NO                           37                            44
  YES                         175                           260
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, continuous
D44V12, 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                          29   171
  DEL PEAK 15(5Q12.1) WILD-TYPE                        16   270
D44V13, multiclass
                                  clus
vv                                 DEL PEAK 15(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 29
  WHITE                                                    171
                                  clus
vv                                 DEL PEAK 15(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                      270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    13 176
  DEL PEAK 15(5Q12.1) WILD-TYPE  12 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     13  176
  DEL PEAK 15(5Q12.1) WILD-TYPE   12  278
                        clus
vv                       DEL PEAK 15(5Q12.1) MUTATED
  HISPANIC OR LATINO                              13
  NOT HISPANIC OR LATINO                         176
                        clus
vv                       DEL PEAK 15(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           278
[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  85
  DEL PEAK 16(5Q15) WILD-TYPE 175 115
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                        223                         290 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                         85                         115 
$`DEL PEAK 16(5Q15) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 
       15.19         9.30         9.07        17.10        15.52        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH 
        3.55        12.62         4.01         7.76        28.11        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI 
       27.95        11.54         7.10        14.47         7.82        11.05 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7870 
       16.41         6.15         9.14         4.41        33.70        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 
       24.66        71.05        20.52        10.55         6.28        38.04 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
       40.44        12.89        26.86        32.65        12.99        20.55 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 
       43.73        13.05        33.11        34.36        35.54        11.84 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6019 TCGA-CN-6021 
       20.71        30.67        20.68        20.65        14.20         9.07 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A499 TCGA-CN-A63U 
       11.08        10.45        12.95        14.10        17.59        17.29 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-5333 
       11.44        12.07         9.80         2.93        10.42        11.21 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       13.25         4.24        38.76        51.29        33.11        16.73 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI 
       41.88        64.11        23.24        25.81        12.46        31.23 
TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 
       11.77        18.54        16.90        12.46        11.51         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 
        3.09        24.95         9.17        34.06        29.82         5.13 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 
        5.95        48.39       139.43        17.16       129.21        76.24 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 
       17.95       107.51        94.88        80.12        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6940 
       60.49         7.07        43.23        54.74        90.12        26.43 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 
       42.38        15.09        30.08        65.82         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       28.34         4.14       126.15       111.16        18.81        12.66 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 
        5.26        52.31        12.92        21.80        10.75        77.16 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7255 
       36.00        31.36        26.20        17.13        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 
       36.13        18.41        35.54         0.46        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7438 
        0.07        14.89         3.52        16.27       153.86         6.38 
TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A465 
      180.16        45.96         6.51        48.20        60.43         7.07 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 
       35.34        29.79        22.52        10.42        18.84        23.05 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q 
       16.14        24.95        12.36        13.94        12.10        11.11 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
       58.45        30.94        33.86        18.02        14.04        18.90 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61V 
        9.83        12.10        10.65        37.18         3.02        12.62 
TCGA-F7-A61W TCGA-F7-A622 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7917 
        0.46        11.80        13.61        21.11         0.16         1.22 
TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67D 
        6.90        11.84        13.55        11.84        18.15         1.84 
TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX 
       15.42        17.98        15.78        56.75        10.85        47.01 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A652 
       18.97         2.04        29.00        12.99        13.15        11.74 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        7.30        16.70        12.72        14.79        12.43         6.51 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-UF-A719 
       11.57        12.10         9.73         9.76        15.91        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.16        49.22        21.86        13.94        20.75 
TCGA-WA-A7GZ 
       20.55 

$`DEL PEAK 16(5Q15) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        3.35        13.64        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
       57.93        23.84        20.48        53.79        57.44        21.17 
TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
       29.42        30.18         5.69         2.27        13.38        20.48 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
       94.62         4.60        18.35        22.42        36.72        50.20 
TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       44.98        38.40        25.71        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 
       12.69        26.27        23.70         4.67        37.84        21.11 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 
       41.10        14.33        27.58        41.69         8.58        12.39 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
        8.32        16.21        11.54        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
       22.45        56.94        19.53        20.68        19.07         6.74 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        9.24        36.49        20.09        24.16         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        35.01        14.56        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
        7.40        15.91         5.75         4.41         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        7.33         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        46.75        45.80        45.99         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 
       32.38        32.88        34.75        56.58        14.99        70.13 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.04        28.83        44.48        11.61        29.36        32.81 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       14.14        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 
       50.01        39.52        34.52        36.99         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7373 
       10.22        11.34        11.64         7.69        15.75        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        0.99        31.96        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        12.89        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5434 
       29.52        30.58         7.10        35.41        29.95       108.95 
TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       19.20        76.50        91.53        17.92        13.35        23.05 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43         9.60         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        11.24       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7089 
       12.03         6.08        53.95        10.98         2.50        64.83 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 
        7.99         9.01         1.84        71.21       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7406 
       47.47        18.97        95.34         4.96        11.87        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7422 
       17.85       210.97        89.33         9.67        22.85        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 
      100.57        56.48       156.49        54.94        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64        22.19        27.98        24.99       169.38 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 
      159.65        35.47         1.05        88.87        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT 
       56.61        15.25         5.98         6.38         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
        3.62        21.24        23.47        19.92        10.42        10.55 
TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 
       34.36        13.25        25.41         9.60         2.53        11.44 
TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       18.67        25.32        17.72        15.88         7.63        14.30 
TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 
       12.79        35.54        25.48        20.45        12.13        11.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 
       16.11        21.63        20.25        19.23        18.94        17.85 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       20.25        12.43        13.38        15.16        15.06         6.77 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
        0.07        25.74        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 
        0.36        13.84         4.27         3.65        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       12.76        14.50        19.33         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       11.54        13.35        12.43        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05        12.62         3.68         7.13        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T7 TCGA-QK-A64Z 
       51.25        36.82        19.00        75.55        16.01        21.07 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-AA3K TCGA-RS-A6TO 
       17.65         9.34        18.64         5.62         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       13.68        43.59        16.11        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7H4 
       17.03        14.56 

  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                     180.16                      210.97 
  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE 
                     17.130                      19.135 
[1] "0.1 - 180.2 (17.1)" "0.1 - 211.0 (19.1)"
[1] "hr=" "1"  
D45V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 16(5Q15) MUTATED         9       34        33       117         4
  DEL PEAK 16(5Q15) WILD-TYPE      18       43        44       135         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                          18
  STAGE II                         34                          43
  STAGE III                        33                          44
  STAGE IVA                       117                         135
  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 59 40 87
  DEL PEAK 16(5Q15) WILD-TYPE    36 74 59 85
D45V4, multiclass
       clus
vv      DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  T0+T1                        14                          36
  T2                           59                          74
  T3                           40                          59
  T4                           87                          85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 16(5Q15) MUTATED    72  31  75   3
  DEL PEAK 16(5Q15) WILD-TYPE 106  35  90   5
D45V5, multiclass
    clus
vv   DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  N0                        72                         106
  N1                        31                          35
  N2                        75                          90
  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"
D45V6, binary
                             cls
clus                            0   1
  DEL PEAK 16(5Q15) MUTATED    79   0
  DEL PEAK 16(5Q15) WILD-TYPE 104   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     79    0
  DEL PEAK 16(5Q15) WILD-TYPE  104    1
   clus
vv  DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  0                        79                         104
  1                         0                           1
[1] 2 2
[1] FALSE
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(5Q15) MUTATED    50 173
  DEL PEAK 16(5Q15) WILD-TYPE  89 204
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     50  173
  DEL PEAK 16(5Q15) WILD-TYPE   89  204
        clus
vv       DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  FEMALE                        50                          89
  MALE                         173                         204
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q15) MUTATED                                     217
  DEL PEAK 16(5Q15) WILD-TYPE                                   288
                             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                                             217
  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                                               288
  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    38 185
  DEL PEAK 16(5Q15) WILD-TYPE  43 250
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     38  185
  DEL PEAK 16(5Q15) WILD-TYPE   43  250
     clus
vv    DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  NO                         38                          43
  YES                       185                         250
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, continuous
D45V12, 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                          29   180
  DEL PEAK 16(5Q15) WILD-TYPE                        16   261
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 16(5Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               29
  WHITE                                                  180
                                  clus
vv                                 DEL PEAK 16(5Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 16
  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"
D45V14, binary
                             cls
clus                            0   1
  DEL PEAK 16(5Q15) MUTATED    13 187
  DEL PEAK 16(5Q15) WILD-TYPE  12 267
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(5Q15) MUTATED     13  187
  DEL PEAK 16(5Q15) WILD-TYPE   12  267
                        clus
vv                       DEL PEAK 16(5Q15) MUTATED DEL PEAK 16(5Q15) WILD-TYPE
  HISPANIC OR LATINO                            13                          12
  NOT HISPANIC OR LATINO                       187                         267
[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  73
  DEL PEAK 17(5Q35.3) WILD-TYPE 189 127
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                          197                           316 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                           73                           127 
$`DEL PEAK 17(5Q35.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 
       15.19         9.30         9.07        17.10        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01         7.76        28.11        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 
        7.10        14.47        11.05        16.41         6.15         9.14 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
       36.72        50.20        66.28        71.05        20.52         6.28 
TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 
       38.04        40.44        12.89        26.86        32.65        20.55 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5364 
       43.73        13.05        33.11        34.36        35.54        16.21 
TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6024 
       11.84        20.71        20.68        14.20         9.07        11.08 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A499 
       10.45        12.95        24.16        17.42        14.10        17.59 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6225 
       17.29        11.44        12.07         2.93        10.42        13.25 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
        4.24        38.76        51.29        33.11        16.73        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
       64.11        23.24        25.81        12.46        31.23        11.77 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       18.54        16.90        12.46         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
       40.93        35.84         3.45         3.09        24.95         0.99 
TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 
       34.06        29.82         5.13         5.95        48.39        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 
      129.21       108.95        76.24       107.51        94.88        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
       48.59        60.49         7.07        43.23        54.74         9.60 
TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 
       90.12        26.43        11.24        15.09        30.08        65.82 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        7.13         8.42        28.34       126.15       111.16        18.81 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 
        5.26        52.31        21.80        10.75        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7414 
       26.20        17.13        47.97        36.13        18.41         0.46 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7435 
       25.08         0.07        34.09        14.89         3.52       153.86 
TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A465 
        6.38       180.16        45.96         6.51        48.20         7.07 
TCGA-CV-A6JE TCGA-CV-A6JU TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 
       35.34         3.62        10.42        18.84        23.05        11.44 
TCGA-D6-8568 TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5629 
       24.95        14.30        13.94        12.10        11.11        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        14.04        18.90         9.83        12.10 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A622 TCGA-H7-A6C4 
       10.65        37.18        20.25        12.62        11.80        13.61 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-IQ-A61G TCGA-IQ-A61H 
        0.16        25.74         1.22        14.66        11.84        13.55 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       11.84        18.15         1.84        16.08        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-QK-A652 
       56.75        10.85        47.01        18.97        29.00        11.74 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        7.30        16.70        12.72        14.79        12.43         6.51 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71B 
       11.57         9.76        15.91        13.25        54.67        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-WA-A7GZ 
       49.22        21.86        16.11        20.75        20.55 

$`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 
        3.35        13.64        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       57.93        23.84        20.48        53.79        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6DD TCGA-BA-A6DF 
       21.17         3.55        29.42        30.18         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        2.27        13.38        20.48        94.62         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
       18.35        22.42        33.70        44.98        24.66        38.40 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       25.71        10.55        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 
       26.27        23.70         4.67        37.84        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 
       12.99        14.33        27.58        41.69         8.58        12.39 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
        8.32        11.54        11.57        12.49         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       56.94        30.67        20.65        19.53        20.68        19.07 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6998 
        6.74         9.24        36.49        20.09         3.68        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        14.56        12.85        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       15.91         5.75         4.41         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.80        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
       41.19        32.38        32.88        34.75        56.58        14.99 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
       70.13        43.04        28.83        44.48        11.61        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       32.81        14.14        84.23        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 
       58.42        50.01        39.52        34.52        36.99         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 
       11.90        10.22        11.34        11.64         7.69        11.51 
TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 
       15.75        47.34        29.23        31.96         9.17        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        31.10        29.85        29.52        30.58         7.10 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 
       35.41        29.95       139.43        19.20        17.95        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-6433 
       91.53        80.12        17.92        13.35        23.05        21.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       62.43         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 
       21.90       126.08        19.79        12.03        42.38         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7097 
       53.95        10.98         2.50         4.14        64.83        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7183 
        7.99         9.01         1.84        12.92        71.21       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 
       77.16         4.73        47.47        18.97        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       11.87         2.10        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7425 
       89.33         9.67        22.85        25.94       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94        16.27        84.49        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
       16.64        22.19        27.98        24.99       169.38       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
       35.47         1.05        88.87        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61        15.25         5.98         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       22.03        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       10.55        34.36        13.25        25.41         9.60         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       16.14        18.67        25.32        17.72        12.36        15.88 
TCGA-D6-A6EM TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 
        7.63        12.79        58.45        35.54        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       12.13        11.18        16.11        21.63         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       18.94         0.46        17.85        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-8314 
       15.16        15.06        21.11         6.77         0.07        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 
        0.07        14.47         5.29        11.54        13.35        12.43 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
       10.75        14.37         7.96        30.05        12.62         3.68 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
       15.42         7.13        29.92        51.25        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55         2.04        12.99        16.01        13.15        21.07 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       17.65         9.34        18.64         5.62        12.10         9.73 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        12.72        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A7JK TCGA-UF-A7JS 
       13.55        13.68        43.59         2.83        13.94        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
       32.65         2.96        17.03        14.56 

  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE 
                       17.590                        18.805 
[1] "0.1 - 180.2 (17.6)" "0.1 - 211.0 (18.8)"
[1] "hr=" "1.1"
D46V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 17(5Q35.3) MUTATED         8       28        34       100         4
  DEL PEAK 17(5Q35.3) WILD-TYPE      19       49        43       152         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                            19
  STAGE II                           28                            49
  STAGE III                          34                            43
  STAGE IVA                         100                           152
  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  53  41  72
  DEL PEAK 17(5Q35.3) WILD-TYPE    39  80  58 100
D46V4, multiclass
       clus
vv      DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  T0+T1                          11                            39
  T2                             53                            80
  T3                             41                            58
  T4                             72                           100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 17(5Q35.3) MUTATED    65  29  67   2
  DEL PEAK 17(5Q35.3) WILD-TYPE 113  37  98   6
D46V5, multiclass
    clus
vv   DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  N0                          65                           113
  N1                          29                            37
  N2                          67                            98
  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"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q35.3) MUTATED    72   0
  DEL PEAK 17(5Q35.3) WILD-TYPE 111   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q35.3) MUTATED     72    0
  DEL PEAK 17(5Q35.3) WILD-TYPE  111    1
   clus
vv  DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  0                          72                           111
  1                           0                             1
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q35.3) MUTATED    46 151
  DEL PEAK 17(5Q35.3) WILD-TYPE  93 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q35.3) MUTATED     46  151
  DEL PEAK 17(5Q35.3) WILD-TYPE   93  226
        clus
vv       DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  FEMALE                          46                            93
  MALE                           151                           226
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(5Q35.3) MUTATED                                     191
  DEL PEAK 17(5Q35.3) WILD-TYPE                                   314
                               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                                               191
  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                                                 314
  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    34 163
  DEL PEAK 17(5Q35.3) WILD-TYPE  47 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q35.3) MUTATED     34  163
  DEL PEAK 17(5Q35.3) WILD-TYPE   47  272
     clus
vv    DEL PEAK 17(5Q35.3) MUTATED DEL PEAK 17(5Q35.3) WILD-TYPE
  NO                           34                            47
  YES                         163                           272
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, continuous
D46V12, 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                          24   160
  DEL PEAK 17(5Q35.3) WILD-TYPE                        21   281
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 17(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                    160
                                  clus
vv                                 DEL PEAK 17(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   21
  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"
D46V14, binary
                               cls
clus                              0   1
  DEL PEAK 17(5Q35.3) MUTATED    11 167
  DEL PEAK 17(5Q35.3) WILD-TYPE  14 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(5Q35.3) MUTATED     11  167
  DEL PEAK 17(5Q35.3) WILD-TYPE   14  287
                        clus
vv                       DEL PEAK 17(5Q35.3) MUTATED
  HISPANIC OR LATINO                              11
  NOT HISPANIC OR LATINO                         167
                        clus
vv                       DEL PEAK 17(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           287
[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    57  38
  DEL PEAK 18(6P25.3) WILD-TYPE 256 162
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           95                           418 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                           38                           162 
$`DEL PEAK 18(6P25.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-5152 TCGA-BA-5559 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7862 
        3.35        42.35        57.44         4.60         4.41        36.72 
TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4740 
       10.55        23.70        38.04        37.84        41.10        27.58 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6022 
       12.39        16.21         8.52        20.71        19.53         9.24 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A 
       11.08        20.09        24.16        14.10        14.56        12.85 
TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6221 
        7.40         4.41        12.07         6.18        10.42        32.88 
TCGA-CQ-6223 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-6473 TCGA-CR-6478 
       34.75        23.24        32.81        31.23        36.99         6.02 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7388 
       12.46         9.27        39.16         3.09        29.23        27.06 
TCGA-CR-7399 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
        5.95       129.21       108.95        76.24        19.20       107.51 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6934 TCGA-CV-6940 TCGA-CV-6945 
       91.53        80.12         7.07         2.14        26.43        12.03 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7247 TCGA-CV-7248 
       28.34         4.14        18.81         5.26        18.97        17.13 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7430 
       11.87        47.97        18.41        25.08        25.94        16.27 
TCGA-CV-A465 TCGA-CV-A6JT TCGA-CV-A6JY TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EQ 
        7.07        22.03        21.24        23.05        11.44        12.10 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-F7-A50I TCGA-F7-A623 
       11.11        58.45        18.90        20.45         3.02        20.25 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-A61I TCGA-MT-A67G 
        0.16         1.22        14.66         3.65         0.07         3.68 
TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T8 
       15.42        17.98        15.78        56.75        19.00        13.15 
TCGA-QK-A8ZA TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JJ TCGA-UP-A6WW 
       12.10         2.83        42.02        16.11        17.03 

$`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 
       15.19         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        57.93        17.10        23.84        20.48        53.79 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       15.52        21.17        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
        7.76        29.42        28.11        20.45        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        9.14        18.35        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       66.28        24.66        38.40        71.05        20.52        25.71 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       27.19        12.92         8.81         6.28        12.69        26.27 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        40.44        12.89        26.86        32.65        21.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       12.99        20.55        14.33        43.73        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
       33.11        34.36         8.58        35.54         8.32        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
       11.84        11.57        12.49        22.45        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       20.68        20.65        20.68        19.07        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 
        9.07        36.49        10.45        12.95         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
       11.74        35.01        17.59        29.72        21.21        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       15.91        11.44         5.75         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        9.80         7.69        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.80        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       41.19        32.38        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
       38.76        70.13        51.29        33.11        16.73        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
       41.88        28.83        64.11        44.48        11.61        29.36 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       25.81        14.14        12.46        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
       37.87        26.27        58.42        50.01        39.52        34.52 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54        16.90        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
        7.69        11.51        15.75        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.45        24.95         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       30.58         7.10         5.13        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 
      139.43        17.16        17.95        94.88        76.50        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       13.35        23.05        86.83        48.59        60.49        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 
       54.74        21.07        62.43         9.60        90.12         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52         4.73        21.90        11.24       126.08 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7089 
       65.82        10.98         7.13         8.42         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
      126.15       111.16        12.66         7.99         9.01         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 
       95.34         4.96         2.10        36.13        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       17.85       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.07        34.09       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94         3.52        84.49        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       16.64         6.38        22.19        27.98        24.99       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
        2.53        16.14        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES 
       12.36        15.88         7.63        14.30        13.94        12.79 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
       35.54        30.94        33.86        18.02        14.04        25.48 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
        9.83        12.13        12.10        10.65        11.18        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       16.11        21.63        20.25        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       15.06        13.61        21.11         6.77         0.07        25.74 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       22.03        12.66        22.85         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84        13.55        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05         1.84        12.62         7.13        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        10.85        36.82        47.01        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        12.99        16.01        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       17.65         7.30        16.70         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       14.79        12.43         6.51         5.62        11.57         9.73 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
        9.76         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       54.67        43.36        41.16        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       24.16        49.22        21.86        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        20.55        14.56 

  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                       129.21                        210.97 
  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE 
                        17.13                         18.25 
[1] "0.1 - 129.2 (17.1)" "0.1 - 211.0 (18.2)"
[1] "hr=" "1.2"
D47V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 18(6P25.3) MUTATED         2       10        13        58         2
  DEL PEAK 18(6P25.3) WILD-TYPE      25       67        64       194        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                            25
  STAGE II                           10                            67
  STAGE III                          13                            64
  STAGE IVA                          58                           194
  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  19  22  39
  DEL PEAK 18(6P25.3) WILD-TYPE    45 114  77 133
D47V4, multiclass
       clus
vv      DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  T0+T1                           5                            45
  T2                             19                           114
  T3                             22                            77
  T4                             39                           133
[1] 4 2
[1] TRUE
[1] "dimension of 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  36   1
  DEL PEAK 18(6P25.3) WILD-TYPE 149  55 129   7
D47V5, multiclass
    clus
vv   DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  N0                          29                           149
  N1                          11                            55
  N2                          36                           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"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED    27   0
  DEL PEAK 18(6P25.3) WILD-TYPE 156   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED     27    0
  DEL PEAK 18(6P25.3) WILD-TYPE  156    1
   clus
vv  DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  0                          27                           156
  1                           0                             1
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED    19  76
  DEL PEAK 18(6P25.3) WILD-TYPE 120 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED     19   76
  DEL PEAK 18(6P25.3) WILD-TYPE  120  301
        clus
vv       DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  FEMALE                          19                           120
  MALE                            76                           301
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6P25.3) MUTATED                                      93
  DEL PEAK 18(6P25.3) WILD-TYPE                                   412
                               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                                                93
  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                                                 412
  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    18  77
  DEL PEAK 18(6P25.3) WILD-TYPE  63 358
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED     18   77
  DEL PEAK 18(6P25.3) WILD-TYPE   63  358
     clus
vv    DEL PEAK 18(6P25.3) MUTATED DEL PEAK 18(6P25.3) WILD-TYPE
  NO                           18                            63
  YES                          77                           358
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, continuous
D47V12, 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    76
  DEL PEAK 18(6P25.3) WILD-TYPE                        31   365
D47V13, multiclass
                                  clus
vv                                 DEL PEAK 18(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                     76
                                  clus
vv                                 DEL PEAK 18(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                               cls
clus                              0   1
  DEL PEAK 18(6P25.3) MUTATED     5  80
  DEL PEAK 18(6P25.3) WILD-TYPE  20 374
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(6P25.3) MUTATED      5   80
  DEL PEAK 18(6P25.3) WILD-TYPE   20  374
                        clus
vv                       DEL PEAK 18(6P25.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       DEL PEAK 18(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           374
[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    42  31
  DEL PEAK 19(7Q31.1) WILD-TYPE 271 169
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           73                           440 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                           31                           169 
$`DEL PEAK 19(7Q31.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 
       15.19        13.64        26.50        42.35        57.44        15.52 
TCGA-BA-6872 TCGA-BA-A4IH TCGA-BA-A6DE TCGA-BB-7861 TCGA-BB-7872 TCGA-BB-A5HY 
       12.62        20.45        14.47        22.42        38.40        10.55 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 
        6.28        12.69        26.86        32.65        41.10        20.55 
TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6998 
       12.39        56.94        30.67        19.07        10.45        11.74 
TCGA-CN-A49B TCGA-CN-A6V3 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CR-5247 TCGA-CR-6474 
       29.72         9.80        41.19        32.38        11.77        18.54 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7398 TCGA-CR-7399 
       39.16        47.34        40.93         0.99         5.13         5.95 
TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6954 TCGA-CV-6960 
       80.12        86.83        54.74        90.12        65.82        28.34 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7415 TCGA-CV-7429 TCGA-CV-7433 
        2.50       111.16        10.75        22.85         3.52        19.76 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A6JE TCGA-CX-7082 
      153.86         6.38        22.19        35.47        35.34        10.42 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EM TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A623 
       23.05        11.44         7.63        21.63        20.25        20.25 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A5BI 
       14.50        11.84        13.55        18.15        12.43         7.13 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       51.25        47.01         2.04        21.07        11.57         9.73 
TCGA-UF-A7JK 
       13.94 

$`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 
        3.35         9.30        37.28         9.07        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        20.48        53.79        21.17        14.83 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II 
        3.55         4.01         7.76        29.42        28.11        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.60         4.41        18.35        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 
       50.20        44.98        66.28        24.66        71.05        20.52 
TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 
       25.71        27.19        12.92         8.81        26.27        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4733 
       38.04         4.67        40.44        37.84        12.89        21.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       12.99        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       33.11        34.36         8.58        35.54         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        22.45 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       20.71        20.68        20.65        19.53        20.68        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 
        6.74         9.07         9.24        36.49        11.08        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A497 
       12.95        24.16         3.68        17.42        14.10        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       14.56        17.59        12.85        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         7.69         6.18        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        46.75        45.80        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
       10.42        11.21         4.24        32.88        34.75        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        32.81        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       16.90         6.02        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        11.51        15.75         9.27        47.18 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       35.84         3.45         3.09        24.95        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
       29.85        29.52        30.58         7.10        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       17.92        13.35        23.05        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
       43.23        21.07        62.43         9.60         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        5.46        20.52         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      126.08        19.79        12.03        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 
        6.08        53.95        10.98         7.13         8.42         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       126.15        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        47.47        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       26.20        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       47.97         2.10        36.13        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 
       17.85       210.97        89.33         9.67         0.46        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 
      156.49        54.94        16.27        84.49         7.17        16.64 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        24.99       169.38       180.16       159.65         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
        0.76        56.61         7.07        15.25         5.98         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        22.03         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       19.92        22.52        10.42        10.55        18.84        34.36 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
       13.25        25.41         9.60         2.53        16.14        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
       24.95        25.32        17.72        12.36        15.88        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        35.54 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       30.94        33.86        18.02        14.04        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       37.18        16.11         3.02        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
        0.46        17.85        11.80        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       15.06        13.61        21.11         6.77         0.07         0.16 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
       25.74         1.22        14.66        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       15.95        12.76        19.33         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       11.54        11.84        13.35        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
       30.05         1.84        12.62         3.68        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        15.78        56.75        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55        18.97        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        18.64        14.79        12.43         6.51         5.62 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.10         9.76         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.55        13.25        13.68 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       16.11        20.75        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE 
                       20.250                        17.885 
[1] "1.0 - 153.9 (20.2)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.1"
D48V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 19(7Q31.1) MUTATED         3       10        12        42         0
  DEL PEAK 19(7Q31.1) WILD-TYPE      24       67        65       210        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                            24
  STAGE II                           10                            67
  STAGE III                          12                            65
  STAGE IVA                          42                           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 19(7Q31.1) MUTATED       5  22  15  25
  DEL PEAK 19(7Q31.1) WILD-TYPE    45 111  84 147
D48V4, multiclass
       clus
vv      DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  T0+T1                           5                            45
  T2                             22                           111
  T3                             15                            84
  T4                             25                           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"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 19(7Q31.1) MUTATED    18  16  28   0
  DEL PEAK 19(7Q31.1) WILD-TYPE 160  50 137   8
D48V5, multiclass
    clus
vv   DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  N0                          18                           160
  N1                          16                            50
  N2                          28                           137
  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"
D48V6, binary
                               cls
clus                              0   1
  DEL PEAK 19(7Q31.1) MUTATED    26   0
  DEL PEAK 19(7Q31.1) WILD-TYPE 157   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q31.1) MUTATED     26    0
  DEL PEAK 19(7Q31.1) WILD-TYPE  157    1
   clus
vv  DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  0                          26                           157
  1                           0                             1
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(7Q31.1) MUTATED    20  55
  DEL PEAK 19(7Q31.1) WILD-TYPE 119 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q31.1) MUTATED     20   55
  DEL PEAK 19(7Q31.1) WILD-TYPE  119  322
        clus
vv       DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  FEMALE                          20                           119
  MALE                            55                           322
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(7Q31.1) MUTATED                                      73
  DEL PEAK 19(7Q31.1) WILD-TYPE                                   432
                               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                                                73
  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                                                 432
  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  60
  DEL PEAK 19(7Q31.1) WILD-TYPE  66 375
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q31.1) MUTATED     15   60
  DEL PEAK 19(7Q31.1) WILD-TYPE   66  375
     clus
vv    DEL PEAK 19(7Q31.1) MUTATED DEL PEAK 19(7Q31.1) WILD-TYPE
  NO                           15                            66
  YES                          60                           375
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, continuous
D48V12, 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    63
  DEL PEAK 19(7Q31.1) WILD-TYPE                        38   378
D48V13, multiclass
                                  clus
vv                                 DEL PEAK 19(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK 19(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                               cls
clus                              0   1
  DEL PEAK 19(7Q31.1) MUTATED     3  68
  DEL PEAK 19(7Q31.1) WILD-TYPE  22 386
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(7Q31.1) MUTATED      3   68
  DEL PEAK 19(7Q31.1) WILD-TYPE   22  386
                        clus
vv                       DEL PEAK 19(7Q31.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK 19(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                22
  NOT HISPANIC OR LATINO                           386
[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    74  54
  DEL PEAK 20(7Q36.1) WILD-TYPE 239 146
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                          128                           385 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                           54                           146 
$`DEL PEAK 20(7Q36.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6871 
       15.19        13.64        42.35        57.44        15.52         3.55 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A8YP 
        7.76        28.11        20.45        14.47        11.05        16.41 
TCGA-BB-7863 TCGA-BB-7872 TCGA-BB-A6UM TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       33.70        38.40        12.92        12.89        26.86        32.65 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-5355 TCGA-CN-5358 
       41.10        12.99        20.55        14.33        33.11         8.58 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       12.39         8.32        56.94        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 
       19.53        19.07        10.45         3.68        14.10        11.74 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5326 
       17.59        29.72        17.29        11.44         5.75         2.93 
TCGA-CQ-5331 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-A4C7 
       45.99        32.38        32.88        14.99        16.73        11.61 
TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6491 TCGA-CR-7365 
       29.36        11.77        18.54         6.02        11.51        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7398 TCGA-CV-5431 
       40.93        35.84         0.99        32.78         5.13        17.16 
TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6941 
       80.12        54.74         9.60        90.12         9.70        11.24 
TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7180 
       42.38        65.82        28.34         2.50       111.16        10.75 
TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       18.97        47.97        17.85         9.67         0.46        22.85 
TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45U 
       14.89         3.52        19.76       153.86         6.38        35.47 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JU TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7219 
       35.34         6.38         3.62        22.52        10.42        34.36 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-7588 
       23.05        11.44         7.63        14.30        12.10        14.04 
TCGA-DQ-7594 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 
       12.10        21.63        20.25         0.46        11.80        20.25 
TCGA-H7-8502 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A61J 
       15.06         3.65        34.75        14.50        13.55        14.47 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67A TCGA-MZ-A5BI TCGA-P3-A5QE 
       18.15        12.43        14.37        30.05         7.13        51.25 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       47.01         2.04        13.15        11.57         9.73         9.76 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JO TCGA-UF-A7JS 
       13.25        13.68        43.59        62.27        20.75        22.36 
TCGA-UF-A7JT TCGA-WA-A7GZ 
       32.65        20.55 

$`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 
        3.35         9.30        37.28         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
       57.93        17.10        23.84        20.48        53.79        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 
       14.83        12.62         4.01        29.42        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       11.54         7.10         5.69         7.82         2.27        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       20.48         6.15        94.62         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.35        22.42        36.72        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       24.66        71.05        20.52        25.71        10.55        27.19 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        26.27        23.70        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4739 TCGA-CN-4740 
        4.67        40.44        37.84        21.11        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       41.69        13.05        34.36        35.54        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       11.84        11.57        12.49         8.52        22.45        20.71 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       20.68        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A497 
       11.08        20.09        12.95        24.16        17.42        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A640 
       14.56        12.85        21.21         7.40        15.91         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
        6.18        48.20        39.68        21.50        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
       45.80        10.42        11.21         4.24        41.19        34.75 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       56.58        13.25         4.24        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       33.11        43.04        41.88        28.83        64.11        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        34.52        36.99        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64         7.69        12.46        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       47.18        47.34         3.45         3.09        24.95        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       29.85        29.52        30.58         7.10         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.95        48.39       139.43       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       17.92        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 
        7.07        43.23        21.07        62.43         2.14         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 
       20.52         4.73        21.90        26.43       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       12.03        15.09        30.08         6.08        53.95        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 
        7.13         8.42         4.14        64.83       126.15        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       12.66         7.99         9.01         5.26         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       12.92        21.80        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
       47.47        36.00        31.36        26.20        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
        4.96        11.87         2.10        36.13        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       35.54       210.97        89.33        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
       34.09       100.57        56.48       156.49        54.94        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
       84.49         7.17        16.64        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      169.38       180.16       159.65         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        7.07        15.25         5.98        29.79         6.48        22.03 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       21.24        23.47        19.92        10.42        10.55        18.84 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
       13.25        25.41         9.60         2.53        16.14        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EP 
       24.95        25.32        17.72        12.36        15.88        13.94 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
       12.79        11.11        58.45        35.54        30.94        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       18.02        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J 
       10.65        11.18        37.18        16.11         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       18.94        12.62        17.85        12.43        13.38        15.16 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E 
       13.84         4.27         6.90        15.95        12.76        19.33 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
       11.84         0.07         5.29        11.54        11.84        13.35 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       10.75         7.96         1.84        12.62         3.68        15.42 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
       16.08        17.98        29.92        15.78        56.75        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       36.82        19.00        75.55        18.97        29.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        21.07        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        18.64        14.79        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62        12.10         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-UF-A719 TCGA-UF-A71A 
       15.91         7.10        32.45        13.55        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
       43.36        41.16        42.02        44.65        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JV TCGA-UP-A6WW 
       49.22        21.86        16.11        13.94         2.96        17.03 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                         0.46                          0.07 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE 
                       15.965                        18.840 
[1] "0.5 - 153.9 (16.0)" "0.1 - 211.0 (18.8)"
[1] "hr=" "1.3"
D49V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 20(7Q36.1) MUTATED         7       14        19        65         5
  DEL PEAK 20(7Q36.1) WILD-TYPE      20       63        58       187         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                            20
  STAGE II                           14                            63
  STAGE III                          19                            58
  STAGE IVA                          65                           187
  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      14  33  21  48
  DEL PEAK 20(7Q36.1) WILD-TYPE    36 100  78 124
D49V4, multiclass
       clus
vv      DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  T0+T1                          14                            36
  T2                             33                           100
  T3                             21                            78
  T4                             48                           124
[1] 4 2
[1] TRUE
[1] "dimension of 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    39  20  43   4
  DEL PEAK 20(7Q36.1) WILD-TYPE 139  46 122   4
D49V5, multiclass
    clus
vv   DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  N0                          39                           139
  N1                          20                            46
  N2                          43                           122
  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"
D49V6, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q36.1) MUTATED    44   0
  DEL PEAK 20(7Q36.1) WILD-TYPE 139   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.1) MUTATED     44    0
  DEL PEAK 20(7Q36.1) WILD-TYPE  139    1
   clus
vv  DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  0                          44                           139
  1                           0                             1
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q36.1) MUTATED    31  99
  DEL PEAK 20(7Q36.1) WILD-TYPE 108 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.1) MUTATED     31   99
  DEL PEAK 20(7Q36.1) WILD-TYPE  108  278
        clus
vv       DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  FEMALE                          31                           108
  MALE                            99                           278
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q36.1) MUTATED                                     127
  DEL PEAK 20(7Q36.1) WILD-TYPE                                   378
                               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                                               127
  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                                                 378
  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    21 109
  DEL PEAK 20(7Q36.1) WILD-TYPE  60 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.1) MUTATED     21  109
  DEL PEAK 20(7Q36.1) WILD-TYPE   60  326
     clus
vv    DEL PEAK 20(7Q36.1) MUTATED DEL PEAK 20(7Q36.1) WILD-TYPE
  NO                           21                            60
  YES                         109                           326
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, continuous
D49V12, 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   110
  DEL PEAK 20(7Q36.1) WILD-TYPE                        30   331
D49V13, multiclass
                                  clus
vv                                 DEL PEAK 20(7Q36.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    110
                                  clus
vv                                 DEL PEAK 20(7Q36.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   30
  WHITE                                                      331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q36.1) MUTATED     5 115
  DEL PEAK 20(7Q36.1) WILD-TYPE  20 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.1) MUTATED      5  115
  DEL PEAK 20(7Q36.1) WILD-TYPE   20  339
                        clus
vv                       DEL PEAK 20(7Q36.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         115
                        clus
vv                       DEL PEAK 20(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           339
[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   165 133
  DEL PEAK 21(8P23.2) WILD-TYPE 148  67
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          298                           215 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          133                            67 
$`DEL PEAK 21(8P23.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 
        3.35        15.19        37.28        26.50        23.74        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       20.48        53.79        15.52        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
        7.76        30.18        27.95         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 
        7.82        11.05        13.38        16.41         9.14         4.41 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU 
       36.72        33.70        66.28        24.66        38.40        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 
       10.55        27.19         8.81         6.28        12.69        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 
       38.04         4.67        40.44        12.89        41.10        12.99 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 
       14.33        27.58        13.05        34.36        35.54         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
       16.21        11.54        11.84        11.57         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
       56.94        30.67        20.68        20.65        19.53        19.07 
TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 
        6.74        11.08        20.09        12.95         3.68        17.42 
TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63W 
       14.10        35.01        14.56        12.85        29.72        11.44 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 
        4.41        12.07        21.50         2.93        46.75        45.80 
TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       10.42         4.24        34.75        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        51.29        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        28.83        64.11        44.48        11.61 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6471 
       29.36        32.81        31.23        84.23        11.77        39.52 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7367 
       18.54         6.02        11.64        12.46        47.18        47.34 
TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       35.84        24.95        29.23         0.99        31.96         9.17 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7395 
       19.92        17.13        47.01        27.06        29.82        30.58 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        5.95        35.41       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 
       76.24        19.20        94.88        80.12        17.92        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 
       48.59        60.49        62.43         9.60        90.12         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 
        5.46        20.52         4.73        26.43       126.08        19.79 
TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       42.38         6.08        65.82         7.13         8.42        28.34 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        4.14        64.83       126.15        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7236 
        9.01         1.84        12.92        71.21        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 
       47.47        31.36        26.20        18.97        17.13        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7414 
        2.10        36.13        35.54        17.85         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
       22.85        25.08         0.07        34.09       100.57        14.89 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
      156.49        54.94        16.27        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45V 
        6.38        22.19       169.38       180.16        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A465 
       45.96         6.51        48.20        60.43        56.61         7.07 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        5.98        35.34         6.48        22.03         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
       23.47        19.92        10.42        34.36         9.60        23.05 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EO 
       16.14        11.44        24.95        17.72         7.63        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       13.94        12.10        12.79        58.45        35.54        33.86 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       18.02        18.90         9.83        37.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        19.23        18.94         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 
       11.80        20.25        15.16        15.06        13.61         0.07 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 
        0.16        14.66        22.85        13.84         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        19.33        11.84        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN 
        5.29        11.54        18.15         7.96         1.84        15.42 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 
       16.08        17.98        15.78        56.75        47.01        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
       11.74         7.30        16.70        12.72        14.79        12.43 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        11.57        12.10         9.73         9.76         8.32 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       12.72        15.91        13.25         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       42.02        44.65        62.27        16.11        13.94        20.75 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65         2.96        20.55        14.56 

$`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 
        9.30        13.64         9.07        42.35        57.93        17.10 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       57.44        21.17         3.55        29.42        28.11        20.45 
TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
       11.54         2.27        20.48         6.15        94.62         4.60 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-8596 TCGA-BB-8601 
       18.35        22.42        50.20        44.98        71.05        20.52 
TCGA-BB-A6UM TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       12.92        26.27        37.84        26.86        32.65        21.11 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       20.55        43.73        41.69        33.11         8.58        12.39 
TCGA-CN-5369 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
       12.49        20.71        20.68        14.20         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49C 
       36.49        10.45        24.16        11.74        17.59        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY 
        7.40        17.29        15.91         5.75         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 
        7.33         9.80         7.69         6.18        48.20        39.68 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       54.58        45.99        11.21        41.19        32.38        32.88 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
       23.24        25.81        14.14        12.46        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
       26.27        58.42        50.01        34.52        36.99        16.90 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
       11.90        10.22        11.34         7.69        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7379 
        9.27        39.16        40.93         3.45         3.09        34.06 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       26.17        32.78        12.89        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5439 
       29.52         7.10         5.13        29.95        48.39        17.95 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 
      107.51        76.50        91.53        13.35        23.05         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6934 TCGA-CV-6939 TCGA-CV-6941 
       43.23        54.74        21.07         2.14        21.90        11.24 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 
       12.03        15.09        30.08        53.95        10.98         2.50 
TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 
      111.16         5.26        52.31        21.80        10.75       130.88 
TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7406 
       36.00        95.34         4.96        11.87        18.41        57.47 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7432 
      210.97        89.33        25.94        56.48         3.52        84.49 
TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45T TCGA-CV-A45Y TCGA-CV-A461 
      153.86        27.98        24.99       159.65        88.87        67.86 
TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-CV-A6K2 
        0.76        15.25         6.38        29.79        22.52        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6827 
       10.55        18.84        13.25        25.41         2.53        18.67 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 
       25.32        12.36        15.88        11.11        30.94        14.04 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       25.48        20.45        12.13        12.10        10.65        11.18 
TCGA-F7-A61V TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 
       12.62        12.43        13.38        21.11         6.77        25.74 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ 
        1.22        22.03        12.66         0.36         4.27         3.65 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
       12.76        14.50        11.84        13.35        12.43        10.75 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-P3-A5Q5 
       14.37        30.05        12.62         3.68         7.13        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IF 
       51.25        10.85        36.82        19.00        75.55        17.65 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        9.34        18.64         6.51        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JC 
       32.45        13.55        13.68        43.59        54.67        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UP-A6WW 
       24.16        49.22        21.86        22.36        17.03 

  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                         0.07                          0.36 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                        17.85                         18.67 
[1] "0.1 - 180.2 (17.9)" "0.4 - 211.0 (18.7)"
[1] "hr=" "1.5"
D50V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 21(8P23.2) MUTATED        16       44        49       156         9
  DEL PEAK 21(8P23.2) WILD-TYPE      11       33        28        96         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                            11
  STAGE II                           44                            33
  STAGE III                          49                            28
  STAGE IVA                         156                            96
  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      28  74  61 114
  DEL PEAK 21(8P23.2) WILD-TYPE    22  59  38  58
D50V4, multiclass
       clus
vv      DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  T0+T1                          28                            22
  T2                             74                            59
  T3                             61                            38
  T4                            114                            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   103  46 100   5
  DEL PEAK 21(8P23.2) WILD-TYPE  75  20  65   3
D50V5, multiclass
    clus
vv   DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  N0                         103                            75
  N1                          46                            20
  N2                         100                            65
  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"
D50V6, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED   118   1
  DEL PEAK 21(8P23.2) WILD-TYPE  65   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED    118    1
  DEL PEAK 21(8P23.2) WILD-TYPE   65    0
   clus
vv  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  0                         118                            65
  1                           1                             0
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED    87 212
  DEL PEAK 21(8P23.2) WILD-TYPE  52 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED     87  212
  DEL PEAK 21(8P23.2) WILD-TYPE   52  165
        clus
vv       DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  FEMALE                          87                            52
  MALE                           212                           165
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(8P23.2) MUTATED                                     296
  DEL PEAK 21(8P23.2) WILD-TYPE                                   209
                               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                                               296
  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                                                 209
  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    48 251
  DEL PEAK 21(8P23.2) WILD-TYPE  33 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED     48  251
  DEL PEAK 21(8P23.2) WILD-TYPE   33  184
     clus
vv    DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  NO                           48                            33
  YES                         251                           184
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, continuous
D50V12, 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                          26   252
  DEL PEAK 21(8P23.2) WILD-TYPE                        19   189
D50V13, multiclass
                                  clus
vv                                 DEL PEAK 21(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    252
                                  clus
vv                                 DEL PEAK 21(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED    18 259
  DEL PEAK 21(8P23.2) WILD-TYPE   7 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED     18  259
  DEL PEAK 21(8P23.2) WILD-TYPE    7  195
                        clus
vv                       DEL PEAK 21(8P23.2) MUTATED
  HISPANIC OR LATINO                              18
  NOT HISPANIC OR LATINO                         259
                        clus
vv                       DEL PEAK 21(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           195
[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   145  89
  DEL PEAK 22(9P23) WILD-TYPE 168 111
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        234                         279 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                         89                         111 
$`DEL PEAK 22(9P23) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 
       15.19         9.30        13.64         9.07        26.50        17.10 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
       15.52        21.17        14.83         3.55        12.62         7.76 
TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DL 
       29.42        30.18        27.95         5.69        14.47        20.48 
TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-7871 
       16.41         9.14        36.72        33.70        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-CN-4723 
       38.40        71.05        20.52        25.71        10.55        23.70 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 
        4.67        40.44        12.89        26.86        32.65        41.10 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5365 
       20.55        27.58        13.05        34.36        35.54        11.54 
TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
       11.57        20.68         6.74         9.07         9.24        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A49A 
       10.45        20.09        12.95        14.10        35.01        12.85 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5327 
       17.29        15.91        11.44        12.07         2.93        54.58 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       10.42        32.88        56.58        13.25         4.24        14.99 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
       70.13        51.29        33.11        16.73        41.88        64.11 
TCGA-CQ-A4CB TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 
       29.36        31.23        11.77        34.52        18.54        16.90 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       11.64        12.46        11.51        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 
       40.93        24.95        29.23         0.99        17.13        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5430 
       12.89        29.82         7.10         5.13        35.41       139.43 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5973 
      129.21        76.24        19.20        17.95        80.12        86.83 
TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       48.59        43.23         9.60        90.12         2.14         9.70 
TCGA-CV-6937 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6960 TCGA-CV-7090 
       20.52       126.08        12.03        42.38        28.34       126.15 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
      111.16        12.66         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       21.80        71.21        10.75        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7252 TCGA-CV-7253 
       36.00        31.36        26.20        18.97         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 
        2.10        36.13        18.41         9.67        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        0.07        34.09       100.57        16.27        84.49        19.76 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A460 
      153.86        16.64        22.19       169.38        88.87        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JT 
       67.86         0.76        56.61         7.07         6.38        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 
        3.62        21.24        10.42        10.42        18.84        34.36 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
       25.41         9.60        23.05        11.44        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       17.72        12.36        14.30        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 
       11.11        30.94        18.02        14.04        18.90        10.65 
TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C5 
       37.18         3.02         0.46        20.25        15.16        21.11 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ 
        0.07         0.16        25.74        22.85        13.84         3.65 
TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D 
       15.95        11.84        14.47        18.15         7.96         1.84 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 
        7.13        17.98        15.78        56.75        47.01        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB 
        2.04        13.15        21.07        16.70        12.72        14.79 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ 
       12.43         6.51         5.62         9.73         9.76        15.91 
TCGA-T2-A6X2 TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       32.45        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       42.02        44.65        62.27        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       16.11        13.94        22.36        17.03        20.55        14.56 

$`DEL PEAK 22(9P23) WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
        3.35        37.28        23.74        42.35        57.93        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH 
       20.48        53.79        57.44         4.01        28.11        20.45 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
       11.54         7.10         7.82         2.27        11.05        13.38 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        6.15        94.62         4.60         4.41        18.35        22.42 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       50.20        44.98        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 
       12.69        26.27        38.04        37.84        21.11        12.99 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       14.33        43.73        41.69        33.11         8.58        12.39 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
        8.32        16.21        11.84        12.49         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        20.71        30.67        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       19.07        14.20        36.49        24.16         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       11.74        14.56        17.59        29.72        21.21         7.40 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        5.75         4.41         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 
        7.69         6.18        48.20        39.68        21.50        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.80        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       34.75        38.76        43.04        28.83        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       23.24        32.81        25.81        14.14        12.46        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       36.99         6.02        11.90        10.22        11.34         7.69 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7376 
       15.75         9.27        35.84         3.45         3.09        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        19.92        26.17        32.78        47.01 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 
       30.02        31.10        29.85        29.52        30.58         5.95 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 
       29.95        48.39        17.16       108.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 
       76.50        91.53        17.92        13.35        23.05        60.49 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6938 
        7.07        54.74        21.07        62.43         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 
       21.90        26.43        11.24        19.79        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 
        2.50         4.14        64.83        18.81         7.99         9.01 
TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7407 
      130.88        17.13        95.34        47.97        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7424 
       17.85       210.97        89.33         0.46        25.08        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-7438 
       56.48       156.49        54.94         3.52         7.17         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        24.99       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       45.96         6.51        48.20        15.25         5.98        35.34 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 
       29.79         6.48        23.47        19.92        22.52        10.55 
TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM 
       13.25         2.53        16.14        18.67        15.88         7.63 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        35.54        33.86        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       12.13        12.10        11.18        16.11        21.63        20.25 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       19.23        18.94        12.62        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7917 TCGA-HD-8224 
       13.38        15.06        13.61         6.77         1.22        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03        12.66         0.36         4.27         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K 
       12.76        14.50        19.33        13.55         0.07         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.54        11.84        13.35        12.43        10.75        14.37 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05        12.62         3.68        15.42        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 
       51.25        10.85        36.82        19.00        75.55        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       12.99        16.01        11.74        17.65         7.30         9.34 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       18.64        11.57        12.10         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7JC 
        6.87         7.10        13.55        13.25        13.68        17.95 
TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV 
       20.75        32.65         2.96 

  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                     169.38                      210.97 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                     18.475                      17.850 
[1] "0.1 - 169.4 (18.5)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.1"
D51V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 22(9P23) MUTATED        11       34        33       122         6
  DEL PEAK 22(9P23) WILD-TYPE      16       43        44       130         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                          16
  STAGE II                         34                          43
  STAGE III                        33                          44
  STAGE IVA                       122                         130
  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      19 57 47 88
  DEL PEAK 22(9P23) WILD-TYPE    31 76 52 84
D51V4, multiclass
       clus
vv      DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  T0+T1                        19                          31
  T2                           57                          76
  T3                           47                          52
  T4                           88                          84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2 N3
  DEL PEAK 22(9P23) MUTATED   88 30 75  3
  DEL PEAK 22(9P23) WILD-TYPE 90 36 90  5
D51V5, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  N0                        88                          90
  N1                        30                          36
  N2                        75                          90
  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"
D51V6, binary
                             cls
clus                           0  1
  DEL PEAK 22(9P23) MUTATED   84  1
  DEL PEAK 22(9P23) WILD-TYPE 99  0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     84    1
  DEL PEAK 22(9P23) WILD-TYPE   99    0
   clus
vv  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  0                        84                          99
  1                         1                           0
[1] 2 2
[1] FALSE
D51V7, binary
                             cls
clus                            0   1
  DEL PEAK 22(9P23) MUTATED    53 182
  DEL PEAK 22(9P23) WILD-TYPE  86 195
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     53  182
  DEL PEAK 22(9P23) WILD-TYPE   86  195
        clus
vv       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  FEMALE                        53                          86
  MALE                         182                         195
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(9P23) MUTATED                                     231
  DEL PEAK 22(9P23) WILD-TYPE                                   274
                             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                                             231
  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                                               274
  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    35 200
  DEL PEAK 22(9P23) WILD-TYPE  46 235
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     35  200
  DEL PEAK 22(9P23) WILD-TYPE   46  235
     clus
vv    DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  NO                         35                          46
  YES                       200                         235
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, continuous
D51V12, 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                          27   191
  DEL PEAK 22(9P23) WILD-TYPE                        18   250
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 22(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               27
  WHITE                                                  191
                                  clus
vv                                 DEL PEAK 22(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 18
  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"
D51V14, binary
                             cls
clus                            0   1
  DEL PEAK 22(9P23) MUTATED    13 198
  DEL PEAK 22(9P23) WILD-TYPE  12 256
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     13  198
  DEL PEAK 22(9P23) WILD-TYPE   12  256
                        clus
vv                       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  HISPANIC OR LATINO                            13                          12
  NOT HISPANIC OR LATINO                       198                         256
[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   172 124
  DEL PEAK 23(9P21.3) WILD-TYPE 141  76
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          296                           217 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          124                            76 
$`DEL PEAK 23(9P21.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6868 
       15.19        13.64         9.07        26.50        17.10        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83         3.55        12.62         7.76        29.42 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP 
       30.18        27.95         5.69        14.47        20.48        16.41 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
        9.14         4.41        36.72        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A480 TCGA-CN-4723 
       71.05        20.52        25.71        10.55        12.69        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       38.04         4.67        40.44        37.84        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
       32.65        41.10        20.55        43.73        27.58        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       33.11        34.36        35.54         8.32        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
       11.57        12.49        22.45        30.67        20.68        19.53 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
       19.07         6.74         9.07         9.24        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A49A 
       20.09        12.95        14.10        11.74        35.01        12.85 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 
       17.29        11.44        12.07         9.80        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        2.93        54.58        10.42        41.19        32.88        34.75 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58        13.25         4.24        14.99        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 
       16.73        43.04        41.88        28.83        64.11        23.24 
TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
       29.36        11.77        34.52        18.54        16.90         6.02 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7372 
       12.46        11.51        47.18        39.16        40.93        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 
       29.23         0.99        31.96        26.17        17.13        27.06 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 
       29.82         7.10         5.13         5.95        35.41       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       17.16       129.21       108.95        76.24        19.20        17.95 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
       80.12        17.92        13.35        86.83        48.59        43.23 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6955 
       20.52        26.43        11.24        12.03        42.38        10.98 
TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        7.13        28.34        64.83       111.16        12.66         7.99 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 
        5.26         1.84        52.31        12.92        21.80        10.75 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       77.16         4.73        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
       18.97         4.96        11.87         2.10        36.13        18.41 
TCGA-CV-7407 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 
       35.54        89.33         9.67        22.85        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
       34.09       100.57        56.48       156.49         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 
       84.49        19.76         7.17       153.86         6.38        22.19 
TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
      169.38        35.47         6.51        88.87        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JT TCGA-CV-A6JU 
        0.76        56.61         7.07         6.38        22.03         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       21.24        23.47        22.52        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 
       18.84        34.36         9.60        23.05        11.44        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       25.32        17.72        12.36        14.30        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
       12.79        11.11        35.54        30.94        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
       18.90        10.65        37.18        16.11        20.25         3.02 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 
       12.62         0.46        11.80        20.25        13.38        15.06 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
       21.11         0.07         0.16        25.74         1.22        14.66 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 
       12.66        22.85         0.36        13.84         3.65         6.90 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J 
       15.95        12.76        14.50        19.33        11.84        14.47 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D 
       11.84        13.35        18.15        10.75         7.96         1.84 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 
        7.13        17.98        15.78        47.01        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH 
        2.04        29.00        16.01        13.15        21.07        16.70 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       14.79        12.43         6.51         5.62        11.57        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 
        9.73         9.76         8.32         6.87        15.91        32.45 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       43.59        54.67         2.83        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        62.27        17.95        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       16.11        13.94        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

$`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 
        3.35         9.30        37.28        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A4IG 
       23.84        20.48        53.79        57.44         4.01        28.11 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
       20.45        11.54         7.10         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
       13.38         6.15        94.62         4.60        18.35        22.42 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       33.70        50.20        44.98        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 
        6.28        26.27        21.11        12.99        14.33        41.69 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 
        8.58        12.39        11.84         8.52        56.94        20.71 
TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 
       20.65        20.68        14.20        36.49        24.16         3.68 
TCGA-CN-6996 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       17.42        14.56        17.59        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       15.91         5.75         4.41         2.70        10.09         7.33 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        7.69         6.18        48.20        46.75        45.80        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-A4C6 
       11.21         4.24        32.38        38.76        70.13        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       11.61        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       39.52        36.99        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
        7.69        15.75         9.27        47.34        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7385 TCGA-CR-7386 
        3.09         9.17        34.06        19.92        32.78        47.01 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       12.89        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       29.95        48.39       107.51        94.88        76.50        91.53 
TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6938 
       23.05        60.49         7.07        54.74        21.07         4.73 
TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       21.90       126.08        19.79        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 
       53.95        65.82         8.42         2.50         4.14       126.15 
TCGA-CV-7095 TCGA-CV-7100 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7250 
       18.81         9.01        71.21       130.88        17.13        95.34 
TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7414 TCGA-CV-7416 
       47.97        57.47        17.85       210.97         0.46        25.08 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R 
       14.89        54.94        16.64        27.98        24.99       180.16 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A468 TCGA-CV-A6JD 
      159.65         1.05        45.96        48.20        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6K0 TCGA-D6-6515 TCGA-D6-6516 
       35.34        29.79         6.48        19.92        13.25        25.41 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-DQ-5624 
        2.53        16.14        18.67        15.88         7.63        58.45 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       33.86        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A624 
       11.18        21.63        19.23        18.94        17.85        12.43 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-8314 TCGA-HD-A634 TCGA-HL-7533 
       15.16        13.61         6.77        22.03         4.27        34.75 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-MT-A51W 
       13.55         0.07         5.29        11.54        12.43        14.37 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05        12.62         3.68        15.42        16.08        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T6 
       56.75        51.25        10.85        36.82        75.55        12.99 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       11.74        17.65         7.30         9.34        12.72        18.64 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       12.72        16.96         7.10        13.55        13.25        13.68 
TCGA-UF-A7JO 
       20.75 

  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                       17.935                        18.810 
[1] "0.1 - 169.4 (17.9)" "0.1 - 211.0 (18.8)"
[1] "hr=" "1.3"
D52V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 23(9P21.3) MUTATED        14       42        42       161         7
  DEL PEAK 23(9P21.3) WILD-TYPE      13       35        35        91         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                            13
  STAGE II                           42                            35
  STAGE III                          42                            35
  STAGE IVA                         161                            91
  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      23  72  63 113
  DEL PEAK 23(9P21.3) WILD-TYPE    27  61  36  59
D52V4, multiclass
       clus
vv      DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  T0+T1                          23                            27
  T2                             72                            61
  T3                             63                            36
  T4                            113                            59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 23(9P21.3) MUTATED   112  37 101   4
  DEL PEAK 23(9P21.3) WILD-TYPE  66  29  64   4
D52V5, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  N0                         112                            66
  N1                          37                            29
  N2                         101                            64
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED   104   1
  DEL PEAK 23(9P21.3) WILD-TYPE  79   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED    104    1
  DEL PEAK 23(9P21.3) WILD-TYPE   79    0
   clus
vv  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  0                         104                            79
  1                           1                             0
[1] 2 2
[1] FALSE
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    80 217
  DEL PEAK 23(9P21.3) WILD-TYPE  59 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     80  217
  DEL PEAK 23(9P21.3) WILD-TYPE   59  160
        clus
vv       DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  FEMALE                          80                            59
  MALE                           217                           160
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P21.3) MUTATED                                     292
  DEL PEAK 23(9P21.3) WILD-TYPE                                   213
                               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                                               292
  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                                                 213
  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    44 253
  DEL PEAK 23(9P21.3) WILD-TYPE  37 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     44  253
  DEL PEAK 23(9P21.3) WILD-TYPE   37  182
     clus
vv    DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  NO                           44                            37
  YES                         253                           182
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, continuous
D52V12, 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                          32   249
  DEL PEAK 23(9P21.3) WILD-TYPE                        13   192
D52V13, multiclass
                                  clus
vv                                 DEL PEAK 23(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 32
  WHITE                                                    249
                                  clus
vv                                 DEL PEAK 23(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    15 255
  DEL PEAK 23(9P21.3) WILD-TYPE  10 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     15  255
  DEL PEAK 23(9P21.3) WILD-TYPE   10  199
                        clus
vv                       DEL PEAK 23(9P21.3) MUTATED
  HISPANIC OR LATINO                              15
  NOT HISPANIC OR LATINO                         255
                        clus
vv                       DEL PEAK 23(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           199
[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    62  44
  DEL PEAK 24(9Q21.11) WILD-TYPE 251 156
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                           106                            407 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                            44                            156 
$`DEL PEAK 24(9Q21.11) MUTATED`
TCGA-BA-4074 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4II 
       15.19        14.83         3.55        12.62         7.76        30.18 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-CN-4730 
       20.48        16.41        66.28        25.71        27.19        26.86 
TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5367 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 
       27.58        34.36        11.57        19.07         6.74        10.45 
TCGA-CN-6989 TCGA-CQ-5332 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
       20.09        10.42        14.99        16.73        41.88        64.11 
TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6491 TCGA-CR-7364 
       29.36        11.77        34.52        18.54        11.51        47.18 
TCGA-CR-7365 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CV-5430 
       39.16        35.84        24.95         0.99        31.96       139.43 
TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 
       76.24        94.88        86.83        20.52        11.24        12.03 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7252 
      111.16        18.81         1.84        77.16        31.36         4.96 
TCGA-CV-7254 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7432 
       47.97         9.67        25.08         0.07       100.57        84.49 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A6JU 
      153.86        22.19         6.51        88.87        56.61         3.62 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EO 
       18.84        23.05        11.44        25.32        17.72        14.30 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-F7-7848 
       13.94        12.79        30.94        18.02        18.90        37.18 
TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7753 
        3.02         0.46        20.25        13.61        21.11         0.16 
TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A67D TCGA-MZ-A5BI 
       14.66        22.85         3.65        18.15         1.84         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-QK-A6IJ 
       17.98        15.78        47.01        18.97         2.04        12.72 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       14.79        12.43         5.62        11.57        12.10         9.73 
TCGA-T2-A6WZ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7JD TCGA-UF-A7JJ 
       15.91        43.59        54.67         2.83        24.16        16.11 
TCGA-UF-A7JK TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94         2.96        17.03        20.55 

$`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 
        3.35         9.30        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF 
       53.79        57.44        15.52        21.17         4.01        29.42 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       28.11        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 
       14.47         7.82         2.27        11.05        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
       94.62         9.14         4.60         4.41        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
       36.72        33.70        50.20        44.98        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       71.05        20.52        10.55        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
       12.69        26.27        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       37.84        12.89        32.65        21.11        41.10        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       20.55        14.33        43.73        41.69        13.05        33.11 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        35.54         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.84        12.49         8.52        22.45        56.94        20.71 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       30.67        20.68        20.65        19.53        20.68        14.20 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 
        9.07         9.24        36.49        11.08        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       45.99        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
       34.75        56.58        13.25         4.24        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       51.29        33.11        43.04        28.83        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64         7.69        12.46        15.75         9.27 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7377 
       47.34        40.93         3.45         3.09        29.23         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       29.52        30.58         7.10         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
       29.95        48.39        17.16       129.21       108.95        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95       107.51        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       13.35        23.05        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
       54.74        21.07        62.43         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 
        9.70         5.46         4.73        21.90        26.43       126.08 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       126.15        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        5.26        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 
      130.88         4.73        47.47        36.00        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
       17.13        95.34        11.87         2.10        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 
       57.47        35.54        17.85       210.97        89.33         0.46 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
       22.85        25.94        34.09        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
       54.94         3.52        16.27        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
        6.38        27.98        24.99       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       35.47         1.05        45.96        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
        0.76         7.07        15.25         5.98        35.34         6.38 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        22.03        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 
       22.52        10.42        10.42        10.55        34.36        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       25.41         9.60         2.53        16.14        18.67        24.95 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 
       12.36        15.88         7.63        12.10        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       35.54        33.86        14.04        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 
       20.25        19.23        18.94        12.62        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 
       12.43        13.38        15.16        15.06         6.77         0.07 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
       25.74         1.22        22.03        12.66         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         6.90        34.75        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.54        11.84        13.35        12.43        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
        7.96        30.05        12.62         3.68        15.42        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       29.92        56.75        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
       11.74        17.65         7.30        16.70         9.34        18.64 
TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        6.51         9.76         8.32        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71B 
        7.10        32.45        13.55        13.25        13.68        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
       41.16        42.02        44.65        62.27        17.95        49.22 
TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 
       21.86        20.75        22.36        32.65        14.56 

  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE 
                        18.085                         17.950 
[1] "0.1 - 153.9 (18.1)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.1"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 24(9Q21.11) MUTATED         4       16        17        52         2
  DEL PEAK 24(9Q21.11) WILD-TYPE      23       61        60       200        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                             23
  STAGE II                            16                             61
  STAGE III                           17                             60
  STAGE IVA                           52                            200
  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  31  16  39
  DEL PEAK 24(9Q21.11) WILD-TYPE    41 102  83 133
D53V4, multiclass
       clus
vv      DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  T0+T1                            9                             41
  T2                              31                            102
  T3                              16                             83
  T4                              39                            133
[1] 4 2
[1] TRUE
[1] "dimension of 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    39  17  33   1
  DEL PEAK 24(9Q21.11) WILD-TYPE 139  49 132   7
D53V5, multiclass
    clus
vv   DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  N0                           39                            139
  N1                           17                             49
  N2                           33                            132
  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"
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(9Q21.11) MUTATED    46   1
  DEL PEAK 24(9Q21.11) WILD-TYPE 137   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(9Q21.11) MUTATED     46    1
  DEL PEAK 24(9Q21.11) WILD-TYPE  137    0
   clus
vv  DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  0                           46                            137
  1                            1                              0
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(9Q21.11) MUTATED    24  82
  DEL PEAK 24(9Q21.11) WILD-TYPE 115 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(9Q21.11) MUTATED     24   82
  DEL PEAK 24(9Q21.11) WILD-TYPE  115  295
        clus
vv       DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  FEMALE                           24                            115
  MALE                             82                            295
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9Q21.11) MUTATED                                     106
  DEL PEAK 24(9Q21.11) WILD-TYPE                                   399
                                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                                                106
  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                                                  399
  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  89
  DEL PEAK 24(9Q21.11) WILD-TYPE  64 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(9Q21.11) MUTATED     17   89
  DEL PEAK 24(9Q21.11) WILD-TYPE   64  346
     clus
vv    DEL PEAK 24(9Q21.11) MUTATED DEL PEAK 24(9Q21.11) WILD-TYPE
  NO                            17                             64
  YES                           89                            346
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, continuous
D53V12, 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                          13    85
  DEL PEAK 24(9Q21.11) WILD-TYPE                        32   356
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 24(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      85
                                  clus
vv                                 DEL PEAK 24(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    32
  WHITE                                                       356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                                cls
clus                               0   1
  DEL PEAK 24(9Q21.11) MUTATED     5  90
  DEL PEAK 24(9Q21.11) WILD-TYPE  20 364
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(9Q21.11) MUTATED      5   90
  DEL PEAK 24(9Q21.11) WILD-TYPE   20  364
                        clus
vv                       DEL PEAK 24(9Q21.11) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 24(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            364
[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    44  33
  DEL PEAK 25(9Q34.3) WILD-TYPE 269 167
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           77                           436 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                           33                           167 
$`DEL PEAK 25(9Q34.3) MUTATED`
TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7864 
        3.55         7.76        13.38         9.14         4.41        50.20 
TCGA-BB-7870 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-6018 
       66.28        25.71        27.19        41.10        27.58        19.07 
TCGA-CN-6020 TCGA-CN-A63U TCGA-CN-A63Y TCGA-CQ-5327 TCGA-CQ-6227 TCGA-CQ-6228 
        6.74        17.29         5.75        54.58         4.24        14.99 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6472 
       16.73        41.88        64.11        14.14        11.77        34.52 
TCGA-CR-6474 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7399 
       18.54        47.18        24.95         0.99        12.89         5.95 
TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-6441 
      139.43       108.95        76.24        94.88        86.83         9.60 
TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-7090 TCGA-CV-7091 
       20.52        11.24        12.03        42.38       126.15       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7104 TCGA-CV-7243 TCGA-CV-7252 TCGA-CV-7255 
       18.81        12.66        12.92        31.36         4.96         2.10 
TCGA-CV-7413 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Q 
        9.67         0.07       100.57       153.86        22.19       169.38 
TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JU TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I 
       60.43        56.61         3.62        18.02        37.18         3.02 
TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8635 TCGA-IQ-7630 TCGA-KU-A66T TCGA-MZ-A5BI 
       21.11         0.16        22.85        15.95        18.15         7.13 
TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       56.75        18.97        12.72        14.79         5.62        12.10 
TCGA-QK-A8ZB TCGA-UF-A719 TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JK 
        9.73        54.67        24.16        16.11        13.94 

$`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 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       26.50        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       20.48        53.79        57.44        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01        29.42        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       27.95        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        2.27        11.05        20.48        16.41         6.15        94.62 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 
        4.60        18.35        22.42        36.72        33.70        44.98 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A6UM 
       24.66        38.40        71.05        20.52        10.55        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        8.81         6.28        12.69        26.27        23.70        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        40.44        37.84        12.89        26.86        32.65 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
       21.11        12.99        20.55        14.33        43.73        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        33.11        34.36         8.58        12.39        35.54 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.52        22.45        56.94        20.71        30.67        20.68 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
       20.65        19.53        20.68        14.20         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
       36.49        11.08        10.45        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       17.59        12.85        29.72        21.21         7.40        15.91 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
       11.44         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        9.80         7.69         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        2.93        46.75        45.80        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
        4.24        41.19        32.38        32.88        34.75        56.58 
TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       13.25        38.76        70.13        51.29        33.11        43.04 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       28.83        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       25.81        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 
       26.27        58.42        50.01        39.52        36.99        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        6.02        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
       12.46        11.51        15.75         9.27        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 
       40.93        35.84         3.45         3.09        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        29.82        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
       29.52        30.58         7.10         5.13        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       48.39        17.16       129.21        19.20        17.95       107.51 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43        90.12         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 
       21.90        26.43       126.08        19.79        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7100 
       28.34         2.50         4.14        64.83         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        5.26         1.84        52.31        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
      130.88        77.16         4.73        47.47        36.00        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       18.97        17.13        95.34        11.87        47.97        36.13 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       18.41        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        0.46        22.85        25.08        25.94        34.09        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17        16.64         6.38        27.98        24.99 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 
       88.87        48.20        67.86         0.76         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        22.03 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       23.05         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       25.32        17.72        12.36        15.88         7.63        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        35.54 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       30.94        33.86        14.04        18.90        25.48        20.45 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
        9.83        12.13        12.10        10.65        11.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       21.63        20.25        19.23        18.94        12.62         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
       15.06        13.61         6.77         0.07        25.74         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       14.66        22.03        12.66         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        34.75        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        13.55         0.07        14.47         5.29        11.54 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       11.84        13.35        12.43        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 
       30.05         1.84        12.62         3.68        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        15.78        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       47.01        19.00        75.55         2.04        29.00        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        11.74        17.65         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       16.70         9.34        18.64        12.43         6.51        11.57 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
        9.76         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       17.95        49.22        21.86        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE 
                       18.150                        17.965 
[1] "0.1 - 169.4 (18.1)" "0.1 - 211.0 (18.0)"
[1] "hr=" "1.1"
D54V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 25(9Q34.3) MUTATED         5       15        11        36         2
  DEL PEAK 25(9Q34.3) WILD-TYPE      22       62        66       216        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                            22
  STAGE II                           15                            62
  STAGE III                          11                            66
  STAGE IVA                          36                           216
  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  25
  DEL PEAK 25(9Q34.3) WILD-TYPE    42 110  85 147
D54V4, multiclass
       clus
vv      DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  T0+T1                           8                            42
  T2                             23                           110
  T3                             14                            85
  T4                             25                           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"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 25(9Q34.3) MUTATED    29   9  25   1
  DEL PEAK 25(9Q34.3) WILD-TYPE 149  57 140   7
D54V5, multiclass
    clus
vv   DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  N0                          29                           149
  N1                           9                            57
  N2                          25                           140
  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"
D54V6, binary
                               cls
clus                              0   1
  DEL PEAK 25(9Q34.3) MUTATED    26   1
  DEL PEAK 25(9Q34.3) WILD-TYPE 157   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9Q34.3) MUTATED     26    1
  DEL PEAK 25(9Q34.3) WILD-TYPE  157    0
   clus
vv  DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  0                          26                           157
  1                           1                             0
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 25(9Q34.3) MUTATED    22  56
  DEL PEAK 25(9Q34.3) WILD-TYPE 117 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9Q34.3) MUTATED     22   56
  DEL PEAK 25(9Q34.3) WILD-TYPE  117  321
        clus
vv       DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  FEMALE                          22                           117
  MALE                            56                           321
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9Q34.3) MUTATED                                      78
  DEL PEAK 25(9Q34.3) WILD-TYPE                                   427
                               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                                                78
  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                                                 427
  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  66
  DEL PEAK 25(9Q34.3) WILD-TYPE  69 369
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9Q34.3) MUTATED     12   66
  DEL PEAK 25(9Q34.3) WILD-TYPE   69  369
     clus
vv    DEL PEAK 25(9Q34.3) MUTATED DEL PEAK 25(9Q34.3) WILD-TYPE
  NO                           12                            69
  YES                          66                           369
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, continuous
D54V12, 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    60
  DEL PEAK 25(9Q34.3) WILD-TYPE                        36   381
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 25(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     60
                                  clus
vv                                 DEL PEAK 25(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      381
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                               cls
clus                              0   1
  DEL PEAK 25(9Q34.3) MUTATED     5  64
  DEL PEAK 25(9Q34.3) WILD-TYPE  20 390
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9Q34.3) MUTATED      5   64
  DEL PEAK 25(9Q34.3) WILD-TYPE   20  390
                        clus
vv                       DEL PEAK 25(9Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       DEL PEAK 25(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           390
[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    88  78
  DEL PEAK 26(10P15.3) WILD-TYPE 225 122
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           166                            347 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                            78                            122 
$`DEL PEAK 26(10P15.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
        9.30        13.64         9.07        57.44        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI 
       14.83        12.62         4.01         7.76        29.42        11.05 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A47Z 
       66.28        24.66        20.52        25.71        10.55         6.28 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 
       23.70        38.04         4.67        20.55        33.11        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       35.54         8.32        56.94        30.67        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 
       14.20         6.74        10.45        20.09        17.42        11.74 
TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       11.44        48.20         2.93        34.75        56.58        13.25 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
       14.99        51.29        16.73        41.88        64.11        11.61 
TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       18.54        11.64        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 
        3.45         3.09        24.95        29.23         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 
       19.92        26.17        17.13        47.01        12.89         5.13 
TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-5979 
       76.24       107.51        80.12        17.92        60.49        43.23 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6950 
       90.12         2.14         5.46        26.43       126.08        15.09 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
        6.08        65.82         2.50         4.14        64.83       126.15 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 
       12.66         9.01         5.26         1.84        21.80        71.21 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       77.16        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7252 TCGA-CV-7263 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 
        4.96        18.41         0.46        25.94       100.57        14.89 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45U TCGA-CV-A45W 
       54.94        84.49         7.17         6.38        35.47        45.96 
TCGA-CV-A45X TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K1 
        6.51         7.07         5.98        22.03        21.24        22.52 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-5631 
       34.36         9.60        11.44        13.94        30.94        18.02 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
       14.04        25.48        21.63        20.25         3.02        12.62 
TCGA-F7-A620 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-IQ-A61G TCGA-IQ-A61H 
       17.85        22.85         0.36        13.84        11.84        13.55 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MT-A7BN 
       14.47         5.29        18.15        12.43         7.96        15.42 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 
       47.01        75.55        18.97         2.04        29.00        13.15 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        17.65        16.70        18.64        11.57        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HJ 
        9.73         8.32         6.87        15.91         7.10        13.25 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD 
       43.59         2.83        43.36        41.16        17.95        24.16 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-WA-A7H4 
       16.11        13.94        20.55        14.56 

$`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 
        3.35        15.19        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6871 
       57.93        17.10        23.84        20.48        53.79         3.55 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       28.11        20.45        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69        14.47         7.82         2.27        13.38        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15        94.62         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.35        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       38.40        71.05        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       26.27        40.44        37.84        12.89        26.86        32.65 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       21.11        41.10        12.99        14.33        43.73        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5364 TCGA-CN-5365 
       41.69        13.05        34.36         8.58        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       11.84        11.57        12.49         8.52        22.45        20.71 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       20.65        19.53        20.68         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A497 
       11.08        12.95        24.16         3.68        14.10        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       14.56        17.59        12.85        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       17.29        15.91         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       10.09         7.33         9.80         7.69         6.18        39.68 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50        54.58        46.75        45.80        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6227 
       11.21         4.24        41.19        32.38        32.88         4.24 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
       38.76        70.13        33.11        43.04        28.83        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        32.81        25.81        14.14        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       31.23        84.23        11.77        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
       58.42        50.01        39.52        34.52        36.99        16.90 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        6.02        11.90        10.22        11.34         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7374 TCGA-CR-7376 
       11.51        15.75         9.27        47.18         0.99        31.96 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       32.78        27.06        29.82        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       29.52        30.58         7.10         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
       48.39       139.43        17.16       129.21       108.95        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 
       17.95        94.88        76.50        91.53        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       86.83        48.59         7.07        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        9.60         9.70        20.52         4.73        21.90        11.24 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6955 
       19.79        12.03        42.38        30.08        53.95        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        7.13         8.42        28.34       111.16        18.81         7.99 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       52.31        12.92        10.75       130.88         4.73        47.47 
TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 
       95.34        11.87        47.97         2.10        36.13        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 
       35.54        17.85       210.97        89.33         9.67        22.85 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
       25.08         0.07        34.09        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O 
       16.27        19.76       153.86        16.64        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y 
       24.99       169.38       180.16       159.65         1.05        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       48.20        60.43        67.86         0.76        56.61        15.25 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JZ 
       35.34         6.38        29.79         6.48         3.62        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 
       19.92        10.42        10.42        10.55        18.84        13.25 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       25.41        23.05         2.53        16.14        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       25.32        17.72        12.36        15.88         7.63        14.30 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        11.11        58.45        35.54        33.86 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       18.90        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W 
       11.18        37.18        16.11        19.23        18.94         0.46 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.61        21.11         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A634 TCGA-HD-A6HZ 
        1.22        14.66        22.03        12.66         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
        0.07        11.54        11.84        13.35        10.75        14.37 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05         1.84        12.62         3.68         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        56.75        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IG 
       36.82        19.00        12.99        16.01        11.74         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        14.79        12.43         6.51         5.62 
TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL 
        9.76        12.72        16.96        32.45        13.55        13.68 
TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH 
       54.67        42.02        44.65        62.27        49.22        21.86 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       20.75        22.36        32.65         2.96        17.03 

  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                          0.36                           0.07 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                        126.15                         210.97 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                        17.885                         18.810 
[1] "0.4 - 126.2 (17.9)" "0.1 - 211.0 (18.8)"
[1] "hr=" "1.4"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 26(10P15.3) MUTATED         5       23        22        94         3
  DEL PEAK 26(10P15.3) WILD-TYPE      22       54        55       158         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                             22
  STAGE II                            23                             54
  STAGE III                           22                             55
  STAGE IVA                           94                            158
  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  42  32  66
  DEL PEAK 26(10P15.3) WILD-TYPE    42  91  67 106
D55V4, multiclass
       clus
vv      DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  T0+T1                            8                             42
  T2                              42                             91
  T3                              32                             67
  T4                              66                            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 26(10P15.3) MUTATED    48  22  65   1
  DEL PEAK 26(10P15.3) WILD-TYPE 130  44 100   7
D55V5, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  N0                           48                            130
  N1                           22                             44
  N2                           65                            100
  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"
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED    57   0
  DEL PEAK 26(10P15.3) WILD-TYPE 126   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     57    0
  DEL PEAK 26(10P15.3) WILD-TYPE  126    1
   clus
vv  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  0                           57                            126
  1                            0                              1
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED    41 126
  DEL PEAK 26(10P15.3) WILD-TYPE  98 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     41  126
  DEL PEAK 26(10P15.3) WILD-TYPE   98  251
        clus
vv       DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  FEMALE                           41                             98
  MALE                            126                            251
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(10P15.3) MUTATED                                     167
  DEL PEAK 26(10P15.3) WILD-TYPE                                   338
                                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                                                167
  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                                                  338
  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    33 134
  DEL PEAK 26(10P15.3) WILD-TYPE  48 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     33  134
  DEL PEAK 26(10P15.3) WILD-TYPE   48  301
     clus
vv    DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  NO                            33                             48
  YES                          134                            301
[1] 2 2
[1] FALSE
D55V10, continuous
D55V11, continuous
D55V12, 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   139
  DEL PEAK 26(10P15.3) WILD-TYPE                        24   302
D55V13, multiclass
                                  clus
vv                                 DEL PEAK 26(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     139
                                  clus
vv                                 DEL PEAK 26(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       302
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED     7 147
  DEL PEAK 26(10P15.3) WILD-TYPE  18 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED      7  147
  DEL PEAK 26(10P15.3) WILD-TYPE   18  307
                        clus
vv                       DEL PEAK 26(10P15.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          147
                        clus
vv                       DEL PEAK 26(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            307
[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    90  69
  DEL PEAK 27(10P11.21) WILD-TYPE 223 131
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                            159                             354 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                             69                             131 
$`DEL PEAK 27(10P11.21) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
       15.19         9.30         9.07        57.44        15.52        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DI TCGA-BA-A8YP 
       12.62         4.01         7.76        27.95        11.05        16.41 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-C9-A47Z 
       66.28        38.40        20.52        25.71        10.55         6.28 
TCGA-CN-4723 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       23.70        20.55        33.11        35.54         8.32        16.21 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       56.94        30.67        20.68        19.07        14.20         6.74 
TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63W TCGA-CN-A6V6 
       10.45        17.42        11.74        12.85        11.44         7.69 
TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
       48.20         2.93        10.42        41.19        34.75        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
       13.25        14.99        51.29        16.73        41.88        64.11 
TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7365 
       11.61        31.23        18.54         6.02        11.64        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
       47.34        40.93        35.84         3.45        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 
        0.99        19.92        26.17        17.13        47.01        12.89 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5444 TCGA-CV-5966 
       29.82         5.13        17.16        76.24        80.12        17.92 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6940 
       86.83        60.49        43.23        90.12         5.46        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-6962 
       11.24       126.08        15.09        65.82         2.50         4.14 
TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 
      126.15        12.66         9.01         5.26         1.84        71.21 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 
       36.00        31.36        26.20        18.97        17.13         4.96 
TCGA-CV-7263 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 
       18.41         0.46        25.94       100.57        14.89        54.94 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A465 
       84.49         7.17         6.38        35.47        45.96         7.07 
TCGA-CV-A6JD TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
        5.98        21.24        22.52        34.36         9.60        23.05 
TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5629 TCGA-DQ-5631 
       11.44        12.36        13.94        12.10        30.94        18.02 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
       14.04        25.48        12.13        20.25         3.02        12.62 
TCGA-F7-A61W TCGA-HD-7753 TCGA-HD-A633 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
        0.46         0.16        13.84        11.84        13.55        14.47 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MZ-A7D7 
        5.29        11.84        18.15        12.43         7.96        17.98 
TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z 
       56.75        75.55         2.04        29.00        13.15        21.07 
TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K 
       16.70        18.64        11.57        12.10         9.73         8.32 
TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JC 
        7.10        13.25        43.59         2.83        43.36        17.95 
TCGA-UF-A7JD TCGA-WA-A7GZ TCGA-WA-A7H4 
       24.16        20.55        14.56 

$`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 
        3.35        13.64        37.28        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
       57.93        17.10        23.84        20.48        53.79        21.17 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
        3.55        29.42        28.11        20.45        30.18        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
        7.10         5.69        14.47         7.82         2.27        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       20.48         6.15        94.62         9.14         4.60         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.35        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       24.66        71.05        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       26.27        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
       26.86        32.65        21.11        41.10        12.99        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
       43.73        27.58        41.69        13.05        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       12.39        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 
       22.45        20.71        20.65        19.53        20.68         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        9.24        36.49        11.08        20.09        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
        3.68        14.10        35.01        14.56        17.59        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        17.29        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 
       12.07         2.70        10.09         7.33         9.80         6.18 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       39.68        21.50        54.58        46.75        45.80        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 
       11.21         4.24        32.38        32.88         4.24        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       70.13        33.11        43.04        28.83        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        32.81        25.81        14.14        12.46        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        34.52        36.99        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34         7.69        12.46        11.51        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7385 
       47.18         3.09        31.96         9.17        34.06        32.78 
TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       27.06        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        7.10         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 
       76.50        91.53        13.35        23.05        48.59         7.07 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
       54.74        21.07        62.43         9.60         2.14         9.70 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       20.52         4.73        21.90        19.79        12.03        42.38 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       30.08         6.08        53.95        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7103 
       28.34        64.83       111.16        18.81         7.99        52.31 
TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       12.92        21.80        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       47.47        95.34        11.87        47.97         2.10        36.13 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 
       22.85        25.08         0.07        34.09        56.48       156.49 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
        3.52        16.27        19.76       153.86        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        24.99       169.38       180.16       159.65         1.05 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 
        6.51        88.87        48.20        60.43        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61        15.25        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 
       22.03         3.62        23.47        19.92        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 
       10.55        18.84        13.25        25.41         2.53        16.14 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
       18.67        24.95        25.32        17.72        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       14.30        12.79        11.11        58.45        35.54        33.86 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.90        20.45         9.83        12.10        10.65        11.18 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 
       37.18        16.11        21.63        19.23        18.94        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
       13.61        21.11         6.77         0.07        25.74         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
       14.66        22.03        12.66        22.85         0.36         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
       19.33         0.07        11.54        13.35        10.75        14.37 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         3.68        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       16.08        29.92        15.78        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 
       47.01        19.00        18.97        12.99        16.01        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
       17.65         7.30         9.34        12.72        14.79        12.43 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        6.51         5.62         9.76        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71D 
       15.91        32.45        13.55        13.68        54.67        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       42.02        44.65        62.27        49.22        21.86        16.11 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.94        20.75        22.36        32.65         2.96        17.03 

  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                           0.16                            0.07 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                         126.15                          210.97 
  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE 
                         17.130                          18.985 
[1] "0.2 - 126.2 (17.1)" "0.1 - 211.0 (19.0)"
[1] "hr=" "1.3"
D56V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 27(10P11.21) MUTATED         8       19        22        88
  DEL PEAK 27(10P11.21) WILD-TYPE      19       58        55       164
                                 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                              19
  STAGE II                             19                              58
  STAGE III                            22                              55
  STAGE IVA                            88                             164
  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  41  30  62
  DEL PEAK 27(10P11.21) WILD-TYPE    40  92  69 110
D56V4, multiclass
       clus
vv      DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  T0+T1                            10                              40
  T2                               41                              92
  T3                               30                              69
  T4                               62                             110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 27(10P11.21) MUTATED    49  21  59   2
  DEL PEAK 27(10P11.21) WILD-TYPE 129  45 106   6
D56V5, multiclass
    clus
vv   DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  N0                            49                             129
  N1                            21                              45
  N2                            59                             106
  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"
D56V6, binary
                                 cls
clus                                0   1
  DEL PEAK 27(10P11.21) MUTATED    55   0
  DEL PEAK 27(10P11.21) WILD-TYPE 128   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10P11.21) MUTATED     55    0
  DEL PEAK 27(10P11.21) WILD-TYPE  128    1
   clus
vv  DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  0                            55                             128
  1                             0                               1
[1] 2 2
[1] FALSE
D56V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(10P11.21) MUTATED    35 125
  DEL PEAK 27(10P11.21) WILD-TYPE 104 252
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10P11.21) MUTATED     35  125
  DEL PEAK 27(10P11.21) WILD-TYPE  104  252
        clus
vv       DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  FEMALE                            35                             104
  MALE                             125                             252
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P11.21) MUTATED                                     158
  DEL PEAK 27(10P11.21) WILD-TYPE                                   347
                                 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                                                 158
  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                                                   347
  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    33 127
  DEL PEAK 27(10P11.21) WILD-TYPE  48 308
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10P11.21) MUTATED     33  127
  DEL PEAK 27(10P11.21) WILD-TYPE   48  308
     clus
vv    DEL PEAK 27(10P11.21) MUTATED DEL PEAK 27(10P11.21) WILD-TYPE
  NO                             33                              48
  YES                           127                             308
[1] 2 2
[1] FALSE
D56V10, continuous
D56V11, continuous
D56V12, 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   129
  DEL PEAK 27(10P11.21) WILD-TYPE                        22   312
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 27(10P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      129
                                  clus
vv                                 DEL PEAK 27(10P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                        312
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                                 cls
clus                                0   1
  DEL PEAK 27(10P11.21) MUTATED     9 139
  DEL PEAK 27(10P11.21) WILD-TYPE  16 315
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(10P11.21) MUTATED      9  139
  DEL PEAK 27(10P11.21) WILD-TYPE   16  315
                        clus
vv                       DEL PEAK 27(10P11.21) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           139
                        clus
vv                       DEL PEAK 27(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             315
[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    80  57
  DEL PEAK 28(10Q23.31) WILD-TYPE 233 143
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            137                             376 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                             57                             143 
$`DEL PEAK 28(10Q23.31) MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 
       15.19         9.30         9.07        42.35        17.10        57.44 
TCGA-BA-6869 TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7861 
       21.17        28.11        27.95        11.05        16.41        22.42 
TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-5355 
       66.28        20.52         6.28        38.04        40.44        33.11 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
       12.39        35.54        56.94        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49A 
        6.74         9.07        11.08        11.74        17.59        12.85 
TCGA-CN-A63U TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6225 
       17.29         7.69         6.18        10.42        32.88        13.25 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6477 
       14.99        51.29        64.11        50.01        18.54        16.90 
TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       11.90        11.64        39.16        40.93        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7398 
       24.95        29.23         0.99        17.13        47.01         5.13 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5973 
       17.16       129.21       108.95        76.24        19.20        86.83 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6941 
        7.07        43.23        90.12         9.70        26.43        11.24 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 
       12.03        15.09        28.34         2.50         4.14       126.15 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       12.66         5.26        52.31        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 
       17.13        18.41        57.47         0.46        25.94       100.57 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A465 
       14.89        84.49         6.38        45.96        60.43         7.07 
TCGA-CV-A6JY TCGA-D6-6823 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       21.24        23.05        12.36        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 
       11.11        18.02        14.04        18.90        25.48        12.13 
TCGA-DQ-7596 TCGA-H7-A76A TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
       11.18         6.77         3.65        11.84        13.55        14.47 
TCGA-IQ-A61K TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A5BI 
        5.29        18.15        12.43         7.96        15.42         7.13 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T5 
       16.08        17.98        51.25        47.01        19.00        29.00 
TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K 
       16.70        18.64        14.79        11.57        12.10         8.32 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       15.91         7.10        13.25        43.59        54.67        43.36 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       44.65        17.95        17.03        20.55        14.56 

$`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 
        3.35        13.64        37.28        26.50        23.74        57.93 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
       23.84        20.48        53.79        15.52        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01         7.76        29.42        20.45        30.18 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       13.38        20.48         6.15        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.35        36.72        33.70        50.20        44.98 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        25.71        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
       12.92         8.81        12.69        26.27        23.70         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       37.84        12.89        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       13.05        34.36         8.58         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       11.84        11.57        12.49         8.52        22.45        20.71 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6023 
       30.67        20.65        19.53        20.68         9.24        36.49 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       10.45        20.09        12.95        24.16         3.68        17.42 
TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       14.10        35.01        14.56        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
       10.09         7.33         9.80        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        2.93        54.58        46.75        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
        4.24        41.19        32.38        34.75        56.58         4.24 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       38.76        70.13        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       28.83        44.48        11.61        23.24        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       25.81        14.14        12.46        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6472 
       54.67        37.87        26.27        58.42        39.52        34.52 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       36.99         6.02        10.22        11.34         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7371 
       11.51        15.75         9.27        47.18        47.34         3.09 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       31.96         9.17        34.06        19.92        26.17        32.78 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       29.52        30.58         7.10         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       48.39       139.43        17.95       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
       91.53        80.12        17.92        13.35        23.05        48.59 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       60.49        54.74        21.07        62.43         9.60         2.14 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 
        5.46        20.52         4.73        21.90       126.08        19.79 
TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        7.13         8.42        64.83       111.16        18.81         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        9.01         1.84        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 
      130.88        77.16         4.73        47.47        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 
        4.96        11.87        47.97         2.10        36.13        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 
       17.85       210.97        89.33         9.67        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
        0.07        34.09        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
       16.27        19.76         7.17       153.86        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        24.99       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 
        1.05         6.51        88.87        48.20        67.86         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
       56.61        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        22.03         3.62        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       10.42        10.42        10.55        18.84        34.36        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
       25.41         9.60         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       24.95        25.32        17.72        15.88         7.63        14.30 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 
       58.45        35.54        30.94        33.86        20.45         9.83 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       12.10        10.65        37.18        16.11        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        19.23        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
       13.61        21.11         0.07         0.16        25.74         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
       14.66        22.03        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         6.90        34.75        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 
       19.33         0.07        11.54        11.84        13.35        10.75 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 
       14.37        30.05         1.84        12.62         3.68        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T3 
       15.78        56.75        10.85        36.82        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        12.99        16.01        13.15        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z7 
       17.65         7.30         9.34        12.72        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62         9.73         9.76        12.72        16.96         6.87 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E 
       32.45        13.55        13.68         2.83        41.16        42.02 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       62.27        24.16        49.22        21.86        16.11        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       20.75        22.36        32.65         2.96 

  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                           0.46                            0.07 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                         129.21                          210.97 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                          17.13                           18.97 
[1] "0.5 - 129.2 (17.1)" "0.1 - 211.0 (19.0)"
[1] "hr=" "1.1"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 28(10Q23.31) MUTATED         3       21        22        64
  DEL PEAK 28(10Q23.31) WILD-TYPE      24       56        55       188
                                 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                              24
  STAGE II                             21                              56
  STAGE III                            22                              55
  STAGE IVA                            64                             188
  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  39  28  42
  DEL PEAK 28(10Q23.31) WILD-TYPE    42  94  71 130
D57V4, multiclass
       clus
vv      DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T0+T1                             8                              42
  T2                               39                              94
  T3                               28                              71
  T4                               42                             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
  DEL PEAK 28(10Q23.31) MUTATED    46  15  45   2
  DEL PEAK 28(10Q23.31) WILD-TYPE 132  51 120   6
D57V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                            46                             132
  N1                            15                              51
  N2                            45                             120
  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"
D57V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    46   0
  DEL PEAK 28(10Q23.31) WILD-TYPE 137   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     46    0
  DEL PEAK 28(10Q23.31) WILD-TYPE  137    1
   clus
vv  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  0                            46                             137
  1                             0                               1
[1] 2 2
[1] FALSE
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    26 111
  DEL PEAK 28(10Q23.31) WILD-TYPE 113 266
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     26  111
  DEL PEAK 28(10Q23.31) WILD-TYPE  113  266
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            26                             113
  MALE                             111                             266
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10Q23.31) MUTATED                                     136
  DEL PEAK 28(10Q23.31) WILD-TYPE                                   369
                                 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                                                 136
  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                                                   369
  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    23 114
  DEL PEAK 28(10Q23.31) WILD-TYPE  58 321
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     23  114
  DEL PEAK 28(10Q23.31) WILD-TYPE   58  321
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                             23                              58
  YES                           114                             321
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, continuous
D57V12, 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   115
  DEL PEAK 28(10Q23.31) WILD-TYPE                        28   326
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 28(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      115
                                  clus
vv                                 DEL PEAK 28(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     28
  WHITE                                                        326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     9 118
  DEL PEAK 28(10Q23.31) WILD-TYPE  16 336
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      9  118
  DEL PEAK 28(10Q23.31) WILD-TYPE   16  336
                        clus
vv                       DEL PEAK 28(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           118
                        clus
vv                       DEL PEAK 28(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             336
[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    97  64
  DEL PEAK 29(11P15.5) WILD-TYPE 216 136
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           161                            352 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            64                            136 
$`DEL PEAK 29(11P15.5) MUTATED`
TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        9.07        17.10        15.52        14.83         3.55        12.62 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
        7.76        28.11        20.45        30.18        27.95        11.54 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-8596 
        5.69        14.47        16.41         4.41        66.28        71.05 
TCGA-BB-A6UO TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 
        8.81        38.04        37.84        12.89        41.10        12.99 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
       43.73        27.58        34.36        12.39         8.32        11.54 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6020 
       11.84        56.94        30.67        20.68        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 
        9.07        10.45        20.09        12.95        14.10        11.74 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A6UY TCGA-CQ-5326 TCGA-CQ-5332 
       21.21        17.29         5.75        10.09         2.93        10.42 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       32.88         4.24        23.24        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       54.67        16.90         6.02        10.22        11.34        11.64 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7399 
        0.99        17.13        32.78        27.06        12.89         5.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5978 TCGA-CV-6441 
       48.39       139.43       129.21        17.95         7.07         9.60 
TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 
       90.12         5.46        20.52        26.43       126.08        12.03 
TCGA-CV-6948 TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       42.38         7.13         4.14       111.16        18.81        12.66 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7235 
        9.01         5.26         1.84        52.31        21.80        77.16 
TCGA-CV-7245 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7415 
       26.20        11.87        36.13        18.41        35.54        22.85 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A45R 
       25.08         0.07       100.57        16.27       153.86       180.16 
TCGA-CV-A45U TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JU TCGA-CX-7082 
       35.47        88.87        48.20        60.43         3.62        10.42 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        12.36        13.94        12.79        11.11        58.45 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       30.94        18.90        12.10        11.18        37.18        16.11 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7917 
       20.25         3.02        20.25        13.61         0.16         1.22 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61G 
       14.66        22.03        22.85         3.65        14.50        11.84 
TCGA-KU-A66T TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 
       18.15         3.68        15.42         7.13        16.08        15.78 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 
       36.82        19.00         2.04        29.00        12.99        13.15 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J 
       17.65        16.70         6.51        11.57        12.10         9.76 
TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        8.32        15.91        13.25        43.59        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JH 
       43.36        41.16        42.02        62.27        21.86 

$`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 
        3.35        15.19         9.30        13.64        37.28        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       23.74        42.35        57.93        23.84        20.48        53.79 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DF 
       57.44        21.17         4.01        29.42         7.10         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
        2.27        11.05        13.38        20.48         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.60        18.35        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HU 
       50.20        44.98        24.66        38.40        20.52        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       10.55        27.19        12.92         6.28        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       23.70         4.67        40.44        26.86        32.65        21.11 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       20.55        14.33        41.69        13.05        33.11         8.58 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       35.54        16.21        11.57        12.49         8.52        22.45 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6022 
       20.71        20.65        19.53        20.68        19.07         9.24 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A497 
       36.49        11.08        24.16         3.68        17.42        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
       14.56        17.59        12.85        29.72         7.40        15.91 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 
       11.44         4.41        12.07         2.70         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
        7.69         6.18        48.20        39.68        21.50        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       46.75        45.80        45.99        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-6229 
       32.38        34.75        56.58        13.25        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
       70.13        51.29        33.11        16.73        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       28.83        64.11        44.48        11.61        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       25.81        14.14        12.46        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       50.01        39.52        34.52        36.99        18.54        11.90 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        11.51        15.75         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
       39.16        47.34        40.93        35.84         3.45         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95        29.23        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       26.17        47.01        29.82        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
       29.52        30.58         7.10         5.13        35.41        29.95 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
       17.16       108.95        76.24        19.20       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       76.50        91.53        80.12        17.92        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       86.83        48.59        60.49        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
       62.43         2.14         9.70         4.73        21.90        11.24 
TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       19.79        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
       10.98         8.42        28.34         2.50        64.83       126.15 
TCGA-CV-7099 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 
        7.99        12.92        71.21        10.75       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       47.47        36.00        31.36        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
        4.96        47.97         2.10        57.47        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
       89.33         9.67         0.46        25.94        34.09        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49        54.94         3.52        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17        16.64         6.38        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A461 
      169.38       159.65         1.05        45.96         6.51        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38        29.79         6.48        22.03        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
       19.92        22.52        10.42        10.55        18.84        34.36 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
       11.44        18.67        25.32        17.72        15.88         7.63 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       14.30        12.10        35.54        33.86        18.02        14.04 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-F7-8489 
       25.48        20.45         9.83        12.13        10.65        21.63 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       19.23        18.94        12.62         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A 
       12.43        13.38        15.16        15.06        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
        0.07        25.74        12.66         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61H 
        6.90        34.75        15.95        12.76        19.33        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       12.43        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       12.62        17.98        29.92        56.75        51.25        10.85 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       47.01        75.55        18.97        16.01        21.07        11.74 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30         9.34        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        5.62         9.73        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
       32.45        13.55        13.68        44.65        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       49.22        16.11        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                        16.080                         19.215 
[1] "0.1 - 180.2 (16.1)" "0.1 - 211.0 (19.2)"
[1] "hr=" "1.1"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 29(11P15.5) MUTATED         5       19        20        79         8
  DEL PEAK 29(11P15.5) WILD-TYPE      22       58        57       173         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                             22
  STAGE II                            19                             58
  STAGE III                           20                             57
  STAGE IVA                           79                            173
  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  28  58
  DEL PEAK 29(11P15.5) WILD-TYPE    36  98  71 114
D58V4, multiclass
       clus
vv      DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T0+T1                           14                             36
  T2                              35                             98
  T3                              28                             71
  T4                              58                            114
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 29(11P15.5) MUTATED    45  18  50   6
  DEL PEAK 29(11P15.5) WILD-TYPE 133  48 115   2
D58V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                           45                            133
  N1                           18                             48
  N2                           50                            115
  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"
D58V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    51   0
  DEL PEAK 29(11P15.5) WILD-TYPE 132   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     51    0
  DEL PEAK 29(11P15.5) WILD-TYPE  132    1
   clus
vv  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  0                           51                            132
  1                            0                              1
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    39 123
  DEL PEAK 29(11P15.5) WILD-TYPE 100 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     39  123
  DEL PEAK 29(11P15.5) WILD-TYPE  100  254
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           39                            100
  MALE                            123                            254
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(11P15.5) MUTATED                                     155
  DEL PEAK 29(11P15.5) WILD-TYPE                                   350
                                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                                                155
  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                                                  350
  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    25 137
  DEL PEAK 29(11P15.5) WILD-TYPE  56 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     25  137
  DEL PEAK 29(11P15.5) WILD-TYPE   56  298
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                            25                             56
  YES                          137                            298
[1] 2 2
[1] FALSE
D58V10, continuous
D58V11, continuous
D58V12, 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   134
  DEL PEAK 29(11P15.5) WILD-TYPE                        24   307
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 29(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     134
                                  clus
vv                                 DEL PEAK 29(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    11 135
  DEL PEAK 29(11P15.5) WILD-TYPE  14 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     11  135
  DEL PEAK 29(11P15.5) WILD-TYPE   14  319
                        clus
vv                       DEL PEAK 29(11P15.5) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          135
                        clus
vv                       DEL PEAK 29(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            319
[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   152  90
  DEL PEAK 30(11Q23.1) WILD-TYPE 161 110
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                           242                            271 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                            90                            110 
$`DEL PEAK 30(11Q23.1) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5153 
       15.19        13.64        37.28         9.07        26.50        57.93 
TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
       17.10        57.44        15.52        14.83         3.55        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
        4.01         7.76        28.11        20.45        30.18        11.54 
TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 
        5.69         2.27        20.48         6.15        94.62         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
       18.35        22.42        44.98        66.28        24.66        71.05 
TCGA-BB-A5HU TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       25.71        12.92         8.81        40.44        37.84        12.89 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       41.10        43.73        41.69        12.39        35.54         8.32 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 
       11.54        11.84        11.57         8.52        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6989 
       20.68        20.65         6.74         9.07        11.08        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
       12.95        24.16         3.68        11.74        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63Y TCGA-CN-A641 
       12.85        29.72        21.21         7.40         5.75        12.07 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6220 
       10.09         7.69         6.18        48.20        10.42        32.38 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7067 
       32.88        56.58         4.24        14.99        38.76        16.73 
TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       11.61        29.36        32.81        84.23        11.77        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7369 
       11.64         7.69        12.46        11.51         9.27        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 
        3.45         3.09         9.17        19.92        17.13        32.78 
TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       27.06         5.95        48.39       139.43        17.16       129.21 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5973 
       17.95       107.51        94.88        91.53        13.35        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 
       48.59        60.49        43.23        54.74        21.07         9.60 
TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 
       90.12         9.70         5.46        20.52        21.90        26.43 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
      126.08        12.03         8.42         2.50       126.15       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 
       18.81        12.66         9.01         5.26         1.84        12.92 
TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7247 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       21.80        77.16        18.97        18.41        57.47        35.54 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.94         0.07        34.09       100.57 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U 
       54.94        84.49        19.76       153.86       180.16        35.47 
TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
       45.96        88.87        60.43        35.34        29.79        10.42 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6EP 
       18.84        34.36        23.05        16.14        17.72        13.94 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       12.79        11.11        14.04        18.90        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
       12.13        12.10        11.18        37.18        16.11        20.25 
TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
        3.02        20.25        15.06        13.61        21.11         6.77 
TCGA-HD-7753 TCGA-HD-8314 TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
        0.16        22.03        34.75        11.84        13.55        14.47 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X 
       11.54        11.84        18.15        12.43        14.37         7.96 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QF 
        1.84         3.68         7.13        17.98        56.75        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 
       36.82        47.01        18.97         2.04        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB 
       13.15        17.65         7.30        16.70        18.64        14.79 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP 
        6.51        11.57        12.10         9.76         8.32        16.96 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71A 
       15.91         7.10        13.25        13.68        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       43.36        42.02        62.27        17.95        24.16        21.86 
TCGA-UF-A7JS TCGA-UP-A6WW 
       22.36        17.03 

$`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 
        3.35         9.30        23.74        42.35        23.84        20.48 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
       53.79        21.17        29.42        27.95         7.10        14.47 
TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4225 
        7.82        11.05        13.38        16.41         9.14         4.60 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY 
       36.72        33.70        50.20        38.40        20.52        10.55 
TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
       27.19         6.28        12.69        26.27        23.70        38.04 
TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
        4.67        26.86        32.65        21.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       14.33        27.58        13.05        33.11        34.36         8.58 
TCGA-CN-5364 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 
       16.21        12.49        22.45        20.71        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6996 
       19.07        14.20         9.24        36.49        10.45        17.42 
TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 
       14.10        35.01        17.29        15.91        11.44         4.41 
TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        2.70         7.33         9.80        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.80        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       41.19        34.75        13.25        70.13        51.29        33.11 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       43.04        41.88        28.83        64.11        44.48        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-6471 TCGA-CR-6492 
       25.81        14.14        12.46        31.23        39.52        15.75 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 
       47.18        39.16        47.34        40.93        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7389 
        0.99        31.96        34.06        26.17        47.01        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5434 TCGA-CV-5435 
        7.10         5.13        35.41        29.95       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5978 
       19.20        76.50        80.12        17.92        23.05         7.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6948 
       62.43         2.14         4.73        11.24        19.79        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7103 
        7.13        28.34         4.14        64.83         7.99        52.31 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21        10.75       130.88         4.73        47.47        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        17.13        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       47.97         2.10        36.13        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 
        9.67        25.08        14.89        56.48       156.49         3.52 
TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       16.27         7.17        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Z 
       24.99       169.38       159.65         1.05         6.51        48.20 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       67.86         0.76        56.61         7.07        15.25         5.98 
TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38         6.48        22.03         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 
       19.92        22.52        10.42        10.55        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        9.60         2.53        11.44        18.67        24.95        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5624 
       12.36        15.88         7.63        14.30        12.10        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7595 
       35.54        30.94        33.86        18.02         9.83        10.65 
TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       21.63        19.23        18.94        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7754 
       11.80        12.43        13.38        15.16         0.07        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
        1.22        14.66        12.66        22.85         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        4.27         3.65         6.90        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61K TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A67A 
       19.33         0.07         5.29        13.35        10.75        30.05 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE 
       12.62        15.42        16.08        29.92        15.78        51.25 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6II 
       19.00        75.55        12.99        21.07        11.74         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-T2-A6WX 
       12.72        12.43         5.62         9.73        12.72         6.87 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JF 
       32.45        13.55        43.59        41.16        44.65        49.22 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ 
       16.11        13.94        20.75        32.65         2.96        20.55 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE 
                        17.685                         19.070 
[1] "0.1 - 180.2 (17.7)" "0.1 - 211.0 (19.1)"
[1] "hr=" "1.1"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 30(11Q23.1) MUTATED        11       33        32       115         6
  DEL PEAK 30(11Q23.1) WILD-TYPE      16       44        45       137         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                             16
  STAGE II                            33                             44
  STAGE III                           32                             45
  STAGE IVA                          115                            137
  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      23 62 45 73
  DEL PEAK 30(11Q23.1) WILD-TYPE    27 71 54 99
D59V4, multiclass
       clus
vv      DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  T0+T1                           23                             27
  T2                              62                             71
  T3                              45                             54
  T4                              73                             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 30(11Q23.1) MUTATED    65  26  93   3
  DEL PEAK 30(11Q23.1) WILD-TYPE 113  40  72   5
D59V5, multiclass
    clus
vv   DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  N0                           65                            113
  N1                           26                             40
  N2                           93                             72
  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"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.1) MUTATED    76   0
  DEL PEAK 30(11Q23.1) WILD-TYPE 107   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.1) MUTATED     76    0
  DEL PEAK 30(11Q23.1) WILD-TYPE  107    1
   clus
vv  DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  0                           76                            107
  1                            0                              1
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.1) MUTATED    43 200
  DEL PEAK 30(11Q23.1) WILD-TYPE  96 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.1) MUTATED     43  200
  DEL PEAK 30(11Q23.1) WILD-TYPE   96  177
        clus
vv       DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  FEMALE                           43                             96
  MALE                            200                            177
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11Q23.1) MUTATED                                     236
  DEL PEAK 30(11Q23.1) WILD-TYPE                                   269
                                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                                                236
  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                                                  269
  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    43 200
  DEL PEAK 30(11Q23.1) WILD-TYPE  38 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.1) MUTATED     43  200
  DEL PEAK 30(11Q23.1) WILD-TYPE   38  235
     clus
vv    DEL PEAK 30(11Q23.1) MUTATED DEL PEAK 30(11Q23.1) WILD-TYPE
  NO                            43                             38
  YES                          200                            235
[1] 2 2
[1] FALSE
D59V10, continuous
D59V11, continuous
D59V12, 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   211
  DEL PEAK 30(11Q23.1) WILD-TYPE                        22   230
D59V13, multiclass
                                  clus
vv                                 DEL PEAK 30(11Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     211
                                  clus
vv                                 DEL PEAK 30(11Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q23.1) MUTATED    15 210
  DEL PEAK 30(11Q23.1) WILD-TYPE  10 244
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q23.1) MUTATED     15  210
  DEL PEAK 30(11Q23.1) WILD-TYPE   10  244
                        clus
vv                       DEL PEAK 30(11Q23.1) MUTATED
  HISPANIC OR LATINO                               15
  NOT HISPANIC OR LATINO                          210
                        clus
vv                       DEL PEAK 30(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            244
[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  26
  DEL PEAK 31(12Q24.33) WILD-TYPE 279 174
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             60                             453 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                             26                             174 
$`DEL PEAK 31(12Q24.33) MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
        9.30        15.52        14.83         4.01         7.76        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-8596 TCGA-CN-4726 
       20.45        27.95        14.47        16.41        71.05         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5374 
       40.44        37.84        43.73        33.11        12.39        56.94 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A49B TCGA-CQ-5332 TCGA-CR-6493 
       11.08        10.45        24.16        29.72        10.42         9.27 
TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5966 TCGA-CV-5976 
        3.45        17.13        29.82       139.43        17.92        48.59 
TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-6948 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 
       54.74         9.70        42.38       126.15       111.16         5.26 
TCGA-CV-7102 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7432 TCGA-CV-7435 
        1.84        47.97         2.10        18.41        84.49       153.86 
TCGA-CV-A6JY TCGA-CX-7219 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-DQ-5629 TCGA-F7-7848 
       21.24        34.36        17.72        13.94        30.94        37.18 
TCGA-H7-A6C5 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MZ-A5BI TCGA-P3-A5Q6 TCGA-P3-A5QA 
       21.11        11.84        18.15         7.13        15.78        56.75 
TCGA-P3-A6T5 TCGA-QK-A8Z7 TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A7JF TCGA-WA-A7GZ 
       29.00         6.51        15.91        54.67        49.22        20.55 

$`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 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-A4IG 
       53.79        57.44        21.17         3.55        12.62        28.11 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        13.38        20.48         6.15        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.60         4.41        18.35        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 
       50.20        44.98        66.28        24.66        38.40        20.52 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z 
       25.71        10.55        27.19        12.92         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4730 
       12.69        26.27        23.70        38.04        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
       27.58        41.69        13.05        34.36         8.58        35.54 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.32        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        8.52        22.45        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 
        9.24        36.49        20.09        12.95         3.68        17.42 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       14.10        11.74        35.01        14.56        17.59        12.85 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        17.29        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.69         6.18        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.80        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       41.19        32.38        32.88        34.75        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        14.99        38.76        70.13        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       16.73        43.04        41.88        28.83        64.11        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       11.61        23.24        29.36        32.81        25.81        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       12.46        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
       11.64         7.69        12.46        11.51        15.75        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
       39.16        47.34        40.93        35.84         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       26.17        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
        5.95        35.41        29.95        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      108.95        76.24        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        80.12        13.35        23.05        86.83 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
       60.49         7.07        43.23        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
       90.12         2.14         5.46        20.52         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
       26.43        11.24       126.08        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       30.08         6.08        53.95        65.82        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7095 
        8.42        28.34         2.50         4.14        64.83        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
       12.66         7.99         9.01        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       71.21        10.75       130.88        77.16         4.73        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
        4.96        11.87        36.13        57.47        35.54        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
      210.97        89.33         9.67         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
       25.94         0.07        34.09       100.57        14.89        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
      156.49        54.94         3.52        16.27        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       16.64         6.38        22.19        27.98        24.99       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      180.16       159.65        35.47         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       88.87        48.20        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        22.03         3.62        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.42        10.55        18.84        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       24.95        25.32        12.36        15.88         7.63        14.30 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        11.11        58.45        35.54        33.86 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       18.02        14.04        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        16.11        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        19.23        18.94        12.62         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       17.85        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.06        13.61         6.77         0.07         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
        1.22        14.66        22.03        12.66        22.85         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       13.84         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       12.76        14.50        19.33        13.55         0.07        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
        5.29        11.54        11.84        13.35        12.43        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         3.68 
TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF 
       15.42        16.08        17.98        29.92        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       36.82        47.01        19.00        75.55        18.97         2.04 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        16.70         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       12.43         5.62        11.57        12.10         9.73         9.76 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        12.72        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.25        13.68        43.59         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       41.16        42.02        44.65        62.27        17.95        24.16 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7H4 
        2.96        17.03        14.56 

  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                           1.84                            0.07 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                         153.86                          210.97 
  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE 
                          20.50                           17.95 
[1] "1.8 - 153.9 (20.5)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1"  
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      24       69        71       219
                                 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                              24
  STAGE II                              8                              69
  STAGE III                             6                              71
  STAGE IVA                            33                             219
  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  14  11  26
  DEL PEAK 31(12Q24.33) WILD-TYPE    47 119  88 146
D60V4, multiclass
       clus
vv      DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  T0+T1                             3                              47
  T2                               14                             119
  T3                               11                              88
  T4                               26                             146
[1] 4 2
[1] TRUE
[1] "dimension of 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    19   6  21   2
  DEL PEAK 31(12Q24.33) WILD-TYPE 159  60 144   6
D60V5, multiclass
    clus
vv   DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  N0                            19                             159
  N1                             6                              60
  N2                            21                             144
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                                 cls
clus                                0   1
  DEL PEAK 31(12Q24.33) MUTATED    19   0
  DEL PEAK 31(12Q24.33) WILD-TYPE 164   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED     19    0
  DEL PEAK 31(12Q24.33) WILD-TYPE  164    1
   clus
vv  DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  0                            19                             164
  1                             0                               1
[1] 2 2
[1] FALSE
D60V7, binary
                                 cls
clus                                0   1
  DEL PEAK 31(12Q24.33) MUTATED    14  46
  DEL PEAK 31(12Q24.33) WILD-TYPE 125 331
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED     14   46
  DEL PEAK 31(12Q24.33) WILD-TYPE  125  331
        clus
vv       DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  FEMALE                            14                             125
  MALE                              46                             331
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(12Q24.33) MUTATED                                      58
  DEL PEAK 31(12Q24.33) WILD-TYPE                                   447
                                 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                                                  58
  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                                                   447
  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  50
  DEL PEAK 31(12Q24.33) WILD-TYPE  71 385
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED     10   50
  DEL PEAK 31(12Q24.33) WILD-TYPE   71  385
     clus
vv    DEL PEAK 31(12Q24.33) MUTATED DEL PEAK 31(12Q24.33) WILD-TYPE
  NO                             10                              71
  YES                            50                             385
[1] 2 2
[1] FALSE
D60V10, continuous
D60V11, continuous
D60V12, 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    48
  DEL PEAK 31(12Q24.33) WILD-TYPE                        35   393
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 31(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       48
                                  clus
vv                                 DEL PEAK 31(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                     35
  WHITE                                                        393
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                                 cls
clus                                0   1
  DEL PEAK 31(12Q24.33) MUTATED     4  51
  DEL PEAK 31(12Q24.33) WILD-TYPE  21 403
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 31(12Q24.33) MUTATED      4   51
  DEL PEAK 31(12Q24.33) WILD-TYPE   21  403
                        clus
vv                       DEL PEAK 31(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            51
                        clus
vv                       DEL PEAK 31(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                  21
  NOT HISPANIC OR LATINO                             403
[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   139  88
  DEL PEAK 32(13Q12.11) WILD-TYPE 174 112
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                            227                             286 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                             88                             112 
$`DEL PEAK 32(13Q12.11) MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 
       15.19         9.07        26.50        42.35        17.10        57.44 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17         3.55        12.62         4.01         7.76 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE 
       28.11        20.45        30.18        11.54         5.69        14.47 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 
       11.05        20.48         9.14         4.41        36.72        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY 
       66.28        24.66        71.05        20.52        25.71        10.55 
TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4730 
       27.19         6.28        23.70        38.04        12.89        26.86 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 
       20.55        43.73        27.58        34.36        35.54         8.32 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       11.57        22.45        56.94        20.71        30.67        20.68 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
       19.07         6.74         9.07         9.24        11.08        10.45 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       24.16        14.10        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V7 
       12.85        21.21         7.40        17.29        11.44         6.18 
TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-7064 
       45.80        32.38        32.88        13.25         4.24        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       33.11        16.73        64.11        11.61        23.24        29.36 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6478 
       25.81        31.23        84.23        11.77        34.52         6.02 
TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       10.22         7.69        12.46         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7385 
       47.34         3.09        24.95         0.99        34.06        32.78 
TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5430 
       47.01        29.82         7.10         5.95        29.95       139.43 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5970 
      129.21       108.95       107.51        94.88        17.92        13.35 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 
       48.59        60.49         7.07        43.23         9.60         2.14 
TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
        9.70        21.90        26.43        11.24       126.08        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6962 
       42.38        15.09        30.08        65.82        28.34         4.14 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 
        1.84        52.31        12.92        21.80        10.75        77.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 
       36.00        26.20        17.13         2.10        18.41        57.47 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7429 
        0.46        22.85        25.94         0.07        34.09         3.52 
TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 
      153.86       180.16        45.96        88.87        67.86        56.61 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CX-7086 
        7.07        35.34         6.38        29.79         3.62        18.84 
TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 
       34.36        23.05        16.14        11.44        24.95        17.72 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 
       30.94        33.86        14.04        18.90         9.83        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 
       11.18        37.18        20.25         3.02         0.46        20.25 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 
       21.11         0.07         0.16        14.66        22.85        13.84 
TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61O TCGA-MT-A67G TCGA-MZ-A5BI 
        3.65        14.50        11.84        11.84         3.68         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 
       16.08        15.78        56.75        47.01        18.97         2.04 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        7.30        16.70        18.64         6.51         5.62        11.57 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HJ 
       12.10         9.73         8.32        12.72        15.91        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E 
       13.68        43.59        54.67         2.83        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS 
       44.65        17.95        21.86        13.94        22.36 

$`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 
        3.35         9.30        13.64        37.28        23.74        57.93 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
       23.84        20.48        53.79        14.83        29.42        27.95 
TCGA-BA-A6DB TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
        7.10         7.82         2.27        13.38        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 
       94.62         4.60        18.35        22.42        33.70        44.98 
TCGA-BB-7872 TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 
       38.40        12.92         8.81        12.69        26.27         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       40.44        37.84        32.65        21.11        41.10        12.99 
TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       14.33        41.69        13.05        33.11         8.58        12.39 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6013 
       16.21        11.54        11.84        12.49         8.52        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 
       19.53        20.68        14.20        36.49        20.09        12.95 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
        3.68        17.42        29.72        15.91         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
       12.07         2.70        10.09         7.33         9.80         7.69 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
       45.99        10.42        11.21         4.24        41.19        34.75 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 
       56.58        14.99        38.76        70.13        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 
       28.83        44.48        32.81        14.14        12.46        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 
       18.54        16.90        11.90        11.34        11.64        11.51 
TCGA-CR-6492 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7376 
       15.75        40.93        35.84         3.45        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 
        9.17        19.92        26.17        17.13        27.06        12.89 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 
       30.02        31.10        29.85        29.52        30.58         5.13 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       35.41        48.39        17.16        76.24        19.20        17.95 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6003 
       76.50        91.53        80.12        23.05        86.83        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       21.07        62.43        90.12         5.46        20.52         4.73 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       19.79         6.08        53.95        10.98         7.13         8.42 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 
        2.50       126.15         5.26        71.21       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       47.47        31.36        18.97        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       47.97        36.13        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        9.67        25.08       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
       54.94        16.27        84.49        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
        6.38        22.19        27.98        24.99       169.38       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 
       35.47         1.05         6.51        48.20        60.43         0.76 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
       15.25         5.98         6.48        22.03        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 
       19.92        22.52        10.42        10.42        10.55        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB 
       25.41         9.60         2.53        18.67        25.32        12.36 
TCGA-D6-A6EK TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       15.88        58.45        35.54        18.02        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S 
       12.13        12.10        16.11        21.63        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       12.62        17.85        11.80        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 
       15.06        13.61         6.77        25.74         1.22        22.03 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       12.66         0.36         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       12.76        19.33        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       11.54        13.35        18.15        12.43        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A7D7 
        7.96        30.05         1.84        12.62        15.42        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
       29.92        51.25        10.85        36.82        19.00        75.55 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       29.00        12.99        16.01        13.15        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-AA3J 
       17.65         9.34        12.72        14.79        12.43         9.76 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-UF-A71B 
       16.96         6.87         7.10        32.45        13.55        43.36 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT 
       62.27        24.16        49.22        16.11        20.75        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                         180.16                          210.97 
  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE 
                         17.950                          18.085 
[1] "0.1 - 180.2 (17.9)" "0.1 - 211.0 (18.1)"
[1] "hr=" "1"  
D61V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 32(13Q12.11) MUTATED         8       26        34       121
  DEL PEAK 32(13Q12.11) WILD-TYPE      19       51        43       131
                                 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                              19
  STAGE II                             26                              51
  STAGE III                            34                              43
  STAGE IVA                           121                             131
  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      16 54 46 85
  DEL PEAK 32(13Q12.11) WILD-TYPE    34 79 53 87
D61V4, multiclass
       clus
vv      DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  T0+T1                            16                              34
  T2                               54                              79
  T3                               46                              53
  T4                               85                              87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 32(13Q12.11) MUTATED    67  33  83   3
  DEL PEAK 32(13Q12.11) WILD-TYPE 111  33  82   5
D61V5, multiclass
    clus
vv   DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  N0                            67                             111
  N1                            33                              33
  N2                            83                              82
  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"
D61V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED    82   1
  DEL PEAK 32(13Q12.11) WILD-TYPE 101   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED     82    1
  DEL PEAK 32(13Q12.11) WILD-TYPE  101    0
   clus
vv  DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  0                            82                             101
  1                             1                               0
[1] 2 2
[1] FALSE
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED    51 178
  DEL PEAK 32(13Q12.11) WILD-TYPE  88 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED     51  178
  DEL PEAK 32(13Q12.11) WILD-TYPE   88  199
        clus
vv       DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  FEMALE                            51                              88
  MALE                             178                             199
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(13Q12.11) MUTATED                                     224
  DEL PEAK 32(13Q12.11) WILD-TYPE                                   281
                                 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                                                 224
  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                                                   281
  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    35 194
  DEL PEAK 32(13Q12.11) WILD-TYPE  46 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED     35  194
  DEL PEAK 32(13Q12.11) WILD-TYPE   46  241
     clus
vv    DEL PEAK 32(13Q12.11) MUTATED DEL PEAK 32(13Q12.11) WILD-TYPE
  NO                             35                              46
  YES                           194                             241
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, continuous
D61V12, 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   188
  DEL PEAK 32(13Q12.11) WILD-TYPE                        19   253
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 32(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      188
                                  clus
vv                                 DEL PEAK 32(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     19
  WHITE                                                        253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                                 cls
clus                                0   1
  DEL PEAK 32(13Q12.11) MUTATED    14 191
  DEL PEAK 32(13Q12.11) WILD-TYPE  11 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(13Q12.11) MUTATED     14  191
  DEL PEAK 32(13Q12.11) WILD-TYPE   11  263
                        clus
vv                       DEL PEAK 32(13Q12.11) MUTATED
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           191
                        clus
vv                       DEL PEAK 32(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             263
[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   137  74
  DEL PEAK 33(13Q14.2) WILD-TYPE 176 126
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                           211                            302 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                            74                            126 
$`DEL PEAK 33(13Q14.2) MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
       15.19         9.07        26.50        42.35        57.93        17.10 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG 
       57.44        21.17         3.55         4.01         7.76        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       20.45        30.18        27.95        11.54         7.10         5.69 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
       11.05        20.48        94.62         9.14         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
       22.42        36.72        50.20        66.28        24.66        71.05 
TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4723 
       20.52        25.71        10.55        27.19         6.28        23.70 
TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 
       38.04        26.86        43.73        27.58        34.36        35.54 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        8.32        11.54        11.57        22.45        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
       20.68        19.07         6.74         9.07         9.24        11.08 
TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       10.45        24.16        11.74        35.01        14.56        17.59 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.85        21.21         7.40        11.44         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 
       48.20        45.80        32.38        56.58        13.25        14.99 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI 
       51.29        33.11        16.73        32.81        25.81        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 
       84.23        11.77        54.67        37.87        58.42        50.01 
TCGA-CR-6472 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7364 
       34.52        16.90         6.02        10.22         7.69        47.18 
TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7386 
       39.16        24.95         0.99        34.06        32.78        47.01 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        7.10         5.95        29.95        48.39       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6940 
      108.95        94.88        60.49         7.07         9.60        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 
       11.24       126.08        42.38        15.09        30.08        65.82 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
       28.34         4.14        64.83       111.16        18.81         7.99 
TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 
        9.01        52.31        12.92        21.80        10.75        77.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7415 
       36.00        26.20        17.13        18.41        57.47        22.85 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7440 
       25.94         0.07        34.09         3.52       153.86        22.19 
TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 
      180.16        45.96        88.87        67.86        56.61         7.07 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6825 
       35.34        29.79        10.42        18.84        34.36        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-DQ-5630 
       11.44        18.67        24.95        17.72        13.94        33.86 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 
       14.04        18.90        25.48         9.83        10.65        11.18 
TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A76A 
       37.18        20.25         3.02         0.46        20.25         6.77 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A633 
        0.16         1.22        14.66        22.03        22.85        13.84 
TCGA-HD-A6HZ TCGA-IQ-A61I TCGA-IQ-A61O TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A67G 
        3.65         0.07        11.84        18.15        12.43         3.68 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        15.78        56.75        51.25        10.85 
TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 
       47.01         2.04        16.01         7.30        16.70        18.64 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K 
        6.51         5.62        11.57        12.10         9.73         8.32 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       16.96        15.91         7.10        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JS 
        2.83        41.16        42.02        44.65        17.95        22.36 
TCGA-UP-A6WW 
       17.03 

$`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 
        3.35         9.30        13.64        37.28        23.74        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF 
       20.48        53.79        15.52        14.83        12.62        29.42 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
       14.47         7.82         2.27        13.38        16.41         6.15 
TCGA-BB-4225 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A6UM TCGA-BB-A6UO 
        4.60        33.70        44.98        38.40        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       12.69        26.27         4.67        40.44        37.84        12.89 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 
       41.69        13.05        33.11         8.58        12.39        16.21 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 
       11.84        12.49         8.52        20.71        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 
       20.68        14.20        36.49        20.09        12.95         3.68 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       17.42        14.10        29.72        17.29        15.91         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
        4.41        12.07         2.70        10.09         7.33         9.80 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       39.68        21.50         2.93        54.58        46.75        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.88        34.75 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        38.76        70.13        43.04        41.88        28.83 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CG 
       64.11        44.48        11.61        23.24        29.36        14.14 
TCGA-CQ-A4CH TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       12.46        26.27        39.52        36.99        18.54        11.90 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64        12.46        11.51        15.75         9.27 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
       47.34        40.93        35.84         3.45         3.09        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 
       31.96         9.17        19.92        26.17        17.13        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
       30.58         5.13        35.41        17.16        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95       107.51        76.50        91.53        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 
       13.35        23.05        86.83        48.59        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       21.07        62.43        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
       20.52         4.73        21.90        19.79        12.03         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 
       53.95        10.98         7.13         8.42         2.50       126.15 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 
       12.66         5.26         1.84        71.21       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       47.47        31.36        18.97        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       47.97         2.10        36.13        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 
       89.33         9.67         0.46        25.08       100.57        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49        54.94        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64         6.38        27.98        24.99       169.38 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 
      159.65        35.47         1.05         6.51        48.20        60.43 
TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT 
        0.76        15.25         5.98         6.38         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       10.55        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ 
       25.32        12.36        15.88         7.63        14.30        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 
       12.79        11.11        58.45        35.54        30.94        18.02 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J 
       20.45        12.13        12.10        16.11        21.63        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       18.94        12.62        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 
       15.16        15.06        13.61        21.11         0.07        25.74 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       12.66         0.36         4.27         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
       12.76        14.50        19.33        11.84        13.55        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
        5.29        11.54        13.35        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       30.05         1.84        12.62        15.42        17.98        29.92 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       36.82        19.00        75.55        18.97        29.00        12.99 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ 
       13.15        21.07        11.74        17.65         9.34        12.72 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-AA3J TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X2 
       14.79        12.43         9.76        12.72         6.87        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       13.55        13.25        43.36        62.27        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV 
       21.86        16.11        13.94        20.75        32.65         2.96 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE 
                        20.250                         17.145 
[1] "0.1 - 180.2 (20.2)" "0.1 - 211.0 (17.1)"
[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       24        34       101         6
  DEL PEAK 33(13Q14.2) WILD-TYPE      16       53        43       151         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                             16
  STAGE II                            24                             53
  STAGE III                           34                             43
  STAGE IVA                          101                            151
  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      22  56  38  66
  DEL PEAK 33(13Q14.2) WILD-TYPE    28  77  61 106
D62V4, multiclass
       clus
vv      DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  T0+T1                           22                             28
  T2                              56                             77
  T3                              38                             61
  T4                              66                            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 33(13Q14.2) MUTATED    62  28  73   4
  DEL PEAK 33(13Q14.2) WILD-TYPE 116  38  92   4
D62V5, multiclass
    clus
vv   DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  N0                           62                            116
  N1                           28                             38
  N2                           73                             92
  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"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q14.2) MUTATED    71   1
  DEL PEAK 33(13Q14.2) WILD-TYPE 112   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q14.2) MUTATED     71    1
  DEL PEAK 33(13Q14.2) WILD-TYPE  112    0
   clus
vv  DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  0                           71                            112
  1                            1                              0
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q14.2) MUTATED    47 166
  DEL PEAK 33(13Q14.2) WILD-TYPE  92 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q14.2) MUTATED     47  166
  DEL PEAK 33(13Q14.2) WILD-TYPE   92  211
        clus
vv       DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  FEMALE                           47                             92
  MALE                            166                            211
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q14.2) MUTATED                                     206
  DEL PEAK 33(13Q14.2) WILD-TYPE                                   299
                                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                                                206
  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                                                  299
  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    34 179
  DEL PEAK 33(13Q14.2) WILD-TYPE  47 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q14.2) MUTATED     34  179
  DEL PEAK 33(13Q14.2) WILD-TYPE   47  256
     clus
vv    DEL PEAK 33(13Q14.2) MUTATED DEL PEAK 33(13Q14.2) WILD-TYPE
  NO                            34                             47
  YES                          179                            256
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, continuous
D62V12, 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   176
  DEL PEAK 33(13Q14.2) WILD-TYPE                        20   265
D62V13, multiclass
                                  clus
vv                                 DEL PEAK 33(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     176
                                  clus
vv                                 DEL PEAK 33(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                                cls
clus                               0   1
  DEL PEAK 33(13Q14.2) MUTATED    13 180
  DEL PEAK 33(13Q14.2) WILD-TYPE  12 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(13Q14.2) MUTATED     13  180
  DEL PEAK 33(13Q14.2) WILD-TYPE   12  274
                        clus
vv                       DEL PEAK 33(13Q14.2) MUTATED
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          180
                        clus
vv                       DEL PEAK 33(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            274
[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    45  28
  DEL PEAK 34(14Q11.2) WILD-TYPE 268 172
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            73                            440 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                            28                            172 
$`DEL PEAK 34(14Q11.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-6871 
        3.35         9.30         9.07        42.35        21.17         3.55 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BB-7862 TCGA-BB-A6UM TCGA-CN-4725 TCGA-CN-4729 
       20.45        27.95        36.72        12.92        38.04        12.89 
TCGA-CN-4735 TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6995 TCGA-CN-A49A 
       41.10        30.67        14.20         6.74         3.68        12.85 
TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6472 
       17.29        10.42        32.88        64.11        11.77        34.52 
TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
       11.64        11.51         9.27        39.16        47.34         3.45 
TCGA-CR-7388 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5435 TCGA-CV-5966 TCGA-CV-6933 
       27.06         5.13         5.95        76.24        17.92        90.12 
TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-7177 TCGA-CV-7180 
        9.70        21.90        26.43        12.03        21.80        10.75 
TCGA-CV-7263 TCGA-CV-7413 TCGA-CV-7423 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45Z 
       18.41         9.67       100.57        84.49       153.86        48.20 
TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 
       60.43        21.24        22.52        11.44        25.32        17.72 
TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-5629 TCGA-F7-7848 TCGA-H7-A6C5 TCGA-H7-A76A 
        7.63        13.94        30.94        37.18        21.11         6.77 
TCGA-HD-7229 TCGA-HD-8224 TCGA-HD-A633 TCGA-MT-A7BN TCGA-P3-A6T0 TCGA-QK-A8Z7 
        0.07        14.66        13.84        15.42        19.00         6.51 
TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF 
        9.76        54.67        43.36        41.16        62.27        49.22 
TCGA-WA-A7GZ 
       20.55 

$`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 
       15.19        13.64        37.28        26.50        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       17.10        23.84        20.48        53.79        57.44        15.52 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
       14.83        12.62         4.01         7.76        29.42        28.11 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       30.18        11.54         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
       94.62         9.14         4.60         4.41        18.35        22.42 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       33.70        50.20        44.98        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO 
       71.05        20.52        25.71        10.55        27.19         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
        6.28        12.69        26.27        23.70         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
       37.84        26.86        32.65        21.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        43.73        27.58        41.69        13.05        33.11 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       34.36         8.58        12.39        35.54         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        20.71        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       19.07         9.07         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       20.09        12.95        24.16        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        14.56        17.59        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       15.91        11.44         5.75         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       45.99        11.21         4.24        41.19        32.38        34.75 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       56.58        13.25         4.24        14.99        38.76        70.13 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       51.29        33.11        16.73        43.04        41.88        28.83 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        32.81        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       26.27        58.42        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       16.90         6.02        11.90        10.22        11.34         7.69 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       12.46        15.75        47.18        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       24.95        29.23         0.99        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
       19.92        26.17        17.13        32.78        47.01        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        7.10        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        19.20        17.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       76.50        91.53        80.12        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       48.59        60.49         7.07        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       62.43         9.60         2.14         5.46        20.52         4.73 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       11.24       126.08        19.79        42.38        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
        6.08        53.95        65.82        10.98         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       28.34         2.50         4.14        64.83       126.15       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       52.31        12.92        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       47.47        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       95.34         4.96        11.87        47.97         2.10        36.13 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 
       57.47        35.54        17.85       210.97        89.33         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 
       22.85        25.08        25.94         0.07        34.09        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 
       56.48       156.49        54.94         3.52        16.27        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17        16.64         6.38        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
        6.51        88.87        67.86         0.76        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 
       22.03         3.62        23.47        19.92        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        34.36        13.25        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB 
       23.05         2.53        16.14        18.67        24.95        12.36 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       15.88        14.30        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       35.54        33.86        18.02        14.04        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       20.45         9.83        12.13        12.10        10.65        11.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       16.11        21.63        20.25         3.02        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       12.62         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7754 
       13.38        15.16        15.06        13.61         0.16        25.74 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
        1.22        22.03        12.66        22.85         0.36         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
        3.65         6.90        34.75        15.95        12.76        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       19.33        11.84        13.55         0.07        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
       11.54        11.84        13.35        18.15        12.43        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         3.68 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.13        16.08        17.98        29.92        15.78        56.75 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        10.85        36.82        47.01        75.55        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       11.74        17.65         7.30        16.70         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       18.64        14.79        12.43         5.62        11.57        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
        9.73         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
        7.10        32.45        13.55        13.25        13.68        43.59 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        2.83        42.02        44.65        17.95        24.16        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7H4 
       17.03        14.56 

  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE 
                        19.000                         17.965 
[1] "0.1 - 153.9 (19.0)" "0.1 - 211.0 (18.0)"
[1] "hr=" "1"  
D63V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 34(14Q11.2) MUTATED         1       15         9        37         1
  DEL PEAK 34(14Q11.2) WILD-TYPE      26       62        68       215        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                             26
  STAGE II                            15                             62
  STAGE III                            9                             68
  STAGE IVA                           37                            215
  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       4  21  13  26
  DEL PEAK 34(14Q11.2) WILD-TYPE    46 112  86 146
D63V4, multiclass
       clus
vv      DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  T0+T1                            4                             46
  T2                              21                            112
  T3                              13                             86
  T4                              26                            146
[1] 4 2
[1] TRUE
[1] "dimension of 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    28  10  22   0
  DEL PEAK 34(14Q11.2) WILD-TYPE 150  56 143   8
D63V5, multiclass
    clus
vv   DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  N0                           28                            150
  N1                           10                             56
  N2                           22                            143
  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"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q11.2) MUTATED    27   0
  DEL PEAK 34(14Q11.2) WILD-TYPE 156   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q11.2) MUTATED     27    0
  DEL PEAK 34(14Q11.2) WILD-TYPE  156    1
   clus
vv  DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  0                           27                            156
  1                            0                              1
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q11.2) MUTATED    15  58
  DEL PEAK 34(14Q11.2) WILD-TYPE 124 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q11.2) MUTATED     15   58
  DEL PEAK 34(14Q11.2) WILD-TYPE  124  319
        clus
vv       DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  FEMALE                           15                            124
  MALE                             58                            319
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(14Q11.2) MUTATED                                      70
  DEL PEAK 34(14Q11.2) WILD-TYPE                                   435
                                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                                                 70
  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                                                  435
  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  62
  DEL PEAK 34(14Q11.2) WILD-TYPE  70 373
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q11.2) MUTATED     11   62
  DEL PEAK 34(14Q11.2) WILD-TYPE   70  373
     clus
vv    DEL PEAK 34(14Q11.2) MUTATED DEL PEAK 34(14Q11.2) WILD-TYPE
  NO                            11                             70
  YES                           62                            373
[1] 2 2
[1] FALSE
D63V10, continuous
D63V11, continuous
D63V12, 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    61
  DEL PEAK 34(14Q11.2) WILD-TYPE                        35   380
D63V13, multiclass
                                  clus
vv                                 DEL PEAK 34(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      61
                                  clus
vv                                 DEL PEAK 34(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       380
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                                cls
clus                               0   1
  DEL PEAK 34(14Q11.2) MUTATED     0  63
  DEL PEAK 34(14Q11.2) WILD-TYPE  25 391
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(14Q11.2) MUTATED      0   63
  DEL PEAK 34(14Q11.2) WILD-TYPE   25  391
                        clus
vv                       DEL PEAK 34(14Q11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 34(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 25
  NOT HISPANIC OR LATINO                            391
[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    49  25
  DEL PEAK 35(14Q32.32) WILD-TYPE 264 175
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             74                             439 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                             25                             175 
$`DEL PEAK 35(14Q32.32) MUTATED`
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-6869 
        3.35         9.07        42.35        57.93        57.44        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 
       14.83         3.55        20.45        16.41        94.62         4.60 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-A6UM TCGA-CN-4728 TCGA-CN-4735 
       18.35        36.72        44.98        12.92        37.84        41.10 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A63U 
       14.20         6.74        12.95         3.68        35.01        17.29 
TCGA-CN-A63Y TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-6221 TCGA-CR-5247 TCGA-CR-5250 
        5.75        10.09         7.69        32.88        11.77        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-7398 TCGA-CR-7399 
       58.42        50.01        34.52        11.90         5.13         5.95 
TCGA-CV-5434 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6433 
      108.95        76.50        91.53        17.92         7.07        21.07 
TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6962 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7263 
        9.70        21.90         4.14        18.97        17.13        18.41 
TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A460 
       57.47        34.09       100.57       153.86        48.20        60.43 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5631 TCGA-DQ-7590 
       21.24        22.52        25.32         7.63        18.02        25.48 
TCGA-DQ-7593 TCGA-DQ-7596 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-8224 TCGA-HD-A6HZ 
       12.13        11.18        21.11         6.77        14.66         3.65 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A6T0 TCGA-T2-A6X0 TCGA-UF-A71D 
       15.42         7.13        16.08        19.00         7.10        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 
       42.02        44.65 

$`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 
       15.19         9.30        13.64        37.28        26.50        23.74 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6872 
       17.10        23.84        20.48        53.79        15.52        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 
        4.01         7.76        29.42        28.11        30.18        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       11.54         7.10         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 
       11.05        13.38        20.48         6.15         9.14         4.41 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       22.42        33.70        50.20        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO 
       71.05        20.52        25.71        10.55        27.19         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        26.27        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
       40.44        12.89        26.86        32.65        21.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       33.11        34.36         8.58        12.39        35.54         8.32 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       22.45        56.94        20.71        30.67        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.53        20.68        19.07         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
       11.08        10.45        20.09        24.16        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       11.74        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
        7.40        15.91        11.44         4.41        12.07         2.70 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        7.33         9.80         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        46.75        45.80        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       11.21         4.24        41.19        32.38        34.75        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       44.48        11.61        23.24        29.36        32.81        25.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        84.23        54.67        37.87 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 
       39.52        36.99        18.54        16.90         6.02        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.34        11.64         7.69        12.46        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        9.27        47.18        39.16        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        3.45         3.09        24.95        29.23         0.99        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
       29.85        29.52        30.58         7.10        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
       48.39       139.43        17.16       129.21        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
       17.95       107.51        94.88        80.12        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 
       86.83        48.59        60.49        43.23        54.74        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
        9.60        90.12         2.14         5.46        20.52         4.73 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
       26.43        11.24       126.08        19.79        12.03        42.38 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
        7.13         8.42        28.34         2.50        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      111.16        18.81        12.66         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        47.47        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       26.20        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7424 
        0.46        22.85        25.08        25.94         0.07        14.89 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       56.48       156.49        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       19.76         7.17        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       24.99       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       45.96         6.51        88.87        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN 
        7.07        15.25         5.98        35.34         6.38        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 
        6.48        22.03         3.62        23.47        19.92        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        34.36        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
        9.60        23.05         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
       24.95        17.72        12.36        15.88        14.30        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        35.54        30.94 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        14.04        18.90        20.45         9.83        12.10 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       10.65        37.18        16.11        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       19.23        18.94        12.62         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
       20.25        12.43        13.38        15.16        15.06        13.61 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
        0.07         0.16        25.74         1.22        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.85         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        12.76        14.50        19.33        11.84        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        1.84        12.62         3.68        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
       56.75        51.25        10.85        36.82        47.01        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       18.97         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        18.64        14.79        12.43         6.51         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       11.57        12.10         9.73         9.76         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87        15.91        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JA 
       13.68        43.59        54.67         2.83        43.36        62.27 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.16        49.22        21.86        16.11        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        22.36        32.65         2.96        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                           3.35                            0.07 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                         153.86                          210.97 
  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE 
                          18.69                           17.95 
[1] "3.4 - 153.9 (18.7)" "0.1 - 211.0 (17.9)"
[1] "hr=" "1.2"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 35(14Q32.32) MUTATED         0       12         9        31
  DEL PEAK 35(14Q32.32) WILD-TYPE      27       65        68       221
                                 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                              27
  STAGE II                             12                              65
  STAGE III                             9                              68
  STAGE IVA                            31                             221
  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       4  19  14  18
  DEL PEAK 35(14Q32.32) WILD-TYPE    46 114  85 154
D64V4, multiclass
       clus
vv      DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  T0+T1                             4                              46
  T2                               19                             114
  T3                               14                              85
  T4                               18                             154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 35(14Q32.32) MUTATED    20   8  20   2
  DEL PEAK 35(14Q32.32) WILD-TYPE 158  58 145   6
D64V5, multiclass
    clus
vv   DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  N0                            20                             158
  N1                             8                              58
  N2                            20                             145
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED    17   0
  DEL PEAK 35(14Q32.32) WILD-TYPE 166   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     17    0
  DEL PEAK 35(14Q32.32) WILD-TYPE  166    1
   clus
vv  DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  0                            17                             166
  1                             0                               1
[1] 2 2
[1] FALSE
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED    13  61
  DEL PEAK 35(14Q32.32) WILD-TYPE 126 316
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     13   61
  DEL PEAK 35(14Q32.32) WILD-TYPE  126  316
        clus
vv       DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  FEMALE                            13                             126
  MALE                              61                             316
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q32.32) MUTATED                                      72
  DEL PEAK 35(14Q32.32) WILD-TYPE                                   433
                                 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                                                  72
  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                                                   433
  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  59
  DEL PEAK 35(14Q32.32) WILD-TYPE  66 376
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED     15   59
  DEL PEAK 35(14Q32.32) WILD-TYPE   66  376
     clus
vv    DEL PEAK 35(14Q32.32) MUTATED DEL PEAK 35(14Q32.32) WILD-TYPE
  NO                             15                              66
  YES                            59                             376
[1] 2 2
[1] FALSE
D64V10, continuous
D64V11, continuous
D64V12, 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    63
  DEL PEAK 35(14Q32.32) WILD-TYPE                        35   378
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 35(14Q32.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       63
                                  clus
vv                                 DEL PEAK 35(14Q32.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                     35
  WHITE                                                        378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                                 cls
clus                                0   1
  DEL PEAK 35(14Q32.32) MUTATED     2  64
  DEL PEAK 35(14Q32.32) WILD-TYPE  23 390
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(14Q32.32) MUTATED      2   64
  DEL PEAK 35(14Q32.32) WILD-TYPE   23  390
                        clus
vv                       DEL PEAK 35(14Q32.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            64
                        clus
vv                       DEL PEAK 35(14Q32.32) WILD-TYPE
  HISPANIC OR LATINO                                  23
  NOT HISPANIC OR LATINO                             390
[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    70  51
  DEL PEAK 36(15Q15.1) WILD-TYPE 243 149
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                           121                            392 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                            51                            149 
$`DEL PEAK 36(15Q15.1) MUTATED`
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
       42.35        57.93        17.10        57.44        15.52        21.17 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DE TCGA-BA-A6DI 
        7.76        29.42        28.11        30.18        14.47        11.05 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       16.41        94.62         4.60        44.98        66.28        24.66 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 
       38.04        37.84        26.86        12.39         8.32         8.52 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 
       20.68        19.53         9.07        11.08        17.42        14.10 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY TCGA-CQ-5326 
       11.74        17.59        11.44        12.07        10.09         2.93 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 
       45.80        10.42        56.58         4.24        38.76        16.73 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-6474 
       64.11        44.48        11.61        25.81        84.23        18.54 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-7373 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5441 
        6.02        11.90        29.23        29.95        76.24        94.88 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6441 
       17.92        13.35        48.59        60.49        43.23         9.60 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
       20.52        26.43        42.38        65.82        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7242 
        4.14        18.81        12.92        21.80        77.16        36.00 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7414 
       31.36        18.97        47.97        36.13        35.54         0.46 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A460 
       14.89        84.49       153.86         6.38       180.16        60.43 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
        7.07         6.38        23.47        34.36         9.60        23.05 
TCGA-D6-6826 TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5631 TCGA-F7-A50I 
       11.44        14.30        11.11        58.45        18.02         3.02 
TCGA-F7-A61S TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-A76A TCGA-IQ-A61E TCGA-IQ-A61H 
       18.94        20.25        12.43         6.77        19.33        13.55 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-P3-A5QA TCGA-P3-A6T3 
       11.84        18.15        15.42         7.13        56.75        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6IG TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZA 
        2.04        29.00         7.30        12.43        11.57        12.10 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JA TCGA-UF-A7JD 
       12.72        15.91        43.59        54.67        62.27        24.16 
TCGA-UF-A7JO 
       20.75 

$`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 
        3.35        15.19         9.30        13.64        37.28         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6870 
       26.50        23.74        23.84        20.48        53.79        14.83 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        3.55        12.62         4.01        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
        7.10         5.69         7.82         2.27        13.38        20.48 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        6.15         9.14         4.41        18.35        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU 
       33.70        50.20        38.40        71.05        20.52        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 
       26.27        23.70         4.67        40.44        12.89        32.65 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       21.11        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       35.54        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 
       22.45        56.94        20.71        30.67        20.65        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
       19.07        14.20         6.74         9.24        36.49        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 
       20.09        12.95        24.16         3.68        35.01        14.56 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       12.85        29.72        21.21         7.40        17.29        15.91 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
        5.75         4.41         2.70         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
        6.18        48.20        39.68        21.50        54.58        46.75 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 
       45.99        11.21         4.24        41.19        32.38        32.88 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       34.75        13.25        14.99        70.13        51.29        33.11 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.04        41.88        28.83        23.24        29.36        32.81 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       14.14        12.46        31.23        11.77        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       16.90        10.22        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       11.51        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
       40.93        35.84         3.45         3.09        24.95         0.99 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       32.78        47.01        27.06        12.89        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.95        35.41        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
      108.95        19.20        17.95       107.51        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
       80.12        23.05        86.83         7.07        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 
       62.43        90.12         2.14         9.70         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
       21.90        11.24       126.08        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 
       30.08         6.08        53.95        10.98         7.13         8.42 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       126.15       111.16        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        5.26         1.84        52.31        71.21        10.75       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
        4.73        47.47        26.20        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
       11.87         2.10        18.41        57.47        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67        22.85        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
       34.09       100.57        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O 
       16.27        19.76         7.17        16.64        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       24.99       169.38       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
        6.51        88.87        48.20        67.86         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       15.25         5.98        35.34        29.79         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
        3.62        21.24        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 
       10.55        18.84        13.25        25.41         2.53        16.14 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       18.67        24.95        25.32        17.72        12.36        15.88 
TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 
        7.63        13.94        12.10        12.79        35.54        30.94 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       33.86        14.04        18.90        25.48        20.45         9.83 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       12.13        12.10        10.65        11.18        37.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       21.63        20.25        19.23        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       11.80        13.38        15.16        15.06        13.61        21.11 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        6.90        34.75        15.95        12.76        14.50        11.84 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 
        0.07        14.47         5.29        11.54        13.35        12.43 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       10.75        14.37         7.96        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE 
        3.68        16.08        17.98        29.92        15.78        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 
       10.85        36.82        47.01        19.00        75.55        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       16.01        13.15        21.07        11.74        17.65        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        12.72        18.64        14.79         6.51         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        9.73         9.76         8.32        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71B 
       32.45        13.55        13.25        13.68         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH 
       41.16        42.02        44.65        17.95        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       16.11        13.94        22.36        32.65         2.96        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 
       20.55        14.56 

  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                          0.46                           0.07 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE 
                        18.970                         17.785 
[1] "0.5 - 180.2 (19.0)" "0.1 - 211.0 (17.8)"
[1] "hr=" "1"  
D65V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 36(15Q15.1) MUTATED         3       23        16        57         3
  DEL PEAK 36(15Q15.1) WILD-TYPE      24       54        61       195         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                             24
  STAGE II                            23                             54
  STAGE III                           16                             61
  STAGE IVA                           57                            195
  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  25  38
  DEL PEAK 36(15Q15.1) WILD-TYPE    44  98  74 134
D65V4, multiclass
       clus
vv      DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  T0+T1                            6                             44
  T2                              35                             98
  T3                              25                             74
  T4                              38                            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 36(15Q15.1) MUTATED    37  14  40   3
  DEL PEAK 36(15Q15.1) WILD-TYPE 141  52 125   5
D65V5, multiclass
    clus
vv   DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  N0                           37                            141
  N1                           14                             52
  N2                           40                            125
  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"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q15.1) MUTATED    34   0
  DEL PEAK 36(15Q15.1) WILD-TYPE 149   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q15.1) MUTATED     34    0
  DEL PEAK 36(15Q15.1) WILD-TYPE  149    1
   clus
vv  DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  0                           34                            149
  1                            0                              1
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q15.1) MUTATED    29  92
  DEL PEAK 36(15Q15.1) WILD-TYPE 110 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q15.1) MUTATED     29   92
  DEL PEAK 36(15Q15.1) WILD-TYPE  110  285
        clus
vv       DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  FEMALE                           29                            110
  MALE                             92                            285
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(15Q15.1) MUTATED                                     120
  DEL PEAK 36(15Q15.1) WILD-TYPE                                   385
                                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                                                120
  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                                                  385
  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    23  98
  DEL PEAK 36(15Q15.1) WILD-TYPE  58 337
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q15.1) MUTATED     23   98
  DEL PEAK 36(15Q15.1) WILD-TYPE   58  337
     clus
vv    DEL PEAK 36(15Q15.1) MUTATED DEL PEAK 36(15Q15.1) WILD-TYPE
  NO                            23                             58
  YES                           98                            337
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, continuous
D65V12, 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                          11   103
  DEL PEAK 36(15Q15.1) WILD-TYPE                        34   338
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 36(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     103
                                  clus
vv                                 DEL PEAK 36(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       338
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q15.1) MUTATED     9 101
  DEL PEAK 36(15Q15.1) WILD-TYPE  16 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q15.1) MUTATED      9  101
  DEL PEAK 36(15Q15.1) WILD-TYPE   16  353
                        clus
vv                       DEL PEAK 36(15Q15.1) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       DEL PEAK 36(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            353
[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    60  34
  DEL PEAK 37(16Q23.1) WILD-TYPE 253 166
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            94                            419 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            34                            166 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-A4IH TCGA-BB-4225 
       13.64         9.07        57.93        57.44        20.45         4.60 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 
        4.41        22.42        36.72        44.98        66.28        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4729 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 
       20.52        10.55        12.89        34.36        35.54         8.32 
TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6996 TCGA-CN-A497 
       56.94        20.68         6.74         9.07        17.42        35.01 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CQ-6224 
       17.59        12.85         7.40        17.29        10.09        56.58 
TCGA-CQ-A4C7 TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6481 
       11.61        84.23        58.42        34.52        36.99        10.22 
TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7398 TCGA-CR-7402 
       11.64        40.93         3.45         0.99         5.13        29.95 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6940 
       94.88        91.53        80.12        17.92         7.07        26.43 
TCGA-CV-6941 TCGA-CV-6962 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7250 TCGA-CV-7261 
       11.24         4.14        77.16         4.73        95.34        36.13 
TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 
       35.54         0.46        25.94        14.89        54.94         3.52 
TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A6JN TCGA-CX-7082 
       84.49         6.38        45.96        60.43        29.79        10.42 
TCGA-CX-7086 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-7588 TCGA-DQ-7589 
       18.84        18.67        17.72         7.63        14.04        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50I TCGA-F7-A622 TCGA-HD-8224 
       25.48        20.45         9.83         3.02        11.80        14.66 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-P3-A5QE 
       19.33        13.55         0.07        12.43         7.13        51.25 
TCGA-P3-A6SW TCGA-QK-A6IF TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-TN-A7HJ TCGA-UF-A719 
       36.82        17.65        12.10        12.72        13.25        54.67 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UP-A6WW 
        2.83        42.02        44.65        17.03 

$`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 
        3.35        15.19         9.30        37.28        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
       42.35        17.10        23.84        20.48        53.79        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       21.17        14.83         3.55        12.62         4.01         7.76 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        28.11        30.18        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 
       20.48        16.41         6.15        94.62         9.14        18.35 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HZ 
       33.70        50.20        24.66        38.40        25.71        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       12.92         8.81         6.28        12.69        26.27        23.70 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        40.44        37.84        26.86        32.65 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       21.11        41.10        12.99        20.55        14.33        43.73 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       27.58        41.69        13.05        33.11         8.58        12.39 
TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       16.21        11.54        11.84        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       22.45        20.71        30.67        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       19.07        14.20         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 
       20.09        12.95        24.16         3.68        14.10        11.74 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       14.56        29.72        21.21        15.91        11.44         5.75 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
        4.41        12.07         2.70         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        6.18        48.20        39.68        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       46.75        45.80        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
       41.19        32.38        32.88        34.75        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
       14.99        38.76        70.13        51.29        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       43.04        41.88        28.83        64.11        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        32.81        25.81        14.14        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
       11.77        54.67        37.87        26.27        50.01        39.52 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 
       18.54        16.90         6.02        11.90        11.34         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        11.51        15.75         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       47.34        35.84         3.09        24.95        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
        9.17        34.06        19.92        26.17        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       29.85        29.52        30.58         7.10         5.95        35.41 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       48.39       139.43        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5970 TCGA-CV-5971 
       19.20        17.95       107.51        76.50        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       86.83        48.59        60.49        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       62.43         9.60        90.12         2.14         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       20.52         4.73        21.90       126.08        19.79        12.03 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       42.38        15.09        30.08         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 
       10.98         7.13         8.42        28.34         2.50        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      126.15       111.16        18.81        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        5.26         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       10.75       130.88        47.47        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        17.13         4.96        11.87        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        17.85       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 
       22.85        25.08         0.07        34.09       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
      156.49        16.27        19.76         7.17       153.86        16.64 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        24.99       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
       35.47         1.05         6.51        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        6.38         6.48        22.03         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 
       19.92        22.52        10.42        10.55        34.36        13.25 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       25.41         9.60        23.05         2.53        16.14        11.44 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
       24.95        25.32        12.36        15.88        14.30        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       12.10        12.79        11.11        58.45        35.54        30.94 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       33.86        18.02        12.13        12.10        10.65        11.18 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
       37.18        16.11        21.63        20.25        19.23        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       12.62         0.46        17.85        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11         6.77         0.07 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
        0.16        25.74         1.22        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
        0.36        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61K 
       15.95        12.76        14.50        11.84        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W 
       11.54        11.84        13.35        18.15        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
        7.96        30.05         1.84        12.62         3.68        15.42 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
       16.08        17.98        29.92        15.78        56.75        10.85 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG 
       12.99        16.01        13.15        21.07        11.74         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       16.70         9.34        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        6.51         5.62        11.57         9.73         9.76         8.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       16.96         6.87        15.91         7.10        32.45        13.55 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC 
       13.68        43.59        43.36        41.16        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.16        49.22        21.86        16.11        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        20.55        14.56 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                         95.34                         210.97 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                         17.82                          18.15 
[1] "0.1 - 95.3 (17.8)"  "0.1 - 211.0 (18.1)"
[1] "hr=" "1.1"
D66V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 37(16Q23.1) MUTATED         2       10        15        41         4
  DEL PEAK 37(16Q23.1) WILD-TYPE      25       67        62       211         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                             25
  STAGE II                            10                             67
  STAGE III                           15                             62
  STAGE IVA                           41                            211
  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       6  22  19  26
  DEL PEAK 37(16Q23.1) WILD-TYPE    44 111  80 146
D66V4, multiclass
       clus
vv      DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  T0+T1                            6                             44
  T2                              22                            111
  T3                              19                             80
  T4                              26                            146
[1] 4 2
[1] TRUE
[1] "dimension of 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  15  28   3
  DEL PEAK 37(16Q23.1) WILD-TYPE 157  51 137   5
D66V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  N0                           21                            157
  N1                           15                             51
  N2                           28                            137
  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"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    24   0
  DEL PEAK 37(16Q23.1) WILD-TYPE 159   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     24    0
  DEL PEAK 37(16Q23.1) WILD-TYPE  159    1
   clus
vv  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  0                           24                            159
  1                            0                              1
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    20  75
  DEL PEAK 37(16Q23.1) WILD-TYPE 119 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     20   75
  DEL PEAK 37(16Q23.1) WILD-TYPE  119  302
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  FEMALE                           20                            119
  MALE                             75                            302
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                                      91
  DEL PEAK 37(16Q23.1) WILD-TYPE                                   414
                                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                                                 91
  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                                                  414
  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  82
  DEL PEAK 37(16Q23.1) WILD-TYPE  68 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     13   82
  DEL PEAK 37(16Q23.1) WILD-TYPE   68  353
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  NO                            13                             68
  YES                           82                            353
[1] 2 2
[1] FALSE
D66V10, continuous
D66V11, continuous
D66V12, 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    80
  DEL PEAK 37(16Q23.1) WILD-TYPE                        35   361
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 37(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      80
                                  clus
vv                                 DEL PEAK 37(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED     4  86
  DEL PEAK 37(16Q23.1) WILD-TYPE  21 368
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      4   86
  DEL PEAK 37(16Q23.1) WILD-TYPE   21  368
                        clus
vv                       DEL PEAK 37(16Q23.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK 37(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            368
[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    67  35
  DEL PEAK 38(16Q23.3) WILD-TYPE 246 165
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                           102                            411 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                            35                            165 
$`DEL PEAK 38(16Q23.3) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-A4IH 
       13.64         9.07        23.74        57.93        57.44        20.45 
TCGA-BA-A6DA TCGA-BA-A6DF TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 
       11.54         7.82         4.60        22.42        36.72        44.98 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4729 TCGA-CN-5356 
       66.28        71.05        20.52        10.55        12.89        34.36 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6996 
       35.54         8.32        56.94        20.68         9.07        17.42 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY 
       35.01        17.59        12.85         7.40        17.29        10.09 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CR-5243 
       39.68        54.58        41.19        56.58        11.61        84.23 
TCGA-CR-6467 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 
       58.42        34.52        36.99        10.22        11.64        40.93 
TCGA-CR-7370 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5441 
        3.45         5.13        29.95       139.43       129.21        94.88 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6940 TCGA-CV-6941 
       91.53        80.12        17.92         7.07        26.43        11.24 
TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7261 
        4.14        18.81        12.66        77.16         4.73        36.13 
TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 
       35.54         0.46        25.94        14.89        54.94         3.52 
TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W TCGA-CV-A460 TCGA-CX-7082 TCGA-CX-7086 
       84.49         6.38        45.96        60.43        10.42        18.84 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
       18.67        17.72         7.63        14.04        18.90        25.48 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50I TCGA-F7-A622 TCGA-HD-8224 TCGA-IQ-A61E 
       20.45         9.83         3.02        11.80        14.66        19.33 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5QE 
       13.55         0.07        12.43         7.13        17.98        51.25 
TCGA-P3-A6SW TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO 
       36.82        13.15        17.65        11.57        12.10        12.72 
TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UP-A6WW 
       13.25        54.67         2.83        42.02        44.65        17.03 

$`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 
        3.35        15.19         9.30        37.28        26.50        42.35 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       17.10        23.84        20.48        53.79        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       14.83         3.55        12.62         4.01         7.76        29.42 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       28.11        30.18        27.95         7.10         5.69        14.47 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        2.27        11.05        13.38        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 
       94.62         9.14         4.41        18.35        33.70        50.20 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        38.40        25.71        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        26.27        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       40.44        37.84        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 
       13.05        33.11         8.58        12.39        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       11.84        11.57        12.49         8.52        22.45        20.71 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        6.74         9.24        36.49        11.08        10.45        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
       12.95        24.16         3.68        14.10        11.74        14.56 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.07         2.70         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       48.20        21.50         2.93        46.75        45.80        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
       10.42        11.21         4.24        32.38        32.88        34.75 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       13.25         4.24        14.99        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       33.11        16.73        43.04        41.88        28.83        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        32.81        25.81        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       12.46        31.23        11.77        54.67        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       50.01        39.52        18.54        16.90         6.02        11.90 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34         7.69        12.46        11.51        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
       47.18        39.16        47.34        35.84         3.09        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       29.23         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       26.17        17.13        32.78        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 
        7.10         5.95        35.41        48.39        17.16       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5970 
       76.24        19.20        17.95       107.51        76.50        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
       23.05        86.83        48.59        60.49        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       21.07        62.43         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 
        5.46        20.52         4.73        21.90       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       12.03        42.38        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       65.82        10.98         7.13         8.42        28.34         2.50 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
       64.83       126.15       111.16         7.99         9.01         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 
        1.84        52.31        12.92        21.80        71.21        10.75 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
      130.88        47.47        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       17.13        95.34         4.96        11.87        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        17.85       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 
       22.85        25.08         0.07        34.09       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
      156.49        16.27        19.76         7.17       153.86        16.64 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        24.99       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
       35.47         1.05         6.51        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        0.76        56.61         7.07        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        6.38        29.79         6.48        22.03         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 
       23.47        19.92        22.52        10.42        10.55        34.36 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
       11.44        24.95        25.32        12.36        15.88        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        11.11        58.45        35.54 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       30.94        33.86        18.02        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
       11.18        37.18        16.11        21.63        20.25        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       18.94        12.62         0.46        17.85        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
        0.07         0.16        25.74         1.22        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.85         0.36        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J 
       34.75        15.95        12.76        14.50        11.84        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 
        5.29        11.54        11.84        13.35        18.15        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         3.68 
TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
       15.42        16.08        29.92        15.78        56.75        10.85 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH 
       12.99        16.01        21.07        11.74         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        18.64        14.79        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62         9.73         9.76         8.32        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
       15.91         7.10        32.45        13.55        13.68        43.59 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       43.36        41.16        62.27        17.95        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        20.55        14.56 

  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                        139.43                         210.97 
  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE 
                        18.325                         18.020 
[1] "0.1 - 139.4 (18.3)" "0.1 - 211.0 (18.0)"
[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        16        47         4
  DEL PEAK 38(16Q23.3) WILD-TYPE      25       65        61       205         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                             25
  STAGE II                            12                             65
  STAGE III                           16                             61
  STAGE IVA                           47                            205
  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       6  23  24  29
  DEL PEAK 38(16Q23.3) WILD-TYPE    44 110  75 143
D67V4, multiclass
       clus
vv      DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  T0+T1                            6                             44
  T2                              23                            110
  T3                              24                             75
  T4                              29                            143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 38(16Q23.3) MUTATED    23  14  34   3
  DEL PEAK 38(16Q23.3) WILD-TYPE 155  52 131   5
D67V5, multiclass
    clus
vv   DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  N0                           23                            155
  N1                           14                             52
  N2                           34                            131
  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"
D67V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.3) MUTATED    27   0
  DEL PEAK 38(16Q23.3) WILD-TYPE 156   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.3) MUTATED     27    0
  DEL PEAK 38(16Q23.3) WILD-TYPE  156    1
   clus
vv  DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  0                           27                            156
  1                            0                              1
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.3) MUTATED    24  78
  DEL PEAK 38(16Q23.3) WILD-TYPE 115 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.3) MUTATED     24   78
  DEL PEAK 38(16Q23.3) WILD-TYPE  115  299
        clus
vv       DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  FEMALE                           24                            115
  MALE                             78                            299
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16Q23.3) MUTATED                                      98
  DEL PEAK 38(16Q23.3) WILD-TYPE                                   407
                                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                                                 98
  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                                                  407
  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  86
  DEL PEAK 38(16Q23.3) WILD-TYPE  65 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.3) MUTATED     16   86
  DEL PEAK 38(16Q23.3) WILD-TYPE   65  349
     clus
vv    DEL PEAK 38(16Q23.3) MUTATED DEL PEAK 38(16Q23.3) WILD-TYPE
  NO                            16                             65
  YES                           86                            349
[1] 2 2
[1] FALSE
D67V10, continuous
D67V11, continuous
D67V12, 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    85
  DEL PEAK 38(16Q23.3) WILD-TYPE                        35   356
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 38(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      85
                                  clus
vv                                 DEL PEAK 38(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.3) MUTATED     6  91
  DEL PEAK 38(16Q23.3) WILD-TYPE  19 363
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.3) MUTATED      6   91
  DEL PEAK 38(16Q23.3) WILD-TYPE   19  363
                        clus
vv                       DEL PEAK 38(16Q23.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       DEL PEAK 38(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            363
[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    56  40
  DEL PEAK 39(17P11.2) WILD-TYPE 257 160
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            96                            417 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            40                            160 
$`DEL PEAK 39(17P11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
        9.30        26.50        20.48        57.44        15.52        14.83 
TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP 
        3.55        20.45        30.18        27.95        14.47        16.41 
TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HU 
       94.62        36.72        44.98        24.66        20.52        25.71 
TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6988 TCGA-CN-A63W 
       38.04        26.86        43.73        56.94        10.45        11.44 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-A4C7 
       32.38        32.88        13.25        14.99        16.73        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 
       23.24        31.23        34.52        11.64        12.46        47.18 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5439 TCGA-CV-5444 
       35.84         3.09        29.82         5.13        17.95        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6948 TCGA-CV-6961 
       17.92        13.35         9.60        20.52        42.38         2.50 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7406 
        1.84        10.75        26.20        47.97        18.41        57.47 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-A45W 
        0.07       100.57        14.89        54.94       153.86        45.96 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JU TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6826 
       60.43         7.07         3.62        18.84        34.36        11.44 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-F7-A620 
       25.32         7.63        14.04        20.45        10.65        17.85 
TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-8635 TCGA-IQ-7630 TCGA-IQ-A61G 
       20.25        21.11         0.16        22.85        15.95        11.84 
TCGA-IQ-A61H TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-P3-A5Q6 TCGA-P3-A5QA 
       13.55         1.84         3.68        15.42        15.78        56.75 
TCGA-P3-A6SX TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6VC TCGA-QK-A8Z7 
       47.01        16.01        13.15        21.07        12.43         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-T2-A6WZ TCGA-UF-A7JH 
        5.62        11.57        12.10         9.73        15.91        21.86 

$`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 
        3.35        15.19        13.64        37.28         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 
       42.35        57.93        17.10        23.84        53.79        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DA 
       12.62         4.01         7.76        29.42        28.11        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        7.10         5.69         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       20.48         6.15         9.14         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
       22.42        33.70        50.20        66.28        38.40        71.05 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       10.55        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       26.27        23.70         4.67        40.44        37.84        12.89 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.65        21.11        41.10        12.99        20.55        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        41.69        13.05        33.11        34.36         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        35.54         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
       11.57        12.49         8.52        22.45        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       20.68        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 
        6.74         9.07         9.24        36.49        11.08        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       12.95        24.16         3.68        17.42        14.10        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        17.29        15.91         5.75         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 
        2.70        10.09         7.33         9.80         7.69         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       48.20        39.68        21.50         2.93        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       45.80        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
       34.75        56.58         4.24        38.76        70.13        51.29 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       33.11        43.04        41.88        28.83        64.11        44.48 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        32.81        25.81        14.14        12.46        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        36.99        18.54        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       10.22        11.34         7.69        11.51        15.75         9.27 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
       39.16        47.34        40.93         3.45        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
        0.99        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       17.13        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
       31.10        29.85        29.52        30.58         7.10         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
       35.41        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
       91.53        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 
       43.23        54.74        21.07        62.43        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        9.70         5.46         4.73        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      126.08        19.79        12.03        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 
       53.95        65.82        10.98         7.13         8.42        28.34 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        4.14        64.83       126.15       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        7.99         9.01         5.26        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       71.21       130.88        77.16         4.73        47.47        36.00 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       31.36        18.97        17.13        95.34         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
        2.10        36.13        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 
        9.67         0.46        22.85        25.08        25.94        34.09 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       56.48       156.49         3.52        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17        16.64         6.38        22.19        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X 
      169.38       180.16       159.65        35.47         1.05         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       88.87        48.20        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        22.03 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
       21.24        23.47        19.92        22.52        10.42        10.42 
TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       10.55        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       16.14        18.67        24.95        17.72        12.36        15.88 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       14.30        13.94        12.10        12.79        11.11        58.45 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 
       35.54        30.94        33.86        18.02        18.90        25.48 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
        9.83        12.13        12.10        11.18        37.18        16.11 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
        0.46        11.80        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
       13.61         6.77         0.07        25.74         1.22        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       22.03        12.66         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I 
        6.90        34.75        12.76        14.50        19.33         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
       14.47         5.29        11.54        11.84        13.35        18.15 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
       12.43        10.75        14.37         7.96        30.05        12.62 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF 
        7.13        16.08        17.98        29.92        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       12.99        11.74        17.65         7.30        16.70         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       12.72        18.64        14.79         9.76         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       16.96         6.87         7.10        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D 
       13.68        43.59        54.67         2.83        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       42.02        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        13.94        20.75        22.36        32.65         2.96 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                        17.935                         18.150 
[1] "0.1 - 153.9 (17.9)" "0.1 - 211.0 (18.1)"
[1] "hr=" "1.2"
D68V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 39(17P11.2) MUTATED         3       20        16        43         3
  DEL PEAK 39(17P11.2) WILD-TYPE      24       57        61       209         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                             24
  STAGE II                            20                             57
  STAGE III                           16                             61
  STAGE IVA                           43                            209
  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  20  30
  DEL PEAK 39(17P11.2) WILD-TYPE    41 105  79 142
D68V4, multiclass
       clus
vv      DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  T0+T1                            9                             41
  T2                              28                            105
  T3                              20                             79
  T4                              30                            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 39(17P11.2) MUTATED    29  17  32   2
  DEL PEAK 39(17P11.2) WILD-TYPE 149  49 133   6
D68V5, multiclass
    clus
vv   DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  N0                           29                            149
  N1                           17                             49
  N2                           32                            133
  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"
D68V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P11.2) MUTATED    33   1
  DEL PEAK 39(17P11.2) WILD-TYPE 150   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED     33    1
  DEL PEAK 39(17P11.2) WILD-TYPE  150    0
   clus
vv  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  0                           33                            150
  1                            1                              0
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P11.2) MUTATED    24  73
  DEL PEAK 39(17P11.2) WILD-TYPE 115 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED     24   73
  DEL PEAK 39(17P11.2) WILD-TYPE  115  304
        clus
vv       DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  FEMALE                           24                            115
  MALE                             73                            304
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(17P11.2) MUTATED                                      94
  DEL PEAK 39(17P11.2) WILD-TYPE                                   411
                                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                                                 94
  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                                                  411
  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  87
  DEL PEAK 39(17P11.2) WILD-TYPE  71 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED     10   87
  DEL PEAK 39(17P11.2) WILD-TYPE   71  348
     clus
vv    DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  NO                            10                             71
  YES                           87                            348
[1] 2 2
[1] FALSE
D68V10, continuous
D68V11, continuous
D68V12, 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                          18    74
  DEL PEAK 39(17P11.2) WILD-TYPE                        27   367
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 39(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                      74
                                  clus
vv                                 DEL PEAK 39(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P11.2) MUTATED     8  82
  DEL PEAK 39(17P11.2) WILD-TYPE  17 372
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED      8   82
  DEL PEAK 39(17P11.2) WILD-TYPE   17  372
                        clus
vv                       DEL PEAK 39(17P11.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           82
                        clus
vv                       DEL PEAK 39(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            372
[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    47  23
  DEL PEAK 40(17Q25.3) WILD-TYPE 266 177
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            70                            443 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                            23                            177 
$`DEL PEAK 40(17Q25.3) MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4II TCGA-BA-A8YP 
        9.30        15.52        14.83         3.55        30.18        16.41 
TCGA-BB-4223 TCGA-BB-4227 TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6011 
       94.62         4.41        23.70        43.73        56.94        30.67 
TCGA-CN-6992 TCGA-CN-A63Y TCGA-CN-A6V6 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 
       12.95         5.75         7.69        10.42        32.88        56.58 
TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6471 TCGA-CR-6474 
       16.73        23.24        54.67        37.87        39.52        18.54 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7404 TCGA-CV-5430 
       10.22        11.64         0.99        32.78        48.39       139.43 
TCGA-CV-5966 TCGA-CV-6948 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
       17.92        42.38         4.14       111.16        18.81         5.26 
TCGA-CV-7248 TCGA-CV-7409 TCGA-D6-6826 TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7588 
       17.13        17.85        11.44        11.11        18.02        14.04 
TCGA-DQ-7594 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7754 TCGA-HD-8224 
       12.10        20.25         3.02        20.25        25.74        14.66 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T 
        3.65        15.95        11.84        13.55        11.84        18.15 
TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA 
       12.43         3.68        15.42        16.08        17.98        56.75 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       51.25        10.85        47.01        12.72        11.57        12.10 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UP-A6WW 
       16.96        15.91        54.67        17.03 

$`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 
        3.35        15.19        13.64        37.28         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
       23.74        42.35        57.93        17.10        23.84        20.48 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       53.79        57.44        21.17        12.62         4.01         7.76 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       29.42        28.11        20.45        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
       20.48         6.15         9.14         4.60        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
       36.72        33.70        50.20        44.98        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       38.40        71.05        20.52        25.71        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        26.27        38.04 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        4.67        40.44        37.84        12.89        26.86        32.65 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
       21.11        41.10        12.99        20.55        14.33        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       41.69        13.05        33.11        34.36         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       35.54         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 
       12.49         8.52        22.45        20.71        20.68        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
       19.53        20.68        19.07        14.20         6.74         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
        9.24        36.49        11.08        10.45        20.09        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        3.68        17.42        14.10        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       17.59        12.85        29.72        21.21         7.40        17.29 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       15.91        11.44         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
        7.33         9.80         6.18        48.20        39.68        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        2.93        54.58        46.75        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
        4.24        41.19        32.38        34.75        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
       14.99        38.76        70.13        51.29        33.11        43.04 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB 
       41.88        28.83        64.11        44.48        11.61        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       32.81        25.81        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 
       11.77        26.27        58.42        50.01        34.52        36.99 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       16.90         6.02        11.90        11.34         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       11.51        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       47.01        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       29.85        29.52        30.58         7.10         5.13         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       35.41        29.95        17.16       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       19.20        17.95       107.51        94.88        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       80.12        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        7.07        43.23        54.74        21.07        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
       90.12         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
       21.90        26.43        11.24       126.08        19.79        12.03 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       15.09        30.08         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
        7.13         8.42        28.34         2.50        64.83       126.15 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       12.66         7.99         9.01         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       21.80        71.21        10.75       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 
       47.47        36.00        31.36        26.20        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
       57.47        35.54       210.97        89.33         9.67         0.46 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
       22.85        25.08        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       14.89        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
       84.49        19.76         7.17       153.86        16.64         6.38 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
       22.19        27.98        24.99       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
       35.47         1.05        45.96         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       60.43        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        22.03 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        34.36        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
        9.60        23.05         2.53        16.14        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
       25.32        17.72        12.36        15.88         7.63        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
       13.94        12.10        12.79        58.45        35.54        30.94 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
       33.86        18.90        25.48        20.45         9.83        12.13 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J 
       10.65        11.18        37.18        16.11        21.63        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        12.62         0.46        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
        0.07         0.16         1.22        22.03        12.66        22.85 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
        0.36        13.84         4.27         6.90        34.75        12.76 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        19.33         0.07        14.47         5.29        11.54 
TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       13.35        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-P3-A6T0 
       12.62         7.13        29.92        15.78        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       75.55        18.97         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        11.74        17.65         7.30        16.70 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        9.34        18.64        14.79        12.43         6.51         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X0 
        9.73         9.76         8.32        12.72         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
       32.45        13.55        13.25        13.68        43.59         2.83 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       43.36        41.16        42.02        44.65        62.27        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.16        49.22        21.86        16.11        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        32.65         2.96        20.55        14.56 

  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                          0.99                           0.07 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                        139.43                         210.97 
  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE 
                         16.57                          18.97 
[1] "1.0 - 139.4 (16.6)" "0.1 - 211.0 (19.0)"
[1] "hr=" "1.1"
D69V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 40(17Q25.3) MUTATED         3        9         8        33         3
  DEL PEAK 40(17Q25.3) WILD-TYPE      24       68        69       219         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                             24
  STAGE II                             9                             68
  STAGE III                            8                             69
  STAGE IVA                           33                            219
  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  25   7  20
  DEL PEAK 40(17Q25.3) WILD-TYPE    44 108  92 152
D69V4, multiclass
       clus
vv      DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  T0+T1                            6                             44
  T2                              25                            108
  T3                               7                             92
  T4                              20                            152
[1] 4 2
[1] TRUE
[1] "dimension of 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    17   8  24   3
  DEL PEAK 40(17Q25.3) WILD-TYPE 161  58 141   5
D69V5, multiclass
    clus
vv   DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  N0                           17                            161
  N1                            8                             58
  N2                           24                            141
  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"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q25.3) MUTATED    22   0
  DEL PEAK 40(17Q25.3) WILD-TYPE 161   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q25.3) MUTATED     22    0
  DEL PEAK 40(17Q25.3) WILD-TYPE  161    1
   clus
vv  DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  0                           22                            161
  1                            0                              1
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q25.3) MUTATED    15  56
  DEL PEAK 40(17Q25.3) WILD-TYPE 124 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q25.3) MUTATED     15   56
  DEL PEAK 40(17Q25.3) WILD-TYPE  124  321
        clus
vv       DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  FEMALE                           15                            124
  MALE                             56                            321
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17Q25.3) MUTATED                                      69
  DEL PEAK 40(17Q25.3) WILD-TYPE                                   436
                                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                                                 69
  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                                                  436
  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  57
  DEL PEAK 40(17Q25.3) WILD-TYPE  67 378
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q25.3) MUTATED     14   57
  DEL PEAK 40(17Q25.3) WILD-TYPE   67  378
     clus
vv    DEL PEAK 40(17Q25.3) MUTATED DEL PEAK 40(17Q25.3) WILD-TYPE
  NO                            14                             67
  YES                           57                            378
[1] 2 2
[1] FALSE
D69V10, continuous
D69V11, continuous
D69V12, 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    58
  DEL PEAK 40(17Q25.3) WILD-TYPE                        37   383
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 40(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      58
                                  clus
vv                                 DEL PEAK 40(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       383
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q25.3) MUTATED     8  57
  DEL PEAK 40(17Q25.3) WILD-TYPE  17 397
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q25.3) MUTATED      8   57
  DEL PEAK 40(17Q25.3) WILD-TYPE   17  397
                        clus
vv                       DEL PEAK 40(17Q25.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 40(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            397
[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   154 109
  DEL PEAK 41(18Q21.2) WILD-TYPE 159  91
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           263                            250 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           109                             91 
$`DEL PEAK 41(18Q21.2) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5557 
        3.35        15.19         9.30        13.64        42.35        20.48 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
       53.79        15.52        14.83         3.55        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD 
        7.76        29.42        30.18        27.95         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7862 
       14.47        11.05        20.48         6.15         9.14        36.72 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A6UO 
       66.28        24.66        38.40        20.52        10.55         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
        6.28        12.69        23.70        38.04         4.67        40.44 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
       37.84        26.86        41.10        20.55        43.73        27.58 
TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
       33.11         8.32        16.21        11.84        11.57         8.52 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
       22.45        20.71        30.67        20.68        19.07        14.20 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
        6.74         9.24        11.08        10.45        12.95        24.16 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A63T 
        3.68        17.42        11.74        35.01        17.59         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5326 
       17.29        11.44         4.41        12.07        21.50         2.93 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       10.42        41.19        32.38        34.75        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        51.29        33.11        16.73 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CI 
       64.11        44.48        11.61        29.36        14.14        31.23 
TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
       11.77        18.54        11.90        11.64        12.46        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
       15.75         9.27        39.16         3.45        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7399 
        0.99         9.17        34.06        17.13        47.01         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       35.41        29.95       129.21        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 
      107.51        94.88        80.12        17.92        13.35        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 
       48.59        60.49        43.23        54.74         9.60        90.12 
TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 
        9.70        20.52        26.43       126.08        12.03        42.38 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       53.95        65.82         7.13        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
       64.83       126.15       111.16        18.81        12.66         5.26 
TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 
       12.92        10.75        77.16         4.73        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7255 
       26.20        18.97        17.13        95.34        11.87         2.10 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7423 
       18.41        35.54        17.85        22.85        25.94       100.57 
TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
       14.89         3.52        16.27        84.49        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X 
      153.86         6.38        22.19        35.47        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT 
       88.87        67.86         7.07         6.38        29.79        22.03 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        3.62        23.47        22.52        18.84        34.36        25.41 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EO 
       23.05        16.14        24.95        25.32        17.72        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
       13.94        12.10        11.11        58.45        30.94        33.86 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 
       14.04        18.90         9.83        10.65        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
       20.25         3.02         0.46        17.85        20.25        15.16 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 
       15.06        13.61        21.11         0.07         0.16         1.22 
TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G 
       14.66        22.85         3.65        15.95        19.33        11.84 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
       13.55        11.54        11.84        13.35        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 
        7.96         1.84        15.42        15.78        56.75        19.00 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        2.04        29.00        16.01        13.15        21.07        11.74 
TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       16.70         5.62        11.57        12.10         9.73         9.76 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71B 
        8.32        12.72        15.91        13.25        54.67        43.36 
TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       41.16        44.65        62.27        17.95        24.16        49.22 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 
       13.94        20.75        22.36        32.65        14.56 

$`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 
       37.28         9.07        26.50        23.74        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DA 
       23.84        57.44        21.17        28.11        20.45        11.54 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 
        7.82         2.27        13.38        16.41        94.62         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.35        22.42        33.70        50.20        44.98 
TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-CN-4722 TCGA-CN-4729 
       71.05        25.71        27.19        12.92        26.27        12.89 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
       32.65        21.11        12.99        14.33        41.69        13.05 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5369 
       34.36         8.58        12.39        35.54        11.54        12.49 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6023 
       56.94        20.65        19.53        20.68         9.07        36.49 
TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       20.09        14.10        14.56        12.85        29.72        21.21 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 
       15.91         5.75         2.70        10.09         7.33         9.80 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 
        7.69         6.18        48.20        39.68        54.58        46.75 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 
       45.80        45.99        11.21         4.24        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.04        41.88        28.83        23.24        32.81        25.81 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       12.46        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 
       50.01        39.52        34.52        36.99        16.90         6.02 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       10.22        11.34         7.69        47.18        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 
       35.84         3.09        31.96        19.92        26.17        32.78 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        29.82        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5430 
       29.52        30.58         7.10         5.13        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5978 
       17.16       108.95        76.50        91.53        23.05         7.07 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
       21.07        62.43         2.14         5.46         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6955 
       11.24        19.79        15.09        30.08         6.08        10.98 
TCGA-CV-6959 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 
        8.42         7.99         9.01         1.84        52.31        21.80 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 
       71.21       130.88        47.47         4.96        47.97        36.13 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 
       57.47       210.97        89.33         9.67         0.46        25.08 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7437 
        0.07        34.09        56.48       156.49        54.94        16.64 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        24.99       169.38       180.16       159.65         1.05 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       48.20        60.43         0.76        56.61        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 
       35.34         6.48        21.24        19.92        10.42        10.42 
TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
       10.55        13.25         9.60         2.53        11.44        18.67 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5631 
       12.36        15.88         7.63        12.79        35.54        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 
       25.48        20.45        12.13        12.10        11.18        16.11 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       19.23        18.94        12.62        11.80        12.43        13.38 
TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
        6.77        25.74        22.03        12.66         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I 
        4.27         6.90        34.75        12.76        14.50         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
       14.47         5.29        12.43        10.75        30.05        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
        3.68         7.13        16.08        17.98        29.92        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T6 
       10.85        36.82        47.01        75.55        18.97        12.99 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       17.65         7.30         9.34        12.72        18.64        14.79 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.43         6.51        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JH 
       13.55        13.68        43.59         2.83        42.02        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       16.11         2.96        17.03        20.55 

  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                        17.850                         18.955 
[1] "0.1 - 153.9 (17.9)" "0.1 - 211.0 (19.0)"
[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       40        39       138         5
  DEL PEAK 41(18Q21.2) WILD-TYPE      11       37        38       114         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                             11
  STAGE II                            40                             37
  STAGE III                           39                             38
  STAGE IVA                          138                            114
  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      26 65 52 97
  DEL PEAK 41(18Q21.2) WILD-TYPE    24 68 47 75
D70V4, multiclass
       clus
vv      DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  T0+T1                           26                             24
  T2                              65                             68
  T3                              52                             47
  T4                              97                             75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2 N3
  DEL PEAK 41(18Q21.2) MUTATED   92 37 93  3
  DEL PEAK 41(18Q21.2) WILD-TYPE 86 29 72  5
D70V5, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  N0                           92                             86
  N1                           37                             29
  N2                           93                             72
  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"
D70V6, binary
                                cls
clus                              0  1
  DEL PEAK 41(18Q21.2) MUTATED   92  1
  DEL PEAK 41(18Q21.2) WILD-TYPE 91  0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED     92    1
  DEL PEAK 41(18Q21.2) WILD-TYPE   91    0
   clus
vv  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  0                           92                             91
  1                            1                              0
[1] 2 2
[1] FALSE
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED    64 200
  DEL PEAK 41(18Q21.2) WILD-TYPE  75 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED     64  200
  DEL PEAK 41(18Q21.2) WILD-TYPE   75  177
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  FEMALE                           64                             75
  MALE                            200                            177
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                                     260
  DEL PEAK 41(18Q21.2) WILD-TYPE                                   245
                                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                                                260
  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                                                  245
  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    45 219
  DEL PEAK 41(18Q21.2) WILD-TYPE  36 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED     45  219
  DEL PEAK 41(18Q21.2) WILD-TYPE   36  216
     clus
vv    DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  NO                            45                             36
  YES                          219                            216
[1] 2 2
[1] FALSE
D70V10, continuous
D70V11, continuous
D70V12, 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   211
  DEL PEAK 41(18Q21.2) WILD-TYPE                        13   230
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  32
  WHITE                                                     211
                                  clus
vv                                 DEL PEAK 41(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    13
  WHITE                                                       230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED    17 225
  DEL PEAK 41(18Q21.2) WILD-TYPE   8 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED     17  225
  DEL PEAK 41(18Q21.2) WILD-TYPE    8  229
                        clus
vv                       DEL PEAK 41(18Q21.2) MUTATED
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          225
                        clus
vv                       DEL PEAK 41(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            229
[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   167 117
  DEL PEAK 42(18Q23) WILD-TYPE 146  83
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         284                          229 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         117                           83 
$`DEL PEAK 42(18Q23) MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5152 
        3.35        15.19         9.30        13.64        26.50        42.35 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
       20.48        53.79        15.52        21.17        14.83         3.55 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62         4.01        29.42        30.18        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
        7.10         5.69        14.47        11.05        20.48        16.41 
TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
        9.14        36.72        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       20.52        10.55        27.19         8.81         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       23.70        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
       26.86        41.10        20.55        43.73        27.58        13.05 
TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 
       33.11        12.39         8.32        16.21        11.84        11.57 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
        8.52        22.45        20.71        30.67        20.68        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
       14.20         6.74         9.24        11.08        10.45        12.95 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 
       24.16         3.68        17.42        11.74        35.01        17.59 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 
       29.72        21.21         7.40        17.29        11.44         4.41 
TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       12.07        21.50         2.93        10.42        41.19        32.38 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.88        34.75        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        51.29        33.11        16.73        64.11        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 
       11.61        29.36        14.14        31.23        11.77        18.54 
TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.90        11.64        12.46        11.51        15.75         9.27 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 
       39.16         3.45        24.95        29.23         0.99         9.17 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       34.06        17.13        47.01         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
       48.39       129.21       108.95        76.24        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 
       94.88        80.12        17.92        13.35        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 
       60.49         7.07        43.23        54.74         9.60        90.12 
TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 
        9.70        20.52        26.43       126.08        12.03        42.38 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
       64.83       126.15       111.16        18.81        12.66         5.26 
TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7242 
        1.84        12.92        10.75        77.16         4.73        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 
       31.36        26.20        18.97        17.13        95.34        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       47.97         2.10        36.13        18.41        35.54        17.85 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 
        9.67        22.85        25.08        34.09       100.57        14.89 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 
        3.52        16.27        84.49        19.76       153.86         6.38 
TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
       22.19       180.16        35.47        45.96         6.51        88.87 
TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
       67.86         7.07         6.38        22.03         3.62        23.47 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
       22.52        10.42        18.84        34.36         9.60        23.05 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO 
       16.14        24.95        25.32        17.72        12.36        14.30 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
       13.94        12.10        12.79        11.11        58.45        30.94 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 
       33.86        14.04        18.90         9.83        10.65        37.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       21.63        20.25         3.02         0.46        17.85        20.25 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
       15.16        15.06        13.61        21.11         0.07         0.16 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E 
        1.22        14.66        22.85         3.65        15.95        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W 
       11.84        13.55        11.54        11.84        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 
        7.96         1.84        15.42        15.78        56.75        19.00 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
        2.04        29.00        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       11.74        16.70         5.62        11.57        12.10         9.73 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 
        9.76         8.32        12.72        15.91        13.25        54.67 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       43.36        41.16        44.65        62.27        17.95        24.16 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       49.22        16.11        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-WA-A7H4 
        2.96        14.56 

$`DEL PEAK 42(18Q23) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       37.28         9.07        23.74        57.93        17.10        23.84 
TCGA-BA-5559 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DF TCGA-BA-A6DG 
       57.44         7.76        28.11        20.45         7.82         2.27 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
       13.38         6.15        94.62         4.60         4.41        18.35 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-A5HU TCGA-BB-A6UM 
       22.42        33.70        50.20        44.98        25.71        12.92 
TCGA-CN-4722 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 
       26.27        32.65        21.11        12.99        14.33        41.69 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5374 
       34.36         8.58        35.54        11.54        12.49        56.94 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6989 
       20.65        19.53        20.68         9.07        36.49        20.09 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 
       14.10        14.56        12.85        15.91         5.75         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5323 
       10.09         7.33         9.80         7.69         6.18        48.20 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       39.68        54.58        46.75        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 
        4.24        70.13        43.04        41.88        28.83        23.24 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       32.81        25.81        12.46        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7364 
       16.90         6.02        10.22        11.34         7.69        47.18 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7380 
       47.34        40.93        35.84         3.09        31.96        19.92 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       26.17        32.78        27.06        12.89        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
      139.43        17.16        19.20        76.50        91.53        23.05 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 
       21.07        62.43         2.14         5.46         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       11.24        19.79        15.09        30.08         6.08        53.95 
TCGA-CV-6955 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 
       10.98         7.99         9.01        52.31        21.80        71.21 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7252 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
      130.88        47.47         4.96        57.47       210.97        89.33 
TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
        0.46        25.94         0.07        56.48       156.49        54.94 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
        7.17        16.64        27.98        24.99       169.38       159.65 
TCGA-CV-A45V TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
        1.05        48.20        60.43         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 
        5.98        35.34        29.79         6.48        21.24        19.92 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6826 
       10.42        10.55        13.25        25.41         2.53        11.44 
TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 
       18.67        15.88         7.63        35.54        18.02        25.48 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50J 
       20.45        12.13        12.10        11.18        16.11        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A76A 
       18.94        12.62        11.80        12.43        13.38         6.77 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       25.74        22.03        12.66         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61J 
        6.90        34.75        12.76        14.50         0.07        14.47 
TCGA-IQ-A61K TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
        5.29        13.35        12.43        10.75        30.05        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
        3.68         7.13        16.08        17.98        29.92        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-QK-A6IF 
       10.85        36.82        47.01        75.55        18.97        17.65 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30         9.34        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z7 TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
        6.51        16.96         6.87         7.10        32.45        13.55 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JH TCGA-UP-A6WW 
       13.68        43.59         2.83        42.02        21.86        17.03 
TCGA-WA-A7GZ 
       20.55 

  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                      180.16                       210.97 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                      17.655                       19.200 
[1] "0.1 - 180.2 (17.7)" "0.1 - 211.0 (19.2)"
[1] "hr=" "1.2"
D71V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 42(18Q23) MUTATED        15       42        43       149         7
  DEL PEAK 42(18Q23) WILD-TYPE      12       35        34       103         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                           12
  STAGE II                          42                           35
  STAGE III                         43                           34
  STAGE IVA                        149                          103
  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      24  69  57 109
  DEL PEAK 42(18Q23) WILD-TYPE    26  64  42  63
D71V4, multiclass
       clus
vv      DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  T0+T1                         24                           26
  T2                            69                           64
  T3                            57                           42
  T4                           109                           63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2 N3
  DEL PEAK 42(18Q23) MUTATED   98 39 97  5
  DEL PEAK 42(18Q23) WILD-TYPE 80 27 68  3
D71V5, multiclass
    clus
vv   DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  N0                         98                           80
  N1                         39                           27
  N2                         97                           68
  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"
D71V6, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED   102   1
  DEL PEAK 42(18Q23) WILD-TYPE  81   0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED    102    1
  DEL PEAK 42(18Q23) WILD-TYPE   81    0
   clus
vv  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  0                        102                           81
  1                          1                            0
[1] 2 2
[1] FALSE
D71V7, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED    71 213
  DEL PEAK 42(18Q23) WILD-TYPE  68 164
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     71  213
  DEL PEAK 42(18Q23) WILD-TYPE   68  164
        clus
vv       DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  FEMALE                         71                           68
  MALE                          213                          164
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(18Q23) MUTATED                                     281
  DEL PEAK 42(18Q23) WILD-TYPE                                   224
                              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                                              281
  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                                                224
  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    48 236
  DEL PEAK 42(18Q23) WILD-TYPE  33 199
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     48  236
  DEL PEAK 42(18Q23) WILD-TYPE   33  199
     clus
vv    DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  NO                          48                           33
  YES                        236                          199
[1] 2 2
[1] FALSE
D71V10, continuous
D71V11, continuous
D71V12, 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   230
  DEL PEAK 42(18Q23) WILD-TYPE                        12   211
D71V13, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     8
  BLACK OR AFRICAN AMERICAN                                33
  WHITE                                                   230
                                  clus
vv                                 DEL PEAK 42(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED    17 243
  DEL PEAK 42(18Q23) WILD-TYPE   8 211
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     17  243
  DEL PEAK 42(18Q23) WILD-TYPE    8  211
                        clus
vv                       DEL PEAK 42(18Q23) MUTATED
  HISPANIC OR LATINO                             17
  NOT HISPANIC OR LATINO                        243
                        clus
vv                       DEL PEAK 42(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          211
[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  78
  DEL PEAK 43(19P13.3) WILD-TYPE 220 122
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           171                            342 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            78                            122 
$`DEL PEAK 43(19P13.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-6868 
        3.35         9.30        26.50        42.35        57.93        15.52 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DL 
        3.55         4.01         7.76        29.42        11.54        20.48 
TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A5HY 
        4.41        24.66        38.40        71.05        25.71        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4731 
       27.19         8.81         6.28        38.04        12.89        32.65 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-5356 
       41.10        12.99        20.55        14.33        41.69        34.36 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 
       12.39         8.32        11.54         8.52        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6022 
       20.68        20.65        19.53        19.07         6.74         9.24 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A641 
       24.16         3.68        17.42        17.59         7.40        12.07 
TCGA-CN-A642 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-6220 
        2.70         9.80        48.20         2.93        45.80        32.38 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
       34.75        13.25        51.29        41.88        11.61        23.24 
TCGA-CQ-A4CD TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7371 
       32.81        16.90        11.64        47.18        39.16         3.09 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7386 TCGA-CR-7398 TCGA-CR-7399 
       29.23         0.99         9.17        47.01         5.13         5.95 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5970 
      129.21       108.95        76.24        17.95       107.51        13.35 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 
       43.23        54.74         9.60        90.12         5.46        20.52 
TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6961 
       26.43        12.03        15.09         6.08         7.13         2.50 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        18.81        12.66         9.01         5.26         1.84 
TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7253 
       12.92        71.21        10.75        26.20        18.97        11.87 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 
       47.97        36.13        35.54         9.67        22.85        25.08 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45U 
       54.94         3.52        16.27       153.86        22.19        35.47 
TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6516 TCGA-D6-6825 
       67.86         7.07        29.79        22.52        25.41        16.14 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       11.44        25.32         7.63        12.10        12.79        58.45 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 
       14.04        18.90        20.45         9.83        10.65        37.18 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A623 TCGA-HD-7753 
       20.25         3.02        19.23         0.46        20.25         0.16 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I 
       22.85         3.65        34.75        19.33        11.84         0.07 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T4 
       11.54        18.15         7.96        17.98        47.01         2.04 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 
       16.01        13.15        11.74         9.34        12.72         6.51 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO 
        5.62        11.57        12.10         9.73         8.32        12.72 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JK 
       43.59        54.67         2.83        17.95        21.86        13.94 
TCGA-UF-A7JO TCGA-UP-A6WW TCGA-WA-A7GZ 
       20.75        17.03        20.55 

$`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 
       15.19        13.64        37.28         9.07        23.74        17.10 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
       23.84        20.48        53.79        57.44        21.17        14.83 
TCGA-BA-6872 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB 
       12.62        28.11        20.45        30.18        27.95         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        5.69        14.47         7.82         2.27        11.05        13.38 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
       16.41         6.15        94.62         9.14         4.60        18.35 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       22.42        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-8601 TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
       20.52        12.92        12.69        26.27        23.70         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4739 TCGA-CN-4740 
       40.44        37.84        26.86        21.11        43.73        27.58 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5366 
       13.05        33.11         8.58        35.54        16.21        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 
       11.57        12.49        22.45        20.71        20.68        14.20 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        9.07        36.49        11.08        10.45        20.09        12.95 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       14.10        11.74        35.01        14.56        12.85        29.72 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       10.09         7.33         7.69         6.18        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        46.75        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       41.19        32.88        56.58         4.24        14.99        38.76 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 
       70.13        33.11        16.73        43.04        28.83        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       44.48        29.36        25.81        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 
       50.01        39.52        34.52        36.99        18.54         6.02 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       11.90        10.22        11.34         7.69        12.46        11.51 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       15.75         9.27        47.34        40.93        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       24.95        31.96        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
       32.78        27.06        12.89        29.82        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
       29.85        29.52        30.58         7.10        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 
       48.39       139.43        17.16        19.20        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        80.12        17.92        23.05        86.83        48.59 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 
       60.49         7.07        21.07        62.43         2.14         9.70 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        4.73        21.90        11.24       126.08        19.79        42.38 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 
       30.08        53.95        65.82        10.98         8.42        28.34 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7103 TCGA-CV-7177 
        4.14        64.83       126.15         7.99        52.31        21.80 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
      130.88        77.16         4.73        47.47        36.00        31.36 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 
       17.13        95.34         4.96         2.10        18.41        57.47 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 
       17.85       210.97        89.33         0.46        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7432 
       34.09       100.57        14.89        56.48       156.49        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17        16.64         6.38        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X 
      169.38       180.16       159.65         1.05        45.96         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       88.87        48.20        60.43         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34         6.38         6.48        22.03         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
       21.24        23.47        19.92        10.42        10.42        10.55 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        34.36        13.25         9.60        23.05         2.53 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
       18.67        24.95        17.72        12.36        15.88        14.30 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
       13.94        11.11        35.54        30.94        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       25.48        12.13        12.10        11.18        16.11        21.63 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       18.94        12.62        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
       15.16        15.06        13.61        21.11         6.77         0.07 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
       25.74         1.22        14.66        22.03        12.66         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
       13.84         4.27         6.90        15.95        12.76        14.50 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
       13.55        14.47         5.29        11.84        13.35        12.43 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       10.75        14.37        30.05         1.84        12.62         3.68 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        29.92        15.78        56.75 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       51.25        10.85        36.82        19.00        75.55        18.97 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       29.00        12.99        21.07        17.65         7.30        16.70 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX 
       18.64        14.79        12.43         9.76        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.55        13.25        13.68 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
       43.36        41.16        42.02        44.65        62.27        24.16 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV TCGA-WA-A7H4 
       49.22        16.11        22.36        32.65         2.96        14.56 

  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                        17.030                         18.755 
[1] "0.1 - 153.9 (17.0)" "0.1 - 211.0 (18.8)"
[1] "hr=" "1.5"
D72V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 43(19P13.3) MUTATED         6       20        31        92         3
  DEL PEAK 43(19P13.3) WILD-TYPE      21       57        46       160         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                             21
  STAGE II                            20                             57
  STAGE III                           31                             46
  STAGE IVA                           92                            160
  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  41  37  66
  DEL PEAK 43(19P13.3) WILD-TYPE    37  92  62 106
D72V4, multiclass
       clus
vv      DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  T0+T1                           13                             37
  T2                              41                             92
  T3                              37                             62
  T4                              66                            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 43(19P13.3) MUTATED    51  29  63   3
  DEL PEAK 43(19P13.3) WILD-TYPE 127  37 102   5
D72V5, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  N0                           51                            127
  N1                           29                             37
  N2                           63                            102
  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"
D72V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    60   1
  DEL PEAK 43(19P13.3) WILD-TYPE 123   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     60    1
  DEL PEAK 43(19P13.3) WILD-TYPE  123    0
   clus
vv  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  0                           60                            123
  1                            1                              0
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    43 129
  DEL PEAK 43(19P13.3) WILD-TYPE  96 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     43  129
  DEL PEAK 43(19P13.3) WILD-TYPE   96  248
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  FEMALE                           43                             96
  MALE                            129                            248
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                     171
  DEL PEAK 43(19P13.3) WILD-TYPE                                   334
                                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                                                171
  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                                                  334
  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    31 141
  DEL PEAK 43(19P13.3) WILD-TYPE  50 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     31  141
  DEL PEAK 43(19P13.3) WILD-TYPE   50  294
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  NO                            31                             50
  YES                          141                            294
[1] 2 2
[1] FALSE
D72V10, continuous
D72V11, continuous
D72V12, 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   145
  DEL PEAK 43(19P13.3) WILD-TYPE                        29   296
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 43(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     145
                                  clus
vv                                 DEL PEAK 43(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    10 150
  DEL PEAK 43(19P13.3) WILD-TYPE  15 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     10  150
  DEL PEAK 43(19P13.3) WILD-TYPE   15  304
                        clus
vv                       DEL PEAK 43(19P13.3) MUTATED
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          150
                        clus
vv                       DEL PEAK 43(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            304
[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  39
  DEL PEAK 44(19Q13.43) WILD-TYPE 257 161
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             95                             418 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             39                             161 
$`DEL PEAK 44(19Q13.43) MUTATED`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 
        9.30        13.64        26.50        17.10        14.83        12.62 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7871 
        4.01        29.42         7.10         4.41        36.72        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4737 
       71.05        20.52         6.28        38.04         4.67        20.55 
TCGA-CN-5356 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6989 
       34.36        56.94        20.68        19.07         9.07        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63U 
       12.95        24.16        17.42        14.10        12.85        17.29 
TCGA-CN-A641 TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-7064 
       12.07         6.18         2.93        10.42        32.38        51.29 
TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6488 
       41.88        11.61        23.24        31.23        54.67        12.46 
TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5431 
       39.16        29.23         0.99        29.82         5.13        17.16 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 
      108.95        76.24        17.95        43.23        54.74        90.12 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6962 
       26.43        11.24        42.38         7.13        28.34         4.14 
TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7261 
       12.66        10.75        77.16        26.20        47.97        36.13 
TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-A465 TCGA-CV-A6JN 
       35.54        25.08         3.52        16.27         7.07        29.79 
TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EO 
       22.52         9.60        11.44        25.32         7.63        14.30 
TCGA-D6-A6EP TCGA-DQ-7588 TCGA-F7-A61W TCGA-HD-7753 TCGA-IQ-A61I TCGA-IQ-A61L 
       13.94        14.04         0.46         0.16         0.07        11.54 
TCGA-MT-A51X TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 
        7.96        11.74        16.70        12.72         6.51        11.57 
TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JC 
       12.10        15.91        54.67        41.16        17.95 

$`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 
        3.35        15.19        37.28         9.07        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       57.93        23.84        20.48        53.79        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       21.17         3.55         7.76        28.11        20.45        30.18 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       27.95        11.54         5.69        14.47         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       11.05        13.38        20.48        16.41         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
        9.14         4.60        18.35        22.42        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       44.98        66.28        38.40        25.71        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 
       12.92         8.81        12.69        26.27        23.70        40.44 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       37.84        12.89        26.86        32.65        21.11        41.10 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       12.99        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       33.11         8.58        12.39        35.54         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        22.45 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       20.71        30.67        20.65        19.53        20.68        14.20 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6995 
        6.74         9.24        36.49        11.08        10.45         3.68 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       11.74        35.01        14.56        17.59        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
        7.40        15.91        11.44         5.75         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 
       10.09         7.33         9.80         7.69        48.20        39.68 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50        54.58        46.75        45.80        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        41.19        32.88        34.75        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        4.24        14.99        38.76        70.13        33.11        16.73 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.04        28.83        64.11        44.48        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
       25.81        14.14        12.46        84.23        11.77        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       26.27        58.42        50.01        39.52        34.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       18.54        16.90         6.02        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64         7.69        11.51        15.75         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
       47.34        40.93        35.84         3.45         3.09        24.95 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 
       31.96         9.17        34.06        19.92        26.17        17.13 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       32.78        47.01        27.06        12.89        30.02        31.10 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       29.85        29.52        30.58         7.10         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5440 
       29.95        48.39       139.43       129.21        19.20       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 
       23.05        86.83        48.59        60.49         7.07        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
        4.73        21.90       126.08        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 
       30.08         6.08        53.95        65.82        10.98         8.42 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        2.50        64.83       126.15       111.16        18.81         7.99 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 
        9.01         5.26         1.84        52.31        12.92        21.80 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       71.21       130.88         4.73        47.47        36.00        31.36 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       18.97        17.13        95.34         4.96        11.87         2.10 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        57.47        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.94         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 
       14.89        56.48       156.49        54.94        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
        7.17       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       24.99       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       45.96         6.51        88.87        48.20        60.43        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
        0.76        56.61        15.25         5.98        35.34         6.38 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        22.03         3.62        21.24        23.47        19.92 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 
       10.42        10.42        10.55        18.84        34.36        13.25 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       25.41        23.05         2.53        16.14        18.67        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       17.72        12.36        15.88        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
       58.45        35.54        30.94        33.86        18.02        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       25.48        20.45         9.83        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       11.18        37.18        16.11        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       19.23        18.94        12.62        17.85        11.80        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
       12.43        13.38        15.16        15.06        13.61        21.11 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        6.77         0.07        25.74         1.22        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A66S 
       11.84        13.55        14.47         5.29        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
       18.15        12.43        10.75        14.37        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         3.68        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       29.92        15.78        56.75        51.25        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       47.01        19.00        75.55        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        16.01        13.15        21.07        17.65         7.30 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB 
        9.34        18.64        14.79        12.43         5.62         9.73 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        9.76         8.32        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
       32.45        13.55        13.25        13.68        43.59         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
       43.36        42.02        44.65        62.27        24.16        49.22 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       21.86        16.11        13.94        20.75        22.36        32.65 
TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.96        17.03        20.55        14.56 

  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                         108.95                          210.97 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                         17.100                          18.655 
[1] "0.1 - 109.0 (17.1)" "0.1 - 211.0 (18.7)"
[1] "hr=" "1.2"
D73V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 44(19Q13.43) MUTATED         2       13        21        46
  DEL PEAK 44(19Q13.43) WILD-TYPE      25       64        56       206
                                 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                              25
  STAGE II                             13                              64
  STAGE III                            21                              56
  STAGE IVA                            46                             206
  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  25  28  28
  DEL PEAK 44(19Q13.43) WILD-TYPE    45 108  71 144
D73V4, multiclass
       clus
vv      DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  T0+T1                             5                              45
  T2                               25                             108
  T3                               28                              71
  T4                               28                             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 44(19Q13.43) MUTATED    29  14  35   1
  DEL PEAK 44(19Q13.43) WILD-TYPE 149  52 130   7
D73V5, multiclass
    clus
vv   DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  N0                            29                             149
  N1                            14                              52
  N2                            35                             130
  N3                             1                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED    29   0
  DEL PEAK 44(19Q13.43) WILD-TYPE 154   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     29    0
  DEL PEAK 44(19Q13.43) WILD-TYPE  154    1
   clus
vv  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  0                            29                             154
  1                             0                               1
[1] 2 2
[1] FALSE
D73V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED    24  71
  DEL PEAK 44(19Q13.43) WILD-TYPE 115 306
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     24   71
  DEL PEAK 44(19Q13.43) WILD-TYPE  115  306
        clus
vv       DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  FEMALE                            24                             115
  MALE                              71                             306
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19Q13.43) MUTATED                                      93
  DEL PEAK 44(19Q13.43) WILD-TYPE                                   412
                                 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                                                  93
  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                                                   412
  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    18  77
  DEL PEAK 44(19Q13.43) WILD-TYPE  63 358
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     18   77
  DEL PEAK 44(19Q13.43) WILD-TYPE   63  358
     clus
vv    DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  NO                             18                              63
  YES                            77                             358
[1] 2 2
[1] FALSE
D73V10, continuous
D73V11, continuous
D73V12, 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    79
  DEL PEAK 44(19Q13.43) WILD-TYPE                        34   362
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 44(19Q13.43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       79
                                  clus
vv                                 DEL PEAK 44(19Q13.43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     34
  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"
D73V14, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED     7  83
  DEL PEAK 44(19Q13.43) WILD-TYPE  18 371
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED      7   83
  DEL PEAK 44(19Q13.43) WILD-TYPE   18  371
                        clus
vv                       DEL PEAK 44(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                            83
                        clus
vv                       DEL PEAK 44(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             371
[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  77
  DEL PEAK 45(21Q22.3) WILD-TYPE 187 123
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           203                            310 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                            77                            123 
$`DEL PEAK 45(21Q22.3) MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
        3.35         9.30        53.79        57.44        15.52        14.83 
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7864 
        3.55        28.11        27.95        11.54        36.72        50.20 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ 
       24.66        71.05        20.52        25.71        10.55        27.19 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4736 
        6.28        38.04         4.67        37.84        12.89        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       20.55        14.33        43.73        41.69        13.05        33.11 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 
       35.54         8.32        11.54         8.52        56.94        20.71 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6988 
       20.68        19.07        14.20         9.07         9.24        10.45 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A499 
       12.95        24.16        17.42        14.10        11.74        17.59 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5326 TCGA-CQ-5330 
       29.72         7.40        11.44        48.20         2.93        45.80 
TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 
       10.42        32.38        34.75        56.58        13.25        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
       51.29        33.11        16.73        41.88        64.11        44.48 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
       11.61        23.24        25.81        12.46        31.23        11.77 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 
       16.90        11.64        12.46        11.51        39.16        47.34 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7388 
       35.84         3.45         3.09        29.23         0.99        27.06 
TCGA-CR-7389 TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 
       12.89         5.95        17.16        17.95       107.51        80.12 
TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       17.92        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6951 
       54.74         9.60         2.14        20.52        11.24        30.08 
TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
       65.82         7.13         8.42         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 
      126.15       111.16         5.26        52.31        12.92        10.75 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       77.16        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7422 
       47.97        36.13        18.41        17.85        25.08        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45U 
      100.57        14.89        84.49       153.86        22.19        35.47 
TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CX-7082 
       45.96         7.07        29.79         6.48         3.62        10.42 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 
       18.84        34.36        25.41        23.05        16.14        11.44 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 
       17.72        12.36         7.63        12.10        11.11        58.45 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
       30.94        14.04         9.83        16.11        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8501 TCGA-H7-8502 
       19.23        12.62         0.46        17.85        15.16        15.06 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A6HZ 
       21.11         0.07         0.16        12.66        13.84         3.65 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66T 
       19.33        11.84        13.55        14.47        11.54        18.15 
TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX 
        7.96        17.98        15.78        56.75        10.85        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 
       19.00        75.55        18.97         2.04        29.00        13.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 
        7.30        16.70        12.72        14.79         6.51        11.57 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 
        9.76         8.32         7.10         2.83        42.02        44.65 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7H4 
       17.95        24.16        21.86        13.94        14.56 

$`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 
       15.19        13.64        37.28         9.07        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6869 
       42.35        57.93        17.10        23.84        20.48        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II 
       12.62         4.01         7.76        29.42        20.45        30.18 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
        7.10         5.69        14.47         7.82         2.27        11.05 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       13.38        20.48        16.41         6.15        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 
        4.60         4.41        18.35        22.42        33.70        44.98 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 
       66.28        38.40        12.92         8.81        12.69        26.27 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
       23.70        40.44        26.86        32.65        21.11        41.10 
TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5366 
       27.58        34.36         8.58        12.39        16.21        11.84 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
       11.57        12.49        22.45        30.67        20.65        19.53 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6995 
       20.68         6.74        36.49        11.08        20.09         3.68 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       35.01        14.56        12.85        21.21        17.29        15.91 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
        9.80         7.69         6.18        39.68        21.50        54.58 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
       46.75        45.99        11.21         4.24        41.19        32.88 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CB 
        4.24        14.99        70.13        43.04        28.83        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       32.81        14.14        84.23        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
       58.42        50.01        39.52        34.52        36.99        18.54 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6492 
        6.02        11.90        10.22        11.34         7.69        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
        9.27        47.18        40.93        24.95        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       34.06        19.92        26.17        17.13        32.78        47.01 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       29.82        30.02        31.10        29.85        29.52        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        7.10         5.13        35.41        29.95        48.39       139.43 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 
      129.21       108.95        76.24        19.20        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 
       91.53        13.35        23.05        21.07        62.43        90.12 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 
        9.70         5.46         4.73        21.90        26.43       126.08 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        42.38        15.09         6.08        53.95 
TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       10.98        28.34        18.81        12.66         7.99         9.01 
TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
        1.84        21.80        71.21       130.88         4.73        47.47 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7407 
       95.34         4.96        11.87         2.10        57.47        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 
      210.97        89.33         9.67         0.46        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
        0.07        56.48       156.49        54.94         3.52        16.27 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
       19.76         7.17        16.64         6.38        27.98        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
      169.38       180.16       159.65         1.05         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       48.20        60.43        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        5.98        35.34         6.38        22.03        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6517 
       19.92        22.52        10.42        10.55        13.25         9.60 
TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EO 
        2.53        18.67        24.95        25.32        15.88        14.30 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
       13.94        12.79        35.54        33.86        18.02        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       25.48        20.45        12.13        12.10        10.65        11.18 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       37.18        21.63        18.94        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
       13.38        13.61         6.77        25.74         1.22        14.66 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03        22.85         0.36         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61O 
       15.95        12.76        14.50         0.07         5.29        11.84 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
       13.35        12.43        10.75        14.37        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       12.62         3.68        15.42         7.13        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 
       51.25        36.82        12.99        16.01        21.07        11.74 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       17.65         9.34        18.64        12.43         5.62        12.10 
TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 
        9.73        12.72        16.96         6.87        15.91        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       13.55        13.25        13.68        43.59        54.67        43.36 
TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS 
       41.16        62.27        49.22        16.11        20.75        22.36 
TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW TCGA-WA-A7GZ 
       32.65         2.96        17.03        20.55 

  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                         17.72                          18.92 
[1] "0.1 - 153.9 (17.7)" "0.1 - 211.0 (18.9)"
[1] "hr=" "1"  
D74V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 45(21Q22.3) MUTATED        10       32        33       104         6
  DEL PEAK 45(21Q22.3) WILD-TYPE      17       45        44       148         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                             17
  STAGE II                            32                             45
  STAGE III                           33                             44
  STAGE IVA                          104                            148
  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  56  47  71
  DEL PEAK 45(21Q22.3) WILD-TYPE    37  77  52 101
D74V4, multiclass
       clus
vv      DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  T0+T1                           13                             37
  T2                              56                             77
  T3                              47                             52
  T4                              71                            101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 45(21Q22.3) MUTATED    67  32  70   4
  DEL PEAK 45(21Q22.3) WILD-TYPE 111  34  95   4
D74V5, multiclass
    clus
vv   DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  N0                           67                            111
  N1                           32                             34
  N2                           70                             95
  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"
D74V6, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED    70   0
  DEL PEAK 45(21Q22.3) WILD-TYPE 113   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     70    0
  DEL PEAK 45(21Q22.3) WILD-TYPE  113    1
   clus
vv  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  0                           70                            113
  1                            0                              1
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED    50 155
  DEL PEAK 45(21Q22.3) WILD-TYPE  89 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     50  155
  DEL PEAK 45(21Q22.3) WILD-TYPE   89  222
        clus
vv       DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  FEMALE                           50                             89
  MALE                            155                            222
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(21Q22.3) MUTATED                                     201
  DEL PEAK 45(21Q22.3) WILD-TYPE                                   304
                                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                                                201
  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                                                  304
  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    31 174
  DEL PEAK 45(21Q22.3) WILD-TYPE  50 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     31  174
  DEL PEAK 45(21Q22.3) WILD-TYPE   50  261
     clus
vv    DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  NO                            31                             50
  YES                          174                            261
[1] 2 2
[1] FALSE
D74V10, continuous
D74V11, continuous
D74V12, 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   165
  DEL PEAK 45(21Q22.3) WILD-TYPE                        20   276
D74V13, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     165
                                  clus
vv                                 DEL PEAK 45(21Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED     9 180
  DEL PEAK 45(21Q22.3) WILD-TYPE  16 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED      9  180
  DEL PEAK 45(21Q22.3) WILD-TYPE   16  274
                        clus
vv                       DEL PEAK 45(21Q22.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          180
                        clus
vv                       DEL PEAK 45(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            274
[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    85  68
  DEL PEAK 46(XP22.2) WILD-TYPE 228 132
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          153                           360 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           68                           132 
$`DEL PEAK 46(XP22.2) MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-A4IG 
       13.64         9.07        26.50        15.52        12.62        28.11 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7862 
       20.45        27.95        14.47        20.48        16.41        36.72 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4725 
       24.66        71.05        25.71        12.92         8.81        38.04 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5359 
       37.84        12.89        41.10        12.99        20.55        12.39 
TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6023 
       35.54        56.94        20.71        20.68        19.07        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
       11.08        10.45        20.09        12.95        17.42        14.10 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5330 TCGA-CQ-5332 
       12.85        29.72         7.69         6.18        45.80        10.42 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7072 
       41.19        32.38        32.88         4.24        38.76        64.11 
TCGA-CQ-A4C7 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6477 
       11.61        31.23        11.77        54.67        34.52        16.90 
TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7374 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7390 
        7.69         9.27         0.99        19.92        17.13        29.82 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 
        7.10         5.13         5.95       139.43       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6933 
       17.95        13.35        48.59        60.49         9.60        90.12 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6959 
        9.70         5.46        26.43        42.38        30.08         8.42 
TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7236 
       28.34        18.81         5.26         1.84        77.16         4.73 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7407 
       31.36        26.20        18.97        47.97         2.10        35.54 
TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7429 
       17.85         0.46        22.85        25.94        56.48         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45W TCGA-CV-A45X 
       16.27        84.49         6.38       169.38        45.96         6.51 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7082 
       60.43         7.07        29.79        21.24        22.52        10.42 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB 
       18.84        25.41        11.44        18.67        24.95        12.36 
TCGA-D6-A6EM TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
        7.63        11.11        35.54        30.94        18.02        14.04 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W 
       20.45         9.83        37.18        21.63        20.25         0.46 
TCGA-F7-A620 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8635 TCGA-IQ-A61G TCGA-MT-A7BN 
       17.85        21.11         1.22        22.85        11.84        15.42 
TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A6IH 
       51.25        18.97         2.04        29.00        12.99        16.70 
TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71B 
        5.62         9.76        15.91        13.25        54.67        43.36 
TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS 
       42.02        17.95        24.16        21.86        20.75        22.36 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       17.03        20.55        14.56 

$`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 
        3.35        15.19         9.30        37.28        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       57.93        17.10        23.84        20.48        53.79        57.44 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83         3.55         4.01         7.76        29.42 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38         6.15        94.62         9.14         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.35        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z 
       66.28        38.40        20.52        10.55        27.19         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 
       12.69        26.27        23.70         4.67        40.44        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       32.65        21.11        14.33        43.73        27.58        41.69 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 
       13.05        33.11        34.36         8.58         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        22.45 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       30.67        20.65        19.53        20.68        14.20         6.74 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 
        9.07         9.24        24.16         3.68        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       14.56        17.59        21.21         7.40        17.29        15.91 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       11.44         5.75         4.41        12.07         2.70        10.09 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        7.33         9.80        48.20        39.68        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 
       54.58        46.75        45.99        11.21         4.24        34.75 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58        13.25        14.99        70.13        51.29        33.11 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       16.73        43.04        41.88        28.83        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        32.81        25.81        14.14        12.46        84.23 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       18.54         6.02        11.90        10.22        11.34        11.64 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       12.46        11.51        15.75        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       40.93        35.84         3.45         3.09        24.95        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        34.06        26.17        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       27.06        12.89        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
       30.58        35.41        29.95        48.39        17.16       129.21 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20       107.51        94.88        76.50        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       17.92        23.05        86.83         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
       21.07        62.43         2.14        20.52         4.73        21.90 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6952 
       11.24       126.08        19.79        12.03        15.09         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-6962 
       53.95        65.82        10.98         7.13         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       126.15       111.16        12.66         7.99         9.01 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
       52.31        12.92        21.80        71.21        10.75       130.88 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       47.47        36.00        17.13        95.34         4.96        11.87 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       36.13        18.41        57.47       210.97        89.33         9.67 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 
       25.08         0.07        34.09       100.57        14.89       156.49 
TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
       54.94        19.76         7.17       153.86        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        24.99       180.16       159.65        35.47         1.05 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 
       88.87        48.20        67.86         0.76        56.61        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34         6.38         6.48        22.03         3.62 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 
       23.47        19.92        10.42        10.55        34.36        13.25 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4Z9 
        9.60        23.05         2.53        16.14        25.32        17.72 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       15.88        14.30        13.94        12.10        12.79        58.45 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       33.86        18.90        25.48        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       11.18        16.11         3.02        19.23        18.94        12.62 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 
       13.61         6.77         0.07         0.16        25.74        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       22.03        12.66         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       13.55         0.07        14.47         5.29        11.54        11.84 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.35        18.15        12.43        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05         1.84        12.62         3.68         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW 
       17.98        29.92        15.78        56.75        10.85        36.82 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       47.01        19.00        75.55        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       11.74        17.65         7.30         9.34        12.72        18.64 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       14.79        12.43         6.51        11.57        12.10         9.73 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
        8.32        12.72        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A7J9 
       13.55        13.68        43.59         2.83        41.16        44.65 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT TCGA-UF-A7JV 
       62.27        49.22        16.11        13.94        32.65         2.96 

  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                         0.46                          0.07 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                       19.070                        17.225 
[1] "0.5 - 169.4 (19.1)" "0.1 - 211.0 (17.2)"
[1] "hr=" "1.2"
D75V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 46(XP22.2) MUTATED         6       20        22        74         6
  DEL PEAK 46(XP22.2) WILD-TYPE      21       57        55       178         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                            21
  STAGE II                           20                            57
  STAGE III                          22                            55
  STAGE IVA                          74                           178
  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      12  34  40  48
  DEL PEAK 46(XP22.2) WILD-TYPE    38  99  59 124
D75V4, multiclass
       clus
vv      DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  T0+T1                          12                            38
  T2                             34                            99
  T3                             40                            59
  T4                             48                           124
[1] 4 2
[1] TRUE
[1] "dimension of 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    44  17  59   3
  DEL PEAK 46(XP22.2) WILD-TYPE 134  49 106   5
D75V5, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  N0                          44                           134
  N1                          17                            49
  N2                          59                           106
  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"
D75V6, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    46   1
  DEL PEAK 46(XP22.2) WILD-TYPE 137   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     46    1
  DEL PEAK 46(XP22.2) WILD-TYPE  137    0
   clus
vv  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  0                          46                           137
  1                           1                             0
[1] 2 2
[1] FALSE
D75V7, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    34 119
  DEL PEAK 46(XP22.2) WILD-TYPE 105 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     34  119
  DEL PEAK 46(XP22.2) WILD-TYPE  105  258
        clus
vv       DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  FEMALE                          34                           105
  MALE                           119                           258
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                                     148
  DEL PEAK 46(XP22.2) WILD-TYPE                                   357
                               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                                               148
  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                                                 357
  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    29 124
  DEL PEAK 46(XP22.2) WILD-TYPE  52 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     29  124
  DEL PEAK 46(XP22.2) WILD-TYPE   52  311
     clus
vv    DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  NO                           29                            52
  YES                         124                           311
[1] 2 2
[1] FALSE
D75V10, continuous
D75V11, continuous
D75V12, 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   135
  DEL PEAK 46(XP22.2) WILD-TYPE                        32   306
D75V13, multiclass
                                  clus
vv                                 DEL PEAK 46(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                    135
                                  clus
vv                                 DEL PEAK 46(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED     8 134
  DEL PEAK 46(XP22.2) WILD-TYPE  17 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED      8  134
  DEL PEAK 46(XP22.2) WILD-TYPE   17  320
                        clus
vv                       DEL PEAK 46(XP22.2) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         134
                        clus
vv                       DEL PEAK 46(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           320
[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    92  64
  DEL PEAK 47(XP21.3) WILD-TYPE 221 136
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          156                           357 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                           64                           136 
$`DEL PEAK 47(XP21.3) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-A4IH 
       15.19        13.64         9.07        26.50        12.62        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7862 
       27.95        14.47        20.48        16.41         4.41        36.72 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HU TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4725 
       24.66        71.05        25.71        12.92         8.81        38.04 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4742 
       37.84        12.89        41.10        12.99        20.55        13.05 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       12.39        35.54        56.94        20.71        30.67        20.68 
TCGA-CN-6018 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
       19.07        11.08        10.45        20.09        12.95        17.42 
TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A6V7 TCGA-CQ-5327 TCGA-CQ-5330 
       14.10        12.85        29.72         6.18        54.58        45.80 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6227 
       45.99        10.42        41.19        32.38        32.88         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CI 
       38.76        51.29        33.11        64.11        11.61        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7374 
       11.77        54.67        34.52         7.69         9.27         0.99 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       19.92        17.13        29.82         7.10         5.13         5.95 
TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 
      139.43        76.24        17.95        80.12        13.35        48.59 
TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6948 
       60.49         9.60         9.70         5.46        26.43        42.38 
TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 
       30.08         8.42        28.34        18.81         5.26         1.84 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7254 
       77.16         4.73        31.36        26.20        18.97        47.97 
TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7430 
        2.10        35.54        17.85        25.94        56.48        16.27 
TCGA-CV-7432 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45W 
       84.49        16.64         6.38       169.38       180.16        45.96 
TCGA-CV-A45X TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7082 
        6.51        60.43         7.07        21.24        22.52        10.42 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 
       18.84        25.41        23.05        11.44        24.95        17.72 
TCGA-D6-A6EM TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
        7.63        11.11        35.54        30.94        18.02        14.04 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W 
       20.45         9.83        37.18        21.63        20.25         0.46 
TCGA-F7-A620 TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-IQ-A61G 
       17.85        21.11         1.22        22.85         0.36        11.84 
TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 
       18.15         7.96        15.42        51.25        18.97         2.04 
TCGA-P3-A6T6 TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ 
       12.99        16.70         5.62         9.73         9.76        15.91 
TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD 
       13.25        54.67        43.36        42.02        17.95        24.16 
TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       21.86        20.75        22.36        17.03        20.55        14.56 

$`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 
        3.35         9.30        37.28        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       17.10        23.84        20.48        53.79        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       21.17        14.83         3.55         4.01         7.76        29.42 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF 
       28.11        30.18        11.54         7.10         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        13.38         6.15        94.62         9.14 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.60        18.35        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z 
       66.28        38.40        20.52        10.55        27.19         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 
       12.69        26.27        23.70         4.67        40.44        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       32.65        21.11        14.33        43.73        27.58        41.69 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       33.11        34.36         8.58         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 
       11.84        11.57        12.49         8.52        22.45        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
       19.53        20.68        14.20         6.74         9.07         9.24 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       36.49        24.16         3.68        11.74        35.01        14.56 
TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       17.59        21.21         7.40        17.29        15.91        11.44 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 
        5.75         4.41        12.07         2.70        10.09         7.33 
TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        9.80         7.69        48.20        39.68        21.50         2.93 
TCGA-CQ-5329 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       46.75        11.21         4.24        34.75        56.58        13.25 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        70.13        16.73        43.04        41.88        28.83 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        32.81        25.81        14.14 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       12.46        84.23        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
       39.52        36.99        18.54        16.90         6.02        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       10.22        11.34        11.64        12.46        11.51        15.75 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       47.18        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        24.95        29.23        31.96         9.17        34.06 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       26.17        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 
       31.10        29.85        29.52        30.58        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 
       48.39        17.16       129.21       108.95        19.20       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
       94.88        76.50        91.53        17.92        23.05        86.83 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 
        7.07        43.23        54.74        21.07        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 
        2.14        20.52         4.73        21.90        11.24       126.08 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       19.79        12.03        15.09         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       10.98         7.13         2.50         4.14        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 
      111.16        12.66         7.99         9.01        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
       21.80        71.21        10.75       130.88        47.47        36.00 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7263 
       17.13        95.34         4.96        11.87        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       57.47       210.97        89.33         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 
       25.08         0.07        34.09       100.57        14.89       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
       54.94         3.52        19.76         7.17       153.86        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y 
       27.98        24.99       159.65        35.47         1.05        88.87 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       48.20        67.86         0.76        56.61        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       35.34         6.38        29.79         6.48        22.03         3.62 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6515 
       23.47        19.92        10.42        10.55        34.36        13.25 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB 
        9.60         2.53        16.14        18.67        25.32        12.36 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       15.88        14.30        13.94        12.10        12.79        58.45 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
       33.86        18.90        25.48        12.13        12.10        10.65 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       11.18        16.11         3.02        19.23        18.94        12.62 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       11.80        20.25        12.43        13.38        15.16        15.06 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 
       13.61         6.77         0.07         0.16        25.74        14.66 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03        12.66        13.84         4.27         3.65         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H 
       34.75        15.95        12.76        14.50        19.33        13.55 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
        0.07        14.47         5.29        11.54        11.84        13.35 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       12.43        10.75        14.37        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        3.68         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       56.75        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       29.00        16.01        13.15        21.07        11.74        17.65 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30         9.34        12.72        18.64        14.79        12.43 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
        6.51        11.57        12.10         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
        6.87         7.10        32.45        13.55        13.68        43.59 
TCGA-UF-A71A TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ 
        2.83        41.16        44.65        62.27        49.22        16.11 
TCGA-UF-A7JK TCGA-UF-A7JT TCGA-UF-A7JV 
       13.94        32.65         2.96 

  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                        19.02                         17.16 
[1] "0.4 - 180.2 (19.0)" "0.1 - 211.0 (17.2)"
[1] "hr=" "1.1"
D76V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 47(XP21.3) MUTATED         5       23        22        78         6
  DEL PEAK 47(XP21.3) WILD-TYPE      22       54        55       174         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                            22
  STAGE II                           23                            54
  STAGE III                          22                            55
  STAGE IVA                          78                           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 47(XP21.3) MUTATED      11  40  39  50
  DEL PEAK 47(XP21.3) WILD-TYPE    39  93  60 122
D76V4, multiclass
       clus
vv      DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  T0+T1                          11                            39
  T2                             40                            93
  T3                             39                            60
  T4                             50                           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 47(XP21.3) MUTATED    46  19  60   3
  DEL PEAK 47(XP21.3) WILD-TYPE 132  47 105   5
D76V5, multiclass
    clus
vv   DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  N0                          46                           132
  N1                          19                            47
  N2                          60                           105
  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"
D76V6, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED    51   1
  DEL PEAK 47(XP21.3) WILD-TYPE 132   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     51    1
  DEL PEAK 47(XP21.3) WILD-TYPE  132    0
   clus
vv  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  0                          51                           132
  1                           1                             0
[1] 2 2
[1] FALSE
D76V7, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED    37 119
  DEL PEAK 47(XP21.3) WILD-TYPE 102 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     37  119
  DEL PEAK 47(XP21.3) WILD-TYPE  102  258
        clus
vv       DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  FEMALE                          37                           102
  MALE                           119                           258
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(XP21.3) MUTATED                                     151
  DEL PEAK 47(XP21.3) WILD-TYPE                                   354
                               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                                               151
  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                                                 354
  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    30 126
  DEL PEAK 47(XP21.3) WILD-TYPE  51 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     30  126
  DEL PEAK 47(XP21.3) WILD-TYPE   51  309
     clus
vv    DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  NO                           30                            51
  YES                         126                           309
[1] 2 2
[1] FALSE
D76V10, continuous
D76V11, continuous
D76V12, 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   134
  DEL PEAK 47(XP21.3) WILD-TYPE                        31   307
D76V13, multiclass
                                  clus
vv                                 DEL PEAK 47(XP21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                    134
                                  clus
vv                                 DEL PEAK 47(XP21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      307
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED     9 135
  DEL PEAK 47(XP21.3) WILD-TYPE  16 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED      9  135
  DEL PEAK 47(XP21.3) WILD-TYPE   16  319
                        clus
vv                       DEL PEAK 47(XP21.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         135
                        clus
vv                       DEL PEAK 47(XP21.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           319
[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    51  29
  DEL PEAK 48(XQ21.33) WILD-TYPE 262 171
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            80                            433 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            29                            171 
$`DEL PEAK 48(XQ21.33) MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-6872 TCGA-BA-7269 
       15.19        13.64        37.28         9.07        12.62         7.76 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-4225 TCGA-BB-4227 
       20.45        27.95        14.47        20.48         4.60         4.41 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-A5HY TCGA-CN-4729 TCGA-CN-4735 
       36.72        50.20        24.66        10.55        12.89        41.10 
TCGA-CN-5360 TCGA-CN-6011 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A6V3 
       35.54        30.67        12.95        24.16        14.10         9.80 
TCGA-CN-A6V7 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        6.18        32.88         4.24        51.29        33.11        16.73 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-7370 
       31.23        11.77        54.67        34.52         7.69         3.45 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7388 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6935 
        3.09         0.99        27.06        86.83         9.60         9.70 
TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 
       42.38        65.82         7.13        28.34       126.15        18.81 
TCGA-CV-7236 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7430 
        4.73        25.08        25.94         0.07       100.57        16.27 
TCGA-CV-7435 TCGA-CV-A460 TCGA-CV-A6JU TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7219 
      153.86        60.43         3.62        22.52        10.42        34.36 
TCGA-D6-6827 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61W TCGA-IQ-A61G TCGA-IQ-A61J 
       18.67        37.18        20.25         0.46        11.84        14.47 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8Z8 
       15.78        56.75        51.25         2.04        16.70         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-TN-A7HJ TCGA-UF-A7JA TCGA-UF-A7JC 
       12.10         9.73         9.76        13.25        62.27        17.95 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

$`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 
        3.35         9.30        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
       17.10        23.84        20.48        53.79        57.44        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG 
       21.17        14.83         3.55         4.01        29.42        28.11 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       30.18        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
       11.05        13.38        16.41         6.15        94.62         9.14 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
       18.35        22.42        33.70        44.98        66.28        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        25.71        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        6.28        12.69        26.27        23.70        38.04         4.67 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
       40.44        37.84        26.86        32.65        21.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        43.73        27.58        41.69        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 
       33.11        34.36         8.58        12.39         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 
       11.54        11.84        11.57        12.49         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        20.71        20.68        20.65        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       19.07        14.20         6.74         9.07         9.24        36.49 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       11.08        10.45        20.09         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        17.29        15.91        11.44         5.75         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CQ-5323 
       12.07         2.70        10.09         7.33         7.69        48.20 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       39.68        21.50         2.93        54.58        46.75        45.80 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       45.99        10.42        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
       34.75        56.58        13.25        14.99        38.76        70.13 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       43.04        41.88        28.83        64.11        44.48        11.61 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        32.81        25.81        14.14        12.46 
TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       84.23        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       36.99        18.54        16.90         6.02        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64        12.46        11.51        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 
       47.18        39.16        47.34        40.93        35.84        24.95 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       29.23        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
       17.13        32.78        47.01        12.89        29.82        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       31.10        29.85        29.52        30.58         7.10         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.95        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      129.21       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       94.88        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       23.05        48.59        60.49         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 
       21.07        62.43        90.12         2.14         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       126.08        19.79 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       12.03        15.09        30.08         6.08        53.95        10.98 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 
        8.42         2.50         4.14        64.83       111.16        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        7.99         9.01         5.26         1.84        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
       21.80        71.21        10.75       130.88        77.16        47.47 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       36.00        31.36        26.20        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 
        4.96        11.87        47.97         2.10        36.13        18.41 
TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       57.47        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.46        22.85        34.09        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
       54.94         3.52        84.49        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        22.19        27.98        24.99       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      159.65        35.47         1.05        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        67.86         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        22.03 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       21.24        23.47        19.92        10.42        10.55        18.84 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       13.25        25.41         9.60        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        24.95        25.32        17.72        12.36        15.88 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        14.30        13.94        12.10        12.79        11.11 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
       58.45        35.54        30.94        33.86        18.02        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
       18.90        25.48        20.45         9.83        12.13        12.10 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       10.65        11.18        16.11        21.63         3.02        19.23 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       18.94        12.62        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
       13.38        15.16        15.06        13.61        21.11         6.77 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
        0.07         0.16        25.74         1.22        14.66        22.03 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       12.66        22.85         0.36        13.84         4.27         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        6.90        34.75        15.95        12.76        14.50        19.33 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
       13.55         0.07         5.29        11.54        11.84        13.35 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       18.15        12.43        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
        1.84        12.62         3.68        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       17.98        29.92        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       75.55        18.97        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        11.74        17.65         7.30         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3K 
       18.64        14.79        12.43         6.51        11.57         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.72        16.96         6.87        15.91         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.55        13.68        43.59        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       41.16        42.02        44.65        24.16        49.22        21.86 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       16.11        13.94        20.75        22.36        32.65         2.96 
TCGA-WA-A7H4 
       14.56 

  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                         16.88                          18.35 
[1] "0.1 - 153.9 (16.9)" "0.1 - 211.0 (18.4)"
[1] "hr=" "1"  
D77V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 48(XQ21.33) MUTATED         5        6        11        40         3
  DEL PEAK 48(XQ21.33) WILD-TYPE      22       71        66       212         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                             22
  STAGE II                             6                             71
  STAGE III                           11                             66
  STAGE IVA                           40                            212
  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  19  19  24
  DEL PEAK 48(XQ21.33) WILD-TYPE    43 114  80 148
D77V4, multiclass
       clus
vv      DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  T0+T1                            7                             43
  T2                              19                            114
  T3                              19                             80
  T4                              24                            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
  DEL PEAK 48(XQ21.33) MUTATED    19  14  28   1
  DEL PEAK 48(XQ21.33) WILD-TYPE 159  52 137   7
D77V5, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  N0                           19                            159
  N1                           14                             52
  N2                           28                            137
  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"
D77V6, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    26   1
  DEL PEAK 48(XQ21.33) WILD-TYPE 157   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     26    1
  DEL PEAK 48(XQ21.33) WILD-TYPE  157    0
   clus
vv  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  0                           26                            157
  1                            1                              0
[1] 2 2
[1] FALSE
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    20  60
  DEL PEAK 48(XQ21.33) WILD-TYPE 119 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     20   60
  DEL PEAK 48(XQ21.33) WILD-TYPE  119  317
        clus
vv       DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  FEMALE                           20                            119
  MALE                             60                            317
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD AND NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(XQ21.33) MUTATED                                      76
  DEL PEAK 48(XQ21.33) WILD-TYPE                                   429
                                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                                                 76
  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                                                  429
  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  70
  DEL PEAK 48(XQ21.33) WILD-TYPE  71 365
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     10   70
  DEL PEAK 48(XQ21.33) WILD-TYPE   71  365
     clus
vv    DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  NO                            10                             71
  YES                           70                            365
[1] 2 2
[1] FALSE
D77V10, continuous
D77V11, continuous
D77V12, 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    65
  DEL PEAK 48(XQ21.33) WILD-TYPE                        35   376
D77V13, multiclass
                                  clus
vv                                 DEL PEAK 48(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      65
                                  clus
vv                                 DEL PEAK 48(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       376
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED     5  69
  DEL PEAK 48(XQ21.33) WILD-TYPE  20 385
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED      5   69
  DEL PEAK 48(XQ21.33) WILD-TYPE   20  385
                        clus
vv                       DEL PEAK 48(XQ21.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 48(XQ21.33) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            385
[1] 2 2
[1] FALSE
