[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/22506490/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/22508724/transformed.cor.cli.txt"

nPatients in clinical file=528, in cluster file=522, common to both=522
[1]  76 522
[1] "AMP PEAK  1(2Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          107                           415 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          107                           415 
[1] "AMP PEAK  2(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          112                           410 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          112                           410 
[1] "AMP PEAK  3(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           380                            142 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           380                            142 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           240                            282 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           240                            282 
[1] "AMP PEAK  5(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                        205                         317 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                        205                         317 
[1] "AMP PEAK  6(6P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                          110                           412 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                          110                           412 
[1] "AMP PEAK  7(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         96                         426 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         96                         426 
[1] "AMP PEAK  8(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          222                           300 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          222                           300 
[1] "AMP PEAK  9(7Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                          169                           353 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                          169                           353 
[1] "AMP PEAK 10(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                           161                            361 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                           161                            361 
[1] "AMP PEAK 11(8Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                           310                            212 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                           310                            212 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           386                            136 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           386                            136 
[1] "AMP PEAK 13(9P24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                          126                           396 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                          126                           396 
[1] "AMP PEAK 14(9P23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                        124                         398 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                        124                         398 
[1] "AMP PEAK 15(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                          139                           383 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                          139                           383 
[1] "AMP PEAK 16(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                          177                           345 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                          177                           345 
[1] "AMP PEAK 17(11P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                         102                          420 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                         102                          420 
[1] "AMP PEAK 18(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           229                            293 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           229                            293 
[1] "AMP PEAK 19(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                            167                             355 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                            167                             355 
[1] "AMP PEAK 20(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                         103                          419 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                         103                          419 
[1] "AMP PEAK 21(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                           105                            417 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                           105                            417 
[1] "AMP PEAK 22(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                         106                          416 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                         106                          416 
[1] "AMP PEAK 23(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                           105                            417 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                           105                            417 
[1] "AMP PEAK 24(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          91                          431 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          91                          431 
[1] "AMP PEAK 25(18P11.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                            156                             366 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                            156                             366 
[1] "AMP PEAK 26(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                           106                            416 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                           106                            416 
[1] "AMP PEAK 27(20Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE 
                            227                             295 
  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE 
                            227                             295 
[1] "AMP PEAK 28(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                        150                         372 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                        150                         372 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            95                            427 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            95                            427 
[1] "DEL PEAK  2(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          133                           389 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          133                           389 
[1] "DEL PEAK  3(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         48                         474 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         48                         474 
[1] "DEL PEAK  4(2Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           78                           444 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           78                           444 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          121                           401 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          121                           401 
[1] "DEL PEAK  6(2Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          157                           365 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          157                           365 
[1] "DEL PEAK  7(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          348                           174 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          348                           174 
[1] "DEL PEAK  8(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          368                           154 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          368                           154 
[1] "DEL PEAK  9(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          372                           150 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          372                           150 
[1] "DEL PEAK 10(3P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          343                           179 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          343                           179 
[1] "DEL PEAK 11(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          205                           317 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          205                           317 
[1] "DEL PEAK 12(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE 
                          208                           314 
  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE 
                          208                           314 
[1] "DEL PEAK 13(4Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE 
                          156                           366 
  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE 
                          156                           366 
[1] "DEL PEAK 14(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE 
                          169                           353 
  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE 
                          169                           353 
[1] "DEL PEAK 15(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE 
                          213                           309 
  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE 
                          213                           309 
[1] "DEL PEAK 16(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE 
                          215                           307 
  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE 
                          215                           307 
[1] "DEL PEAK 17(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE 
                        226                         296 
  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE 
                        226                         296 
[1] "DEL PEAK 18(5Q35.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE 
                          199                           323 
  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE 
                          199                           323 
[1] "DEL PEAK 19(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE 
                           96                           426 
  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE 
                           96                           426 
[1] "DEL PEAK 20(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           77                           445 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           77                           445 
[1] "DEL PEAK 21(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE 
                          132                           390 
  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE 
                          132                           390 
[1] "DEL PEAK 22(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          305                           217 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          305                           217 
[1] "DEL PEAK 23(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        239                         283 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        239                         283 
[1] "DEL PEAK 24(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          302                           220 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          302                           220 
[1] "DEL PEAK 25(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           108                            414 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           108                            414 
[1] "DEL PEAK 26(9Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE 
                           79                           443 
  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE 
                           79                           443 
[1] "DEL PEAK 27(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           170                            352 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           170                            352 
[1] "DEL PEAK 28(10P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                            163                             359 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                            163                             359 
[1] "DEL PEAK 29(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE 
                            138                             384 
  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE 
                            138                             384 
[1] "DEL PEAK 30(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE 
                           163                            359 
  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE 
                           163                            359 
[1] "DEL PEAK 31(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE 
                           246                            276 
  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE 
                           246                            276 
[1] "DEL PEAK 32(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE 
                             63                             459 
  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE 
                             63                             459 
[1] "DEL PEAK 33(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            233                             289 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            233                             289 
[1] "DEL PEAK 34(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           217                            305 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           217                            305 
[1] "DEL PEAK 35(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                            75                            447 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                            75                            447 
[1] "DEL PEAK 36(14Q32.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE 
                             75                             447 
  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE 
                             75                             447 
[1] "DEL PEAK 37(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           124                            398 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           124                            398 
[1] "DEL PEAK 38(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            98                            424 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            98                            424 
[1] "DEL PEAK 39(16Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE 
                           105                            417 
  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE 
                           105                            417 
[1] "DEL PEAK 40(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                            99                            423 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                            99                            423 
[1] "DEL PEAK 41(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE 
                            71                            451 
  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE 
                            71                            451 
[1] "DEL PEAK 42(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         288                          234 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         288                          234 
[1] "DEL PEAK 43(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           175                            347 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           175                            347 
[1] "DEL PEAK 44(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             97                             425 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             97                             425 
[1] "DEL PEAK 45(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           208                            314 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           208                            314 
[1] "DEL PEAK 46(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          157                           365 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          157                           365 
[1] "DEL PEAK 47(XP21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          159                           363 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          159                           363 
[1] "DEL PEAK 48(XQ21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            80                            442 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            80                            442 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 522 columns.

[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=202,	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=286,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 522 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"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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  49 137 100 173 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   50   137   100   173 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  49 137 100 173 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   50   137   100   173 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
179  68 168   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
179  68 168   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
179  68 168   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
179  68 168   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, 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=19, 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    55  52
  AMP PEAK  1(2Q11.2) WILD-TYPE 246 167
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                          107                           413 
  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                           52                           167 
$`AMP PEAK  1(2Q11.2) MUTATED`
TCGA-BA-4075 TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6024 TCGA-CR-6478 TCGA-CX-7219 
        9.30        51.29        52.08        11.08         6.02        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-4076 TCGA-BA-5555 TCGA-BA-6872 
       30.94        14.04        46.32        13.64        17.10        12.62 
TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 
       29.42        20.48        16.41        50.20        66.28        71.05 
TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 
       56.68        20.55        27.58        13.05        46.32        12.39 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A63T 
       50.07        48.00        19.07        10.45        38.89         7.40 
TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 
       12.39        10.42        13.25        77.56        11.77        16.90 
TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7383 
       11.64        39.16        47.34         3.45        24.95        17.13 
TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
       49.58       139.43        17.16       129.21       108.95        19.20 
TCGA-CV-5440 TCGA-CV-5973 TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 
      107.51        86.83        90.12         5.46        20.52        26.43 
TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7103 
       11.24        15.09        30.08        28.34         4.14        52.31 
TCGA-CV-7178 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7254 
       71.21        36.00        26.20        18.97        95.34        47.97 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7422 
       49.71        18.41        35.54        17.85         0.46        34.09 
TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X 
       14.89       153.86        16.64        35.47        45.96         6.51 
TCGA-CV-A45Z TCGA-CV-A465 TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-8569 TCGA-D6-A4ZB 
       48.20         7.07        35.34        18.84        25.32        12.36 
TCGA-D6-A6EP TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-7229 TCGA-HD-A6HZ TCGA-HD-A6I0 
       13.94        37.58        20.25        33.76         3.65         6.90 
TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-P3-A5Q6 TCGA-P3-A6T5 TCGA-QK-A6IJ TCGA-QK-A6VB 
        5.29        19.04        15.78        29.00        12.72        21.07 
TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-UF-A719 
       12.89        12.20        12.72        15.91        13.55        54.67 
TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-KU-A66T 
        2.83        44.65        55.43        18.05        18.15 

$`AMP PEAK  1(2Q11.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       25.71         9.07         9.24        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       11.61        34.52         0.36        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 
       22.85        48.03         2.96         3.35        15.19         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH 
       15.52        21.17        14.83         4.01        41.85        20.45 
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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        13.38         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ 
       44.98        24.66        38.40        20.52        10.55        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        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 
       57.11        12.99        14.33        45.83        73.61        42.02 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
        8.58        71.31         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        52.08        56.94        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 
       23.90        47.44        28.04        34.13         6.74        32.22 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       17.29        29.72        21.21        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
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        46.95 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       56.58         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.88        43.10        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
       29.49        14.14        12.46        31.23        84.23        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       18.54        11.90        10.22        11.34         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
       22.78        15.75         9.27        47.18        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.09        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        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 
        5.13         5.95        35.41        29.95        48.39        76.24 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95        94.88        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-6934 TCGA-CV-6935 
       54.74        21.07        62.43         9.60         2.14         9.70 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
        4.73        21.90       140.78        19.79        12.03        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-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        64.83       172.67       111.16        18.81        12.66 
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-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
       10.75       130.88        77.16         4.73        89.65        31.36 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7410 
       17.13         4.96        11.87         2.10        57.47       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-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-7438 TCGA-CV-7440 TCGA-CV-A45O 
       84.49        19.76         7.17         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y 
       21.01       169.38       180.16       159.65         1.05        88.87 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        67.86         0.76        56.61        15.25         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        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ 
       23.47        19.92        22.52        10.42        10.55        51.12 
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-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
       11.44        18.67        24.95        17.72        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       22.59        24.95        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
       37.25        33.86        18.02        46.45        20.45        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       39.12        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 
       22.03         0.36        13.84         4.27        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       33.57        13.68        13.84        15.48        19.27        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         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        29.92        71.74 
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-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       18.97         2.04        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 
       21.21        23.15         7.30        21.47         9.34        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       19.73         5.62        14.76        17.82        15.32         8.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA 
       13.25        20.35        64.80        49.51        49.45        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       17.95        24.30        29.46        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        20.55        14.56        13.35 

  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE 
                         0.46                          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 
                        20.48                         21.21 
[1] "0.5 - 153.9 (20.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  1(2Q11.2) MUTATED         2       11        18        59         2
  AMP PEAK  1(2Q11.2) WILD-TYPE      25       65        64       193        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                            65
  STAGE III                          18                            64
  STAGE IVA                          59                           193
  STAGE IVB                           2                            10
  STAGE IVC                           0                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T0+T1  T2  T3  T4
  AMP PEAK  1(2Q11.2) MUTATED       5  19  27  44
  AMP PEAK  1(2Q11.2) WILD-TYPE    45 118  73 129
D1V4, multiclass
       clus
vv      AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  T0+T1                           5                            45
  T2                             19                           118
  T3                             27                            73
  T4                             44                           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  1(2Q11.2) MUTATED    37   9  41   2
  AMP PEAK  1(2Q11.2) WILD-TYPE 142  59 127   6
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  N0                          37                           142
  N1                           9                            59
  N2                          41                           127
  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    36   0
  AMP PEAK  1(2Q11.2) WILD-TYPE 154   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     36    0
  AMP PEAK  1(2Q11.2) WILD-TYPE  154    1
   clus
vv  AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  0                          36                           154
  1                           0                             1
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED    23  84
  AMP PEAK  1(2Q11.2) WILD-TYPE 117 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     23   84
  AMP PEAK  1(2Q11.2) WILD-TYPE  117  298
        clus
vv       AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  FEMALE                          23                           117
  MALE                            84                           298
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED    26  64
  AMP PEAK  1(2Q11.2) WILD-TYPE 136 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED     26   64
  AMP PEAK  1(2Q11.2) WILD-TYPE  136  237
     clus
vv    AMP PEAK  1(2Q11.2) MUTATED AMP PEAK  1(2Q11.2) WILD-TYPE
  NO                           26                           136
  YES                          64                           237
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(2Q11.2) MUTATED                                   106
  AMP PEAK  1(2Q11.2) WILD-TYPE                                 405
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  1(2Q11.2) MUTATED                                                   1
  AMP PEAK  1(2Q11.2) WILD-TYPE                                                 9
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  1(2Q11.2) MUTATED                                                           0
  AMP PEAK  1(2Q11.2) WILD-TYPE                                                         1
D1V9, multiclass
                                                           clus
vv                                                          AMP PEAK  1(2Q11.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               106
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          AMP PEAK  1(2Q11.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 405
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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    88
  AMP PEAK  1(2Q11.2) WILD-TYPE                        36   358
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     88
                                  clus
vv                                 AMP PEAK  1(2Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q11.2) MUTATED     7  91
  AMP PEAK  1(2Q11.2) WILD-TYPE  19 368
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q11.2) MUTATED      7   91
  AMP PEAK  1(2Q11.2) WILD-TYPE   19  368
                        clus
vv                       AMP PEAK  1(2Q11.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          91
                        clus
vv                       AMP PEAK  1(2Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           368
[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    55  57
  AMP PEAK  2(2Q31.2) WILD-TYPE 246 162
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                          112                           408 
  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE 
                           57                           162 
$`AMP PEAK  2(2Q31.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6024 
        9.30        37.28        28.11        30.18         9.07        11.08 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-BA-4076 TCGA-BA-6872 TCGA-BA-A4IF 
       34.36        30.94        14.04        13.64        12.62        29.42 
TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-8596 TCGA-BB-A5HY 
       27.95        20.48        16.41        50.20        71.05        10.55 
TCGA-CN-4728 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-6012 TCGA-CN-6989 TCGA-CN-6994 
       56.68        13.05        12.39        48.00        32.22        38.89 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6225 
        7.40        12.39        45.99        10.42        56.58        13.25 
TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6477 
       14.99        77.56        23.24        31.23        11.77        16.90 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7390 
       39.16         3.45         0.99        19.92        17.13        49.58 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 
      139.43        17.16       129.21       108.95        19.20       107.51 
TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 
        7.07        90.12         9.70        26.43        11.24        12.03 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       15.09        30.08         4.14       111.16        18.81        12.66 
TCGA-CV-7103 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 
       52.31        71.21        77.16        36.00        26.20        18.97 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7418 
       95.34        47.97        49.71        18.41        35.54        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7437 
       34.09       100.57        14.89         3.52       153.86        16.64 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A6JM TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-8569 
        6.51        48.20         6.38        18.84        23.05        25.32 
TCGA-D6-A4ZB TCGA-DQ-7592 TCGA-F7-A623 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       12.36        37.58        20.25         4.27         3.65         6.90 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67D TCGA-MZ-A7D7 
       11.84        37.41        19.04        15.48         1.84        17.98 
TCGA-P3-A5Q6 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A6VB TCGA-QK-A8Z9 
       15.78        29.00        12.99        13.15        21.07        14.76 
TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       12.20        15.91        13.71        54.67         2.83        49.51 
TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-KU-A66T 
       44.65        55.43        18.05        18.15 

$`AMP PEAK  2(2Q31.2) WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 
       20.48        68.48         3.55        25.71        51.29         9.24 
TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       52.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       32.88        70.13        16.73        43.04        11.61        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        6.02         0.36        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 
       22.85        48.03         2.96         3.35        15.19         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-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 
       65.59        15.52        21.17        14.83         4.01        41.85 
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       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HZ 
       44.98        66.28        24.66        38.40        20.52        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        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       73.61        42.02        46.32         8.58        71.31         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-6013 TCGA-CN-6016 
       52.08        56.94        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6995 
       28.04        19.07        34.13         6.74        10.45         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 
       21.50         2.93        54.58        70.45        62.37        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 
        4.24        41.19        32.38        46.95         4.24        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       64.87        53.52        41.88        43.10        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 
       33.60        29.49        14.14        12.46        84.23        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       18.54        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
       12.46        22.78        15.75         9.27        47.18        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       40.93        35.84         3.09        24.95        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        9.17        34.06        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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       24.79         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       76.24        17.95        94.88        76.50        91.53        80.12 
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-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       43.23        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       140.78        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-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 
        8.42        28.34         2.50        64.83       172.67         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-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7252 
      130.88         4.73        89.65        31.36        17.13         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       11.87         2.10        57.47        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7425 
        9.67         0.46        22.85        25.08         0.07        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-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        6.38        22.19        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 
      159.65        35.47         1.05        45.96        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        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ 
       23.47        19.92        22.52        10.42        10.55        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       18.67        24.95        17.72        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
       37.25        33.86        18.02        46.45        20.45        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       39.12        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       33.76        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HL-7533 TCGA-IQ-7630 
       14.66        22.03         0.36        13.84        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       38.53        14.50        37.71         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.68        13.84        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05        12.62         6.25        15.42         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       29.92        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-QK-A64Z 
       19.00        75.55        18.97         2.04        16.01        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J 
       27.39        19.73        12.89         5.62        17.82        15.32 
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-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71E 
        3.12        13.55        13.25        20.35        64.80        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO 
       74.47        17.95        24.30        29.46        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 

  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 
                       19.120                        21.355 
[1] "1.0 - 153.9 (19.1)" "0.1 - 211.0 (21.4)"
[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        15        58         3
  AMP PEAK  2(2Q31.2) WILD-TYPE      25       59        67       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                            59
  STAGE III                          15                            67
  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  27  24  42
  AMP PEAK  2(2Q31.2) WILD-TYPE    43 110  76 131
D2V4, multiclass
       clus
vv      AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  T0+T1                           7                            43
  T2                             27                           110
  T3                             24                            76
  T4                             42                           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    35   9  42   2
  AMP PEAK  2(2Q31.2) WILD-TYPE 144  59 126   6
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  N0                          35                           144
  N1                           9                            59
  N2                          42                           126
  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    32   0
  AMP PEAK  2(2Q31.2) WILD-TYPE 158   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     32    0
  AMP PEAK  2(2Q31.2) WILD-TYPE  158    1
   clus
vv  AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  0                          32                           158
  1                           0                             1
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED    23  89
  AMP PEAK  2(2Q31.2) WILD-TYPE 117 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     23   89
  AMP PEAK  2(2Q31.2) WILD-TYPE  117  293
        clus
vv       AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  FEMALE                          23                           117
  MALE                            89                           293
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED    22  67
  AMP PEAK  2(2Q31.2) WILD-TYPE 140 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED     22   67
  AMP PEAK  2(2Q31.2) WILD-TYPE  140  234
     clus
vv    AMP PEAK  2(2Q31.2) MUTATED AMP PEAK  2(2Q31.2) WILD-TYPE
  NO                           22                           140
  YES                          67                           234
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2Q31.2) MUTATED                                   111
  AMP PEAK  2(2Q31.2) WILD-TYPE                                 400
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  2(2Q31.2) MUTATED                                                   1
  AMP PEAK  2(2Q31.2) WILD-TYPE                                                 9
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  2(2Q31.2) MUTATED                                                           0
  AMP PEAK  2(2Q31.2) WILD-TYPE                                                         1
D2V9, multiclass
                                                           clus
vv                                                          AMP PEAK  2(2Q31.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               111
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          AMP PEAK  2(2Q31.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 400
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          14    90
  AMP PEAK  2(2Q31.2) WILD-TYPE                        34   356
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                     90
                                  clus
vv                                 AMP PEAK  2(2Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   34
  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"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q31.2) MUTATED     9  93
  AMP PEAK  2(2Q31.2) WILD-TYPE  17 366
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q31.2) MUTATED      9   93
  AMP PEAK  2(2Q31.2) WILD-TYPE   17  366
                        clus
vv                       AMP PEAK  2(2Q31.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       AMP PEAK  2(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           366
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q26.33) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  3(3Q26.33) MUTATED   215 164
  AMP PEAK  3(3Q26.33) WILD-TYPE  86  55
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           379                            141 
  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE 
                           164                             55 
$`AMP PEAK  3(3Q26.33) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       32.88        16.73        11.61        34.52         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       34.36        30.94        46.32        12.66        22.85        48.03 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
       13.64         9.07        26.50        23.74        57.93        17.10 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD 
       41.85        29.42        20.45        27.95        11.54         5.69 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        20.48        16.41       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 
        4.80         4.41        22.42        33.70        50.20        66.28 
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-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        26.86        32.81        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       46.32         8.58        12.39        71.31         8.32        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.54        11.84        11.57        52.08        56.94        50.07 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       48.00        23.90        47.44        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 
       10.45        32.22        38.89         3.68        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       25.41        23.57        17.29        29.72        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5329 
       31.69        12.39        12.07        20.88        19.53        70.45 
TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       10.42        32.38        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 
       14.99        38.76        64.87        53.52        41.88        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
       44.48        23.24        29.36        29.49        14.14        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
       36.99        18.54        16.90        11.90        10.22        11.64 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
        7.69        12.46        22.78        15.75        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-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        19.92        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
       27.06        12.89        49.58        24.79         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       29.95        48.39       139.43        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
       76.24        19.20        17.95       107.51        76.50        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
       17.92        13.35        86.83        60.49         7.07        54.74 
TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       21.07        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       21.90        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-6961 
       30.08         6.08        65.82         7.13         8.42         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7100 
        4.14        64.83       172.67       111.16        12.66         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        89.65        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        49.71        18.41        57.47        35.54        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-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7433 
        0.07        34.09       100.57        14.89        16.27        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W 
        7.17       153.86        16.64       180.16        35.47        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 
        6.51        88.87        48.20        60.43        67.86         7.07 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-A4AQ 
       35.34         6.38         3.62        23.47        18.84        51.12 
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        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        58.45        33.86        18.02        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        39.12        41.59        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
        3.02        31.13        18.94        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       11.80        20.25        15.06        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 
       21.93        27.48        27.48        14.66        22.03        13.84 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
        4.27         3.65        34.75        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.68        19.04        15.48 
TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       19.27        14.37         7.96         6.25        15.42         7.13 
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        71.74        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-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
       13.15        21.07        21.21        21.47        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M 
       15.32        12.72        16.96        15.91         7.10        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD 
        2.83        49.51        49.45        44.65        74.47        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ 
       55.43        29.46        13.94        20.75        32.65        20.55 
TCGA-KU-A66T 
       18.15 

$`AMP PEAK  3(3Q26.33) WILD-TYPE`
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-UF-A7JV 
       70.13        43.04        14.04        40.24        21.11         2.96 
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        18.38        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        48.76        52.14        12.49         8.52 
TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       30.67        28.04        17.42        22.32        16.57         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
        2.70        23.44        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-7071 
       62.37        45.99        11.21         4.24        41.19        43.10 
TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6482 TCGA-CR-6493 
       33.60        12.46        26.27        39.52        11.34         9.27 
TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7391 TCGA-CR-7392 
       47.34        29.23        31.96        26.17        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CV-5441 TCGA-CV-5443 
       32.65        44.25        30.58         5.13        94.88        91.53 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6938 
       23.05        48.59        43.23        62.43         9.60         4.73 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-7095 
      140.78        19.79        53.95        10.98        28.34        18.81 
TCGA-CV-7099 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7411 TCGA-CV-7425 TCGA-CV-7427 
        7.99       130.88        77.16        89.33        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       54.94         3.52        84.49         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A463 TCGA-CV-A464 
       21.01       169.38       159.65         1.05         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY 
       15.25         5.98        29.79         6.48        28.01        21.24 
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-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-DQ-5625 
        2.53        11.44        18.67        28.77        22.59        37.25 
TCGA-DQ-7590 TCGA-F7-7848 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       46.45        37.18        12.43        13.38        15.16        20.94 
TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O 
        0.36         6.90        15.95        38.53        14.50        13.84 
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        23.15         7.30         9.34        17.82 
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        18.05        22.36 
TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       17.03        14.56        13.35 

  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 
                         21.07                          21.24 
[1] "0.1 - 211.0 (21.1)" "0.4 - 169.4 (21.2)"
[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       48        62       186        11
  AMP PEAK  3(3Q26.33) WILD-TYPE      11       28        20        66         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                            48                             28
  STAGE III                           62                             20
  STAGE IVA                          186                             66
  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  95  75 128
  AMP PEAK  3(3Q26.33) WILD-TYPE    15  42  25  45
D3V4, multiclass
       clus
vv      AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  T0+T1                           35                             15
  T2                              95                             42
  T3                              75                             25
  T4                             128                             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   122  51 130   7
  AMP PEAK  3(3Q26.33) WILD-TYPE  57  17  38   1
D3V5, multiclass
    clus
vv   AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  N0                          122                             57
  N1                           51                             17
  N2                          130                             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   135   1
  AMP PEAK  3(3Q26.33) WILD-TYPE  55   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED    135    1
  AMP PEAK  3(3Q26.33) WILD-TYPE   55    0
   clus
vv  AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  0                          135                             55
  1                            1                              0
[1] 2 2
[1] FALSE
D3V7, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED    89 291
  AMP PEAK  3(3Q26.33) WILD-TYPE  51  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     89  291
  AMP PEAK  3(3Q26.33) WILD-TYPE   51   91
        clus
vv       AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  FEMALE                           89                             51
  MALE                            291                             91
[1] 2 2
[1] FALSE
D3V8, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED   110 222
  AMP PEAK  3(3Q26.33) WILD-TYPE  52  79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED    110  222
  AMP PEAK  3(3Q26.33) WILD-TYPE   52   79
     clus
vv    AMP PEAK  3(3Q26.33) MUTATED AMP PEAK  3(3Q26.33) WILD-TYPE
  NO                           110                             52
  YES                          222                             79
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(3Q26.33) MUTATED                                   372
  AMP PEAK  3(3Q26.33) WILD-TYPE                                 139
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  3(3Q26.33) MUTATED                                                   8
  AMP PEAK  3(3Q26.33) WILD-TYPE                                                 2
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  3(3Q26.33) MUTATED                                                           0
  AMP PEAK  3(3Q26.33) WILD-TYPE                                                         1
D3V9, multiclass
                                                           clus
vv                                                          AMP PEAK  3(3Q26.33) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                372
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          AMP PEAK  3(3Q26.33) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  139
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          39   319
  AMP PEAK  3(3Q26.33) WILD-TYPE                         9   127
D3V13, multiclass
                                  clus
vv                                 AMP PEAK  3(3Q26.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  39
  WHITE                                                     319
                                  clus
vv                                 AMP PEAK  3(3Q26.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                       127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.33) MUTATED    18 332
  AMP PEAK  3(3Q26.33) WILD-TYPE   8 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.33) MUTATED     18  332
  AMP PEAK  3(3Q26.33) WILD-TYPE    8  127
                        clus
vv                       AMP PEAK  3(3Q26.33) MUTATED
  HISPANIC OR LATINO                               18
  NOT HISPANIC OR LATINO                          332
                        clus
vv                       AMP PEAK  3(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            127
[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   139 100
  AMP PEAK  4(5P15.33) WILD-TYPE 162 119
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           239                            281 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           100                            119 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 
       25.71        51.29        52.08        35.05        32.48        24.39 
TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6478 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       32.88        16.73         6.02        30.94        14.04        46.32 
TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       22.85        48.03         3.35        15.19        13.64         9.07 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       17.10        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
       12.62         4.01        41.85        29.42        27.95         7.10 
TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
       14.47        11.05        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 
        9.14         4.41        18.38        22.42        50.20        44.98 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 
       71.05        20.52         6.28        55.86        38.04        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       26.86        32.81        12.99        20.55        14.33        45.83 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 
       12.39         8.32        11.84        50.07        30.67        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
        6.74        10.45        38.89        25.41        17.29        29.72 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5330 TCGA-CQ-6224 
       31.69        12.39        23.44        20.88        62.37        56.58 
TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 
       13.25        64.87        77.56        33.60        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-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       12.46        15.75         9.27        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7390 
       35.84        34.06        19.92        17.13        12.89        49.58 
TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 
       46.85        24.79         5.13         5.95        48.39        17.16 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
      108.95        76.24        17.95       107.51        76.50        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6936 
       17.92        13.35        86.83         9.60        90.12         5.46 
TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6956 
       20.52        26.43        11.24        12.03        65.82         7.13 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        8.42         2.50       172.67       111.16        18.81        12.66 
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-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7407 
       10.75        77.16        36.00        26.20        47.97        35.54 
TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 
       17.85        25.08         0.07       100.57        14.89         3.52 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z 
      153.86        16.64       180.16        35.47         6.51        48.20 
TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CX-7086 
        0.76         7.07        15.25        35.34         6.38        18.84 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO TCGA-DQ-5624 
        9.60        23.05        24.95        25.32        24.95        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 
       33.86        18.02        46.45        37.58        40.04        41.59 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 
       31.13        18.94         0.46        17.85        20.25        15.06 
TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ 
       20.94        28.47        21.93        27.48        14.66         3.65 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG 
       34.75        15.95        37.71        33.57        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN 
       15.48        19.27        14.37         7.96         1.84        15.42 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX 
        7.13        17.98        15.78        71.74        36.82        47.01 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 
       75.55        18.97         2.04        29.00        12.99        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.07        21.21         7.30        21.47        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T3-A92M TCGA-TN-A7HI 
       15.32         8.32        12.72        15.91        13.71        13.55 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
        2.83        49.51        74.47        55.43        29.46        13.94 
TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S TCGA-KU-A66T 
       22.36        17.03        20.55        13.35        18.15 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-BA-5557 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CQ-5323 
       20.48         9.07         9.24        11.08        19.82        48.20 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 
       70.13        43.04        11.61        34.52         0.36        34.36 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A7JV TCGA-BA-5149 TCGA-BA-5151 
       40.24        21.11        12.66         2.96        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DF 
       42.35        57.93        20.45        11.54         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 
        2.27        13.38         4.80        36.72        33.70        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        38.40        10.55        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 
       12.69        48.76         4.67        56.68        52.14        57.11 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 
       71.31        16.21        11.54        11.57        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       52.08        56.94        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       19.07        32.22         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 
       23.57        21.21         7.40        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       12.07         2.70        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       41.19        32.38        46.95         4.24        14.99        38.76 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       53.52        41.88        43.10        44.48        23.24        29.36 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 
       29.49        14.14        12.46        11.77        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       50.01        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 
       22.78        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        32.65        44.25        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 
      140.78        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        89.65        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        49.71 
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        21.01       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        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.42        10.55        51.12        13.25        25.41 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
        2.53        16.14        11.44        18.67        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77         7.63        22.59        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 
       23.34        37.25        20.45        39.12        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A624 
       21.63        20.25         3.02        24.95        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 
       13.38        15.16        33.76        25.74        27.48        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 
        0.36        13.84         4.27         6.90        38.53        14.50 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H8 
       11.84        37.41         0.07         5.29        13.68        10.75 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
       30.05        12.62         6.25        16.08        29.92        51.25 
TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T7 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A8ZB 
       10.85        19.00        16.01        23.15         9.34        17.82 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HJ 
       16.96         6.87         7.10        32.45         3.12        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
       20.35        64.80        54.67        49.45        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7H4 
       24.30        18.05        20.75        32.65        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 
                         20.55                          21.63 
[1] "0.1 - 180.2 (20.6)" "0.1 - 211.0 (21.6)"
[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        40       113         7
  AMP PEAK  4(5P15.33) WILD-TYPE      19       46        42       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                             46
  STAGE III                           40                             42
  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 64 47 76
  AMP PEAK  4(5P15.33) WILD-TYPE    32 73 53 97
D4V4, multiclass
       clus
vv      AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  T0+T1                           18                             32
  T2                              64                             73
  T3                              47                             53
  T4                              76                             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    64  36  81   4
  AMP PEAK  4(5P15.33) WILD-TYPE 115  32  87   4
D4V5, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  N0                           64                            115
  N1                           36                             32
  N2                           81                             87
  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    84   1
  AMP PEAK  4(5P15.33) WILD-TYPE 106   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     84    1
  AMP PEAK  4(5P15.33) WILD-TYPE  106    0
   clus
vv  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  0                           84                            106
  1                            1                              0
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    54 186
  AMP PEAK  4(5P15.33) WILD-TYPE  86 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     54  186
  AMP PEAK  4(5P15.33) WILD-TYPE   86  196
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                           54                             86
  MALE                            186                            196
[1] 2 2
[1] FALSE
D4V8, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    66 150
  AMP PEAK  4(5P15.33) WILD-TYPE  96 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     66  150
  AMP PEAK  4(5P15.33) WILD-TYPE   96  151
     clus
vv    AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  NO                            66                             96
  YES                          150                            151
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                   234
  AMP PEAK  4(5P15.33) WILD-TYPE                                 277
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  4(5P15.33) MUTATED                                                   5
  AMP PEAK  4(5P15.33) WILD-TYPE                                                 5
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  4(5P15.33) MUTATED                                                           1
  AMP PEAK  4(5P15.33) WILD-TYPE                                                         0
D4V9, multiclass
                                                           clus
vv                                                          AMP PEAK  4(5P15.33) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                234
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          AMP PEAK  4(5P15.33) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  277
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          30   200
  AMP PEAK  4(5P15.33) WILD-TYPE                        18   246
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  30
  WHITE                                                     200
                                  clus
vv                                 AMP PEAK  4(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                       246
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    16 209
  AMP PEAK  4(5P15.33) WILD-TYPE  10 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     16  209
  AMP PEAK  4(5P15.33) WILD-TYPE   10  250
                        clus
vv                       AMP PEAK  4(5P15.33) MUTATED
  HISPANIC OR LATINO                               16
  NOT HISPANIC OR LATINO                          209
                        clus
vv                       AMP PEAK  4(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            250
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5P12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(5P12) MUTATED   122  82
  AMP PEAK  5(5P12) WILD-TYPE 179 137
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                        204                         316 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                         82                         137 
$`AMP PEAK  5(5P12) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6023 
        9.30        68.48        28.11        25.71        51.29        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7067 
       11.08        35.05        32.48        24.39        48.20        16.73 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 
       30.94        46.32        22.85        48.03         3.35        15.19 
TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
        9.07        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       12.62        41.85        29.42        27.95        11.54         7.10 
TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 
       14.47        11.05        20.48         6.15       105.90         4.41 
TCGA-BB-7861 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z 
       22.42        66.28        71.05        20.52        10.55         6.28 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 
       12.89        26.86        32.81        20.55        14.33        13.05 
TCGA-CN-5356 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 
       46.32        11.84        50.07        30.67        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W 
       10.45        38.89        25.41        29.72        31.69        12.39 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5330 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6225 
       23.44        20.88        62.37        41.19        56.58        13.25 
TCGA-CQ-7072 TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 
       77.56        33.60        84.23        58.42        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 
       18.54        16.90        11.64        12.46         9.27        39.16 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7389 
       47.34        40.93        35.84        34.06        17.13        12.89 
TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
       46.85         5.13         5.95        48.39        17.16       129.21 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
       76.24        17.95       107.51        76.50        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6933 
       13.35        86.83         7.07        43.23         9.60        90.12 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6956 
        5.46        20.52        11.24        12.03        65.82         7.13 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
        8.42         2.50       172.67       111.16        18.81         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7242 
        1.84        52.31        12.92        21.80        10.75        36.00 
TCGA-CV-7245 TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 
       26.20        35.54        25.08         0.07       100.57        14.89 
TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z 
        3.52        16.64       180.16        35.47         6.51        48.20 
TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CX-7086 TCGA-D6-6517 
        0.76         7.07        35.34         6.38        18.84         9.60 
TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO TCGA-DQ-5630 TCGA-DQ-5631 
       23.05        24.95        25.32        24.95        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W 
       46.45        37.58        41.59        31.13        18.94         0.46 
TCGA-F7-A620 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       17.85        20.94        28.47        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61O 
       14.66         3.65        15.95        37.71        33.57        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       19.04        15.48        19.27        14.37         7.96         1.84 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       15.42         7.13        16.08        17.98        15.78        71.74 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        75.55        18.97         2.04        29.00 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
       13.15        21.07        21.21         7.30        21.47        12.72 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K 
       21.07        19.73        12.89        14.76        15.32         8.32 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JA 
       12.72        15.91        13.55         2.83        49.51        74.47 
TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S 
       55.43        13.94        22.36        17.03        20.55        13.35 

$`AMP PEAK  5(5P12) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6022 
       37.28        20.48         3.55        30.18         9.07         9.24 
TCGA-CN-A6V1 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       19.82        32.88        70.13        43.04        11.61        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        6.02         0.36        34.36        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-UF-A7JV TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       12.66         2.96        13.64        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6DD TCGA-BA-A6DF 
       57.93        14.83         4.01        20.45         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
        2.27        13.38        16.41         9.14         4.80        18.38 
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-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19        12.92         8.81        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       38.04         4.67        56.68        52.14        57.11        12.99 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       45.83        27.58        73.61        42.02         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 
       71.31         8.32        16.21        11.54        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        8.52        52.08        56.94        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       28.04        19.07        32.22         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       35.01        23.57        17.29        21.21         7.40        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V7 TCGA-CQ-5324 
       16.57         4.41        12.07         2.70        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        54.58        70.45        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
       11.21         4.24        32.38        46.95         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       38.76        64.87        53.52        41.88        43.10        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        29.36        29.49        14.14        12.46        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6480 
       11.77        54.67        37.87        26.27        50.01        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
       10.22        11.34         7.69        22.78        15.75        47.18 
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-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        9.17        19.92        26.17        32.78        47.01        27.06 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       49.58        30.02        32.65        44.25        30.58        24.79 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 
       35.41        29.95       139.43       108.95        19.20        94.88 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 
       91.53        23.05        48.59        60.49        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
       62.43         2.14         9.70         4.73        21.90        26.43 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      140.78        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-7097 
       53.95        10.98        28.34         4.14        64.83        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
        7.99         9.01        71.21       130.88        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       89.65        31.36        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        49.71        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-7418 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
       25.94        34.09        56.48       156.49        54.94        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-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W 
       27.98        21.01       169.38       159.65         1.05        45.96 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       88.87        60.43        67.86        56.61        15.25         5.98 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.42        10.55        51.12        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-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        28.77         7.63        22.59        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7591 TCGA-DQ-7594 
       12.79        23.34        58.45        37.25        20.45        40.04 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       24.95        11.80        20.25        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       15.06        33.76        25.74        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
        4.27         6.90        34.75        38.53        14.50        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A67A 
       37.41         0.07         5.29        13.68        10.75        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6T0 
       12.62         6.25        29.92        51.25        10.85        19.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z8 
       12.99        16.01        23.15         9.34        27.39         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       12.20        17.82        16.96         6.87         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       13.71         3.12        13.25        20.35        64.80        54.67 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ 
       49.45        44.65        17.95        24.30        29.46        18.05 
TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66T 
       20.75        32.65        14.56        18.15 

  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                       0.07                        0.07 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                     180.16                      210.97 
  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE 
                     20.715                      21.565 
[1] "0.1 - 180.2 (20.7)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.1"
D5V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  5(5P12) MUTATED         9       24        37       103         3
  AMP PEAK  5(5P12) WILD-TYPE      18       52        45       149         9
                             vv
clus                          STAGE IVC
  AMP PEAK  5(5P12) MUTATED           0
  AMP PEAK  5(5P12) WILD-TYPE         1
D5V3, multiclass
           clus
vv          AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  STAGE I                           9                          18
  STAGE II                         24                          52
  STAGE III                        37                          45
  STAGE IVA                       103                         149
  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  5(5P12) MUTATED      17  52  46  64
  AMP PEAK  5(5P12) WILD-TYPE    33  85  54 109
D5V4, multiclass
       clus
vv      AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  T0+T1                        17                          33
  T2                           52                          85
  T3                           46                          54
  T4                           64                         109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  5(5P12) MUTATED    58  31  75   2
  AMP PEAK  5(5P12) WILD-TYPE 121  37  93   6
D5V5, multiclass
    clus
vv   AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  N0                        58                         121
  N1                        31                          37
  N2                        75                          93
  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(5P12) MUTATED    73   0
  AMP PEAK  5(5P12) WILD-TYPE 117   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED     73    0
  AMP PEAK  5(5P12) WILD-TYPE  117    1
   clus
vv  AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  0                        73                         117
  1                         0                           1
[1] 2 2
[1] FALSE
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(5P12) MUTATED    48 157
  AMP PEAK  5(5P12) WILD-TYPE  92 225
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED     48  157
  AMP PEAK  5(5P12) WILD-TYPE   92  225
        clus
vv       AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  FEMALE                        48                          92
  MALE                         157                         225
[1] 2 2
[1] FALSE
D5V8, binary
                             cls
clus                            0   1
  AMP PEAK  5(5P12) MUTATED    55 128
  AMP PEAK  5(5P12) WILD-TYPE 107 173
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED     55  128
  AMP PEAK  5(5P12) WILD-TYPE  107  173
     clus
vv    AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  NO                         55                         107
  YES                       128                         173
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(5P12) MUTATED                                   200
  AMP PEAK  5(5P12) WILD-TYPE                                 311
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  5(5P12) MUTATED                                                   4
  AMP PEAK  5(5P12) WILD-TYPE                                                 6
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  5(5P12) MUTATED                                                           1
  AMP PEAK  5(5P12) WILD-TYPE                                                         0
D5V9, multiclass
                                                           clus
vv                                                          AMP PEAK  5(5P12) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                             200
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                         1
                                                           clus
vv                                                          AMP PEAK  5(5P12) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               311
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
D5V11, continuous
D5V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(5P12) MUTATED                                  1     4
  AMP PEAK  5(5P12) WILD-TYPE                                1     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5P12) MUTATED                          22   173
  AMP PEAK  5(5P12) WILD-TYPE                        26   273
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(5P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               22
  WHITE                                                  173
                                  clus
vv                                 AMP PEAK  5(5P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                             cls
clus                            0   1
  AMP PEAK  5(5P12) MUTATED    14 178
  AMP PEAK  5(5P12) WILD-TYPE  12 281
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(5P12) MUTATED     14  178
  AMP PEAK  5(5P12) WILD-TYPE   12  281
                        clus
vv                       AMP PEAK  5(5P12) MUTATED AMP PEAK  5(5P12) WILD-TYPE
  HISPANIC OR LATINO                            14                          12
  NOT HISPANIC OR LATINO                       178                         281
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(6P12.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(6P12.1) MUTATED    60  49
  AMP PEAK  6(6P12.1) WILD-TYPE 241 170
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                          109                           411 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                           49                           170 
$`AMP PEAK  6(6P12.1) MUTATED`
TCGA-BA-4075 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CQ-7067 
        9.30        30.18        25.71         9.24        52.08        16.73 
TCGA-CQ-A4C7 TCGA-DQ-7589 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 
       11.61        46.32        17.10        15.52        12.62         4.01 
TCGA-BA-A6DI TCGA-BB-7870 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 
       11.05        66.28        10.55         6.28        55.86        38.04 
TCGA-CN-4736 TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6020 TCGA-CN-6989 
       12.99        46.32        11.54        11.57         6.74        32.22 
TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A6V6 TCGA-CQ-5329 
       17.29        31.69        12.39         4.41        20.88        70.45 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-A4CE 
       45.99        10.42         4.24        32.38        13.25        29.49 
TCGA-CR-5247 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7399 
       11.77         7.69        40.93        12.89        46.85         5.95 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5442 
       29.95       139.43       129.21        76.24        94.88        76.50 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6945 TCGA-CV-6954 
       60.49        54.74        90.12        20.52        12.03        65.82 
TCGA-CV-6959 TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7248 
        8.42         5.26        71.21        77.16        31.36        17.13 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7435 
       11.87         2.10        35.54        22.85        25.94       153.86 
TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A6JE TCGA-CV-A6JT TCGA-CV-A6JU 
       22.19       180.16        35.47        35.34        28.01         3.62 
TCGA-D6-6823 TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-F7-A623 
       23.05        13.94        23.34        58.45        37.25        20.25 
TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6I0 
       15.06        28.47        21.93        27.48        14.66         6.90 
TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A67D TCGA-MZ-A5BI 
       37.71        13.68        15.48        14.37         1.84         7.13 
TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z7 
       36.82        75.55        18.97         7.30        21.07        12.89 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 
       14.76        12.20        12.72        15.91        13.25        54.67 
TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7H4 
       44.65        24.30        55.43        29.46        13.94        14.56 
TCGA-KU-A66T 
       18.15 

$`AMP PEAK  6(6P12.1) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 
       37.28        20.48        68.48         3.55        28.11        51.29 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.07        11.08        35.05        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 
       48.20        32.88        70.13        43.04        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A4IF 
       23.84        65.59        21.17        14.83        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       20.45        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        7.82         2.27        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 
      105.90         9.14         4.80         4.41        18.38        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-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-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       48.76         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       52.14        57.11        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       73.61        13.05        42.02         8.58        12.39        71.31 
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        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6995 
       28.04        19.07        34.13        10.45        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       17.42        11.74        35.01        25.41        23.57        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 
       21.21         7.40        22.32        16.57        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       23.44        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
       62.37        11.21        41.19        46.95        56.58         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       77.56        44.48        23.24        29.36        33.60        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-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        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        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
       15.75         9.27        47.18        39.16        47.34        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-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
       47.01        27.06        49.58        30.02        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 
       30.58        24.79         5.13        35.41        48.39        17.16 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5443 TCGA-CV-5444 
      108.95        19.20        17.95       107.51        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       17.92        13.35        23.05        86.83        48.59         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-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46         4.73        21.90        26.43        11.24       140.78 
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-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-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       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-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        89.65        36.00        26.20        18.97        95.34 
TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
        4.96        47.97        49.71        18.41        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 
      210.97        89.33         9.67         0.46        25.08         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
        3.52        16.27        84.49        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V 
        6.38        27.98        21.01       169.38       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-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       29.79         6.48        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        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-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       24.95        12.10        12.79        33.86        18.02        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        37.58        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 
       15.16        20.94        33.76        25.74        27.48        22.03 
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-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
        5.29        13.84        19.04        19.27        10.75         7.96 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       30.05        12.62         6.25        15.42        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX 
       29.92        15.78        71.74        51.25        10.85        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 
       19.00         2.04        29.00        12.99        16.01        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21        23.15        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       27.39        19.73         5.62        17.82        15.32         8.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.55        20.35        64.80         2.83        49.51        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       74.47        17.95        18.05        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S 
       17.03        20.55        13.35 

  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                         1.84                          0.07 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                       180.16                        210.97 
  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE 
                        20.88                         21.17 
[1] "1.8 - 180.2 (20.9)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1"  
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  6(6P12.1) MUTATED         4       17        18        52         4
  AMP PEAK  6(6P12.1) WILD-TYPE      23       59        64       200         8
                               vv
clus                            STAGE IVC
  AMP PEAK  6(6P12.1) MUTATED           0
  AMP PEAK  6(6P12.1) WILD-TYPE         1
D6V3, multiclass
           clus
vv          AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  STAGE I                             4                            23
  STAGE II                           17                            59
  STAGE III                          18                            64
  STAGE IVA                          52                           200
  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  6(6P12.1) MUTATED       6  30  26  37
  AMP PEAK  6(6P12.1) WILD-TYPE    44 107  74 136
D6V4, multiclass
       clus
vv      AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  T0+T1                           6                            44
  T2                             30                           107
  T3                             26                            74
  T4                             37                           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  6(6P12.1) MUTATED    38  12  41   2
  AMP PEAK  6(6P12.1) WILD-TYPE 141  56 127   6
D6V5, multiclass
    clus
vv   AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  N0                          38                           141
  N1                          12                            56
  N2                          41                           127
  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(6P12.1) MUTATED    41   0
  AMP PEAK  6(6P12.1) WILD-TYPE 149   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED     41    0
  AMP PEAK  6(6P12.1) WILD-TYPE  149    1
   clus
vv  AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  0                          41                           149
  1                           0                             1
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(6P12.1) MUTATED    26  84
  AMP PEAK  6(6P12.1) WILD-TYPE 114 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED     26   84
  AMP PEAK  6(6P12.1) WILD-TYPE  114  298
        clus
vv       AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  FEMALE                          26                           114
  MALE                            84                           298
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(6P12.1) MUTATED    36  63
  AMP PEAK  6(6P12.1) WILD-TYPE 126 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED     36   63
  AMP PEAK  6(6P12.1) WILD-TYPE  126  238
     clus
vv    AMP PEAK  6(6P12.1) MUTATED AMP PEAK  6(6P12.1) WILD-TYPE
  NO                           36                           126
  YES                          63                           238
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(6P12.1) MUTATED                                   108
  AMP PEAK  6(6P12.1) WILD-TYPE                                 403
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  6(6P12.1) MUTATED                                                   2
  AMP PEAK  6(6P12.1) WILD-TYPE                                                 8
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  6(6P12.1) MUTATED                                                           0
  AMP PEAK  6(6P12.1) WILD-TYPE                                                         1
D6V9, multiclass
                                                           clus
vv                                                          AMP PEAK  6(6P12.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               108
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          AMP PEAK  6(6P12.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 403
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, continuous
D6V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(6P12.1) MUTATED                                  0     1
  AMP PEAK  6(6P12.1) WILD-TYPE                                2    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(6P12.1) MUTATED                          17    87
  AMP PEAK  6(6P12.1) WILD-TYPE                        31   359
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(6P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                     87
                                  clus
vv                                 AMP PEAK  6(6P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      359
[1] 4 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(6P12.1) MUTATED     5  96
  AMP PEAK  6(6P12.1) WILD-TYPE  21 363
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P12.1) MUTATED      5   96
  AMP PEAK  6(6P12.1) WILD-TYPE   21  363
                        clus
vv                       AMP PEAK  6(6P12.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          96
                        clus
vv                       AMP PEAK  6(6P12.1) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           363
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(6Q12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(6Q12) MUTATED    50  45
  AMP PEAK  7(6Q12) WILD-TYPE 251 174
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         95                         425 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         45                         174 
$`AMP PEAK  7(6Q12) MUTATED`
TCGA-BA-4075 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CQ-7067 
        9.30        30.18        25.71         9.24        52.08        16.73 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DI 
        6.02         0.36        34.36        12.62         4.01        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-A5HY TCGA-C9-A47Z 
       20.48        16.41        36.72        66.28        10.55         6.28 
TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5367 
       55.86        12.99        27.58        46.32        11.54        11.57 
TCGA-CN-6010 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A6V6 TCGA-CQ-5329 
       50.07        31.69        12.39         4.41        20.88        70.45 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-A4CE TCGA-CR-5247 
       45.99        10.42         4.24        32.38        29.49        11.77 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7397 TCGA-CV-5430 
        7.69        22.78         3.45        12.89        24.79       139.43 
TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 
      129.21       107.51        76.50        86.83        60.49        54.74 
TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7178 
       90.12        20.52        65.82         8.42         4.14        71.21 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7407 TCGA-CV-7434 
       77.16        31.36        17.13        11.87        35.54         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A461 TCGA-CV-A465 
      153.86        16.64        22.19       180.16        67.86         7.07 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-D6-6823 TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5624 
       35.34         6.38        23.05        13.94        12.10        58.45 
TCGA-DQ-5625 TCGA-HD-7229 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6I0 
       37.25        33.76        21.93        27.48        14.66         6.90 
TCGA-IQ-A61E TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A67D 
       37.71         5.29        13.68        15.48        14.37         1.84 
TCGA-MZ-A5BI TCGA-P3-A5Q6 TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA 
        7.13        15.78         7.30        21.07        14.76        12.20 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A7JD TCGA-KU-A66T 
       12.72        15.91        13.71        24.30        18.15 

$`AMP PEAK  7(6Q12) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 
       37.28        20.48        68.48         3.55        28.11        51.29 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.07        11.08        35.05        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       48.20        32.88        70.13        43.04        11.61        34.52 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       30.94        14.04        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-7269 
       23.84        65.59        15.52        21.17        14.83        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       29.42        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
       14.47         7.82         2.27        13.38         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        9.14         4.80         4.41        18.38        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-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
       27.19        12.92         8.81        12.69        48.76        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       57.11        20.55        14.33        45.83        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       42.02         8.58        12.39        71.31         8.32        16.21 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
       11.84        12.49         8.52        52.08        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       48.00        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 
       21.21         7.40        22.32        16.57        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       23.44        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       62.37        11.21        41.19        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
        4.24        14.99        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       43.10        77.56        44.48        23.24        29.36        33.60 
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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 
       16.90        11.90        10.22        11.34        11.64        12.46 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        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-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        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58         5.13         5.95        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       48.39        17.16       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-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-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 
       30.08         6.08        53.95        10.98         7.13        28.34 
TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        64.83       172.67       111.16        18.81        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-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       21.80        10.75       130.88         4.73        89.65        36.00 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7255 
       26.20        18.97        95.34         4.96        47.97         2.10 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       49.71        18.41        57.47        17.85       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-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-A45O 
        3.52        16.27        84.49        19.76         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       21.01       169.38       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 
        6.51        88.87        48.20        60.43         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       15.25         5.98        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       18.84        51.12        13.25        25.41         9.60         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6ES 
       12.36        28.77         7.63        22.59        24.95        12.79 
TCGA-D6-A74Q TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        33.86        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.04        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         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-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 
       15.06        20.94        28.47        25.74        27.48        22.03 
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-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        11.84        37.41         0.07        33.57 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A 
       13.84        19.04        19.27        10.75         7.96        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       12.62         6.25        15.42        16.08        17.98        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        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-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       13.15        21.07        21.21        23.15        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB 
       12.72        27.39        19.73        12.89         5.62        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       15.32         8.32        16.96         6.87         7.10        32.45 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
        3.12        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        20.55        14.56        13.35 

  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                       0.36                        0.07 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                     180.16                      210.97 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                      18.15                       21.24 
[1] "0.4 - 180.2 (18.1)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D7V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  7(6Q12) MUTATED         3       13        17        44         2
  AMP PEAK  7(6Q12) WILD-TYPE      24       63        65       208        10
                             vv
clus                          STAGE IVC
  AMP PEAK  7(6Q12) MUTATED           0
  AMP PEAK  7(6Q12) WILD-TYPE         1
D7V3, multiclass
           clus
vv          AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  STAGE I                           3                          24
  STAGE II                         13                          63
  STAGE III                        17                          65
  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  7(6Q12) MUTATED       5  26  22  31
  AMP PEAK  7(6Q12) WILD-TYPE    45 111  78 142
D7V4, multiclass
       clus
vv      AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  T0+T1                         5                          45
  T2                           26                         111
  T3                           22                          78
  T4                           31                         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  7(6Q12) MUTATED    30  12  33   2
  AMP PEAK  7(6Q12) WILD-TYPE 149  56 135   6
D7V5, multiclass
    clus
vv   AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  N0                        30                         149
  N1                        12                          56
  N2                        33                         135
  N3                         2                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                             cls
clus                            0   1
  AMP PEAK  7(6Q12) MUTATED    32   0
  AMP PEAK  7(6Q12) WILD-TYPE 158   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED     32    0
  AMP PEAK  7(6Q12) WILD-TYPE  158    1
   clus
vv  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  0                        32                         158
  1                         0                           1
[1] 2 2
[1] FALSE
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(6Q12) MUTATED    27  69
  AMP PEAK  7(6Q12) WILD-TYPE 113 313
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED     27   69
  AMP PEAK  7(6Q12) WILD-TYPE  113  313
        clus
vv       AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  FEMALE                        27                         113
  MALE                          69                         313
[1] 2 2
[1] FALSE
D7V8, binary
                             cls
clus                            0   1
  AMP PEAK  7(6Q12) MUTATED    34  53
  AMP PEAK  7(6Q12) WILD-TYPE 128 248
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED     34   53
  AMP PEAK  7(6Q12) WILD-TYPE  128  248
     clus
vv    AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  NO                         34                         128
  YES                        53                         248
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(6Q12) MUTATED                                    96
  AMP PEAK  7(6Q12) WILD-TYPE                                 415
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  7(6Q12) MUTATED                                                   0
  AMP PEAK  7(6Q12) WILD-TYPE                                                10
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  7(6Q12) MUTATED                                                           0
  AMP PEAK  7(6Q12) WILD-TYPE                                                         1
D7V9, multiclass
                                                           clus
vv                                                          AMP PEAK  7(6Q12) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                              96
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                         0
                                                           clus
vv                                                          AMP PEAK  7(6Q12) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               415
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
D7V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(6Q12) MUTATED                                  0     1
  AMP PEAK  7(6Q12) WILD-TYPE                                2    10
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(6Q12) MUTATED                          14    77
  AMP PEAK  7(6Q12) WILD-TYPE                        34   369
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(6Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                               14
  WHITE                                                   77
                                  clus
vv                                 AMP PEAK  7(6Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                 34
  WHITE                                                    369
[1] 4 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(6Q12) MUTATED     7  83
  AMP PEAK  7(6Q12) WILD-TYPE  19 376
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED      7   83
  AMP PEAK  7(6Q12) WILD-TYPE   19  376
                        clus
vv                       AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             7                          19
  NOT HISPANIC OR LATINO                        83                         376
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(7P11.2) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(7P11.2) MUTATED   108 112
  AMP PEAK  8(7P11.2) WILD-TYPE 193 107
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          220                           300 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                          112                           107 
$`AMP PEAK  8(7P11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
        9.30        30.18        25.71         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 
       35.05        32.48        16.73        43.04        11.61         6.02 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-HD-8634 TCGA-BA-4074 
       34.36        30.94        14.04        46.32        12.66        15.19 
TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       13.64        26.50        17.10        14.83        12.62        41.85 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7863 
       14.47         2.27        11.05        20.48         9.14        33.70 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4722 
       66.28        71.05        20.52        10.55         6.28        48.76 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 
        4.67        12.89        26.86        32.81        20.55        14.33 
TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
       45.83        46.32         8.58        12.39         8.32        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
       11.84        11.57        30.67        48.00        23.90         6.74 
TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
       10.45         3.68        17.29        29.72         7.40        22.32 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 
       12.39         4.41        12.07        70.45        62.37         4.24 
TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 
       32.38        13.25        38.76        41.88        77.56        23.24 
TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7365 
       12.46        18.54        16.90        11.64        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       47.34         3.45        29.23         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 
       26.17        12.89        49.58        24.79         5.13       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
       17.16       129.21        17.95       107.51        76.50        80.12 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       48.59         7.07        90.12         2.14         9.70         5.46 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 
       26.43        11.24        12.03        15.09        30.08        53.95 
TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7091 
       65.82         8.42        28.34         4.14       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 
       18.81         5.26         1.84        21.80        10.75        77.16 
TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        4.73        36.00        31.36        26.20        18.97        17.13 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7418 
        2.10        18.41        35.54        17.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7429 
        0.07        34.09       100.57        14.89        56.48         3.52 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X 
      153.86        16.64        22.19        35.47         1.05         6.51 
TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ 
       48.20         0.76         6.38         6.48        28.01        23.47 
TCGA-CV-A6K0 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 
       19.92        18.84        25.41         9.60        23.05        11.44 
TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ 
       18.67        25.32        28.77         7.63        13.94        12.10 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 
       58.45        37.25        18.02        37.58        37.18        32.71 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A622 TCGA-HD-7229 TCGA-HD-7753 
        3.02        31.13        18.94        11.80        33.76        28.47 
TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7631 TCGA-IQ-7632 
       21.93        27.48        13.84         3.65        38.53        14.50 
TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51W 
       37.41         5.29        13.84        19.04        15.48        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 
        7.96        30.05         1.84         6.25        15.42        17.98 
TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 
       15.78        47.01        18.97         2.04        12.99        13.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       21.47         9.34        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M 
       12.20         8.32        12.72        15.91        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD 
        3.12        13.25         2.83        49.45        44.65        24.30 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-KU-A66T 
       29.46        13.94        20.55        18.15 

$`AMP PEAK  8(7P11.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 
       37.28        20.48        68.48         3.55        28.11        51.29 
TCGA-CN-6021 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
        9.07        19.82        24.39        48.20        32.88        70.13 
TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D 
       34.52         0.36        40.24        21.11        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
        2.96         3.35         9.07        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF 
       23.84        65.59        15.52        21.17         4.01        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF 
       20.45        27.95        11.54         7.10         5.69         7.82 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
       13.38        16.41         6.15       105.90         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       18.38        22.42        36.72        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4723 
       38.40        27.19        12.92         8.81        12.69        55.86 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 
       38.04        56.68        52.14        57.11        12.99        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5369 
       73.61        13.05        42.02        71.31        16.21        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        56.94        50.07        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
       19.07        34.13        32.22        38.89        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y 
       35.01        25.41        23.57        21.21        31.69        16.57 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 
        2.93        54.58        45.99        10.42        11.21        41.19 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        56.58         4.24        14.99        64.87        53.52 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       43.10        44.48        29.36        33.60        29.49        14.14 
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-6473 TCGA-CR-6480 TCGA-CR-6481 
       58.42        50.01        39.52        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        22.78        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        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       32.65        44.25        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       140.78        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        89.65        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        49.71        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 
       21.01       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-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 
       10.55        51.12        13.25         2.53        16.14        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q 
       17.72        12.36        22.59        24.95        12.79        23.34 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       33.86        46.45        20.45        40.04        39.12        41.59 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       21.63        20.25        24.95         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7754 
       12.43        13.38        15.16        15.06        20.94        25.74 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
       27.48        14.66        22.03         0.36         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J 
       34.75        15.95        37.71        11.84         0.07        33.57 
TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 
       13.68        19.27        10.75        12.62         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       29.92        71.74        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       75.55        29.00        16.01        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8ZB TCGA-QK-AA3J 
        7.30        12.72        27.39        21.07        17.82        15.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
       16.96         6.87         7.10        13.55        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ 
       54.67        49.51        74.47        17.95        55.43        18.05 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        17.03        14.56        13.35 

  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                       172.67                        210.97 
  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE 
                        18.28                         22.95 
[1] "0.1 - 172.7 (18.3)" "0.1 - 211.0 (23.0)"
[1] "hr=" "1.7"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  8(7P11.2) MUTATED        10       33        37       113         7
  AMP PEAK  8(7P11.2) WILD-TYPE      17       43        45       139         5
                               vv
clus                            STAGE IVC
  AMP PEAK  8(7P11.2) MUTATED           1
  AMP PEAK  8(7P11.2) WILD-TYPE         0
D8V3, multiclass
           clus
vv          AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  STAGE I                            10                            17
  STAGE II                           33                            43
  STAGE III                          37                            45
  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  8(7P11.2) MUTATED      14 58 53 79
  AMP PEAK  8(7P11.2) WILD-TYPE    36 79 47 94
D8V4, multiclass
       clus
vv      AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  T0+T1                          14                            36
  T2                             58                            79
  T3                             53                            47
  T4                             79                            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  8(7P11.2) MUTATED    76  28  79   4
  AMP PEAK  8(7P11.2) WILD-TYPE 103  40  89   4
D8V5, multiclass
    clus
vv   AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  N0                          76                           103
  N1                          28                            40
  N2                          79                            89
  N3                           4                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    76   1
  AMP PEAK  8(7P11.2) WILD-TYPE 114   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     76    1
  AMP PEAK  8(7P11.2) WILD-TYPE  114    0
   clus
vv  AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  0                          76                           114
  1                           1                             0
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    61 161
  AMP PEAK  8(7P11.2) WILD-TYPE  79 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     61  161
  AMP PEAK  8(7P11.2) WILD-TYPE   79  221
        clus
vv       AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  FEMALE                          61                            79
  MALE                           161                           221
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    72 119
  AMP PEAK  8(7P11.2) WILD-TYPE  90 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     72  119
  AMP PEAK  8(7P11.2) WILD-TYPE   90  182
     clus
vv    AMP PEAK  8(7P11.2) MUTATED AMP PEAK  8(7P11.2) WILD-TYPE
  NO                           72                            90
  YES                         119                           182
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(7P11.2) MUTATED                                   219
  AMP PEAK  8(7P11.2) WILD-TYPE                                 292
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  8(7P11.2) MUTATED                                                   2
  AMP PEAK  8(7P11.2) WILD-TYPE                                                 8
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  8(7P11.2) MUTATED                                                           1
  AMP PEAK  8(7P11.2) WILD-TYPE                                                         0
D8V9, multiclass
                                                           clus
vv                                                          AMP PEAK  8(7P11.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               219
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          AMP PEAK  8(7P11.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 292
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, continuous
D8V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(7P11.2) MUTATED                                  1     4
  AMP PEAK  8(7P11.2) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(7P11.2) MUTATED                          29   182
  AMP PEAK  8(7P11.2) WILD-TYPE                        19   264
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 29
  WHITE                                                    182
                                  clus
vv                                 AMP PEAK  8(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                               cls
clus                              0   1
  AMP PEAK  8(7P11.2) MUTATED    10 198
  AMP PEAK  8(7P11.2) WILD-TYPE  16 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P11.2) MUTATED     10  198
  AMP PEAK  8(7P11.2) WILD-TYPE   16  261
                        clus
vv                       AMP PEAK  8(7P11.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         198
                        clus
vv                       AMP PEAK  8(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           261
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(7Q21.3) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(7Q21.3) MUTATED    79  90
  AMP PEAK  9(7Q21.3) WILD-TYPE 222 129
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                          169                           351 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                           90                           129 
$`AMP PEAK  9(7Q21.3) MUTATED`
TCGA-BA-4075 TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 TCGA-CQ-7067 
        9.30        51.29        52.08        11.08        32.48        16.73 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       11.61         6.02        34.36        30.94        14.04        46.32 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DE TCGA-BA-A6DI 
       15.52        14.83        12.62        41.85        14.47        11.05 
TCGA-BA-A8YP TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       16.41        33.70        66.28        71.05        20.52        10.55 
TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       48.76        12.89        57.11        14.33        45.83        27.58 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
       46.32         8.58        71.31         8.32        11.54        11.84 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
       11.57        50.07        30.67        48.00        23.90         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       10.45        32.22         3.68        17.29        29.72         7.40 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6225 
       22.32        12.39        12.07         2.93        10.42        13.25 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-6491 TCGA-CR-7367 
       41.88        77.56        23.24        11.77        22.78        47.34 
TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 
        3.45        17.13        27.06        12.89        49.58         5.95 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
      139.43        17.16       129.21       108.95        76.24        17.95 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6933 
      107.51        76.50        80.12         7.07         9.60        90.12 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 
        9.70         5.46        26.43        11.24        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7177 
       30.08        28.34         4.14       172.67         5.26        21.80 
TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 
       71.21        77.16        26.20        18.97        17.13        47.97 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7414 
       49.71        18.41        35.54        17.85         9.67         0.46 
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-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45V 
       56.48        19.76       153.86        22.19        35.47         1.05 
TCGA-CV-A45Z TCGA-CV-A463 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-CX-7086 
       48.20         0.76        35.34         6.38        23.47        18.84 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EO 
       25.41        11.44        18.67        25.32        28.77        24.95 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 
       13.94        23.34        37.25        18.02        37.58        32.71 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7753 
        3.02        31.13        18.94        20.25        15.06        28.47 
TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 
       21.93        27.48        14.66         3.65        34.75        38.53 
TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-MT-A51W TCGA-MT-A51X 
       37.41         5.29        13.84        19.04        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T4 
       30.05         6.25        17.98        15.78        47.01         2.04 
TCGA-P3-A6T6 TCGA-QK-A6VC TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO TCGA-T3-A92M 
       12.99        19.73        12.20        15.32        12.72        13.71 
TCGA-T3-A92N TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JS 
        3.12        54.67         2.83        44.65        74.47        22.36 
TCGA-WA-A7GZ 
       20.55 

$`AMP PEAK  9(7Q21.3) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 
       25.71         9.07         9.24        35.05        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CX-7082 
       48.20        32.88        70.13        43.04        34.52         0.36 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
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-5558 TCGA-BA-6869 
       42.35        57.93        17.10        23.84        65.59        21.17 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        29.42        20.45        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 
      105.90         9.14         4.80         4.41        18.38        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-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        4.67        56.68        26.86        32.81        52.14        12.99 
TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5364 
       20.55        73.61        13.05        42.02        12.39        16.21 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 
       12.49         8.52        52.08        56.94        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       19.07        34.13        38.89        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A640 
       25.41        23.57        21.21        31.69        16.57         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        62.37        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
       41.19        32.38        46.95        56.58         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       38.76        64.87        53.52        43.10        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        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-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       39.16        40.93        35.84         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-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       32.78        47.01        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       30.58        24.79         5.13        35.41        29.95        48.39 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       19.20        94.88        91.53        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-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 
       62.43         2.14        20.52         4.73        21.90       140.78 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       19.79        42.38         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 
        7.13         8.42         2.50        64.83       111.16        18.81 
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-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       10.75       130.88         4.73        89.65        36.00        31.36 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7410 
       95.34         4.96        11.87         2.10        57.47       210.97 
TCGA-CV-7411 TCGA-CV-7415 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
       89.33        22.85       156.49        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
       84.49         7.17        16.64         6.38        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      169.38       180.16       159.65        45.96         6.51        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-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 
       29.79         6.48        28.01         3.62        21.24        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       22.52        10.42        10.55        51.12        13.25         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       23.05         2.53        16.14        24.95        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 
        7.63        22.59        12.10        12.79        58.45        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       46.45        20.45        40.04        39.12        41.59        37.18 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       21.63        20.25        24.95         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       12.43        13.38        15.16        20.94        33.76        25.74 
TCGA-HD-7832 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       27.48        22.03         0.36        13.84         4.27         6.90 
TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        14.50        37.71        11.84         0.07        33.57 
TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D TCGA-MT-A67F 
       13.68        15.48        19.27        10.75         1.84        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        71.74        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       10.85        36.82        19.00        75.55        18.97        29.00 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 
       21.47         9.34        12.72        27.39        21.07        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62        14.76        17.82         8.32        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        20.35 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       64.80        49.51        49.45        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW 
       29.46        18.05        13.94        20.75        32.65        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                       172.67                        210.97 
  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE 
                        19.76                         21.21 
[1] "0.1 - 172.7 (19.8)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.5"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK  9(7Q21.3) MUTATED         9       22        28        84         6
  AMP PEAK  9(7Q21.3) WILD-TYPE      18       54        54       168         6
                               vv
clus                            STAGE IVC
  AMP PEAK  9(7Q21.3) MUTATED           0
  AMP PEAK  9(7Q21.3) WILD-TYPE         1
D9V3, multiclass
           clus
vv          AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  STAGE I                             9                            18
  STAGE II                           22                            54
  STAGE III                          28                            54
  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  9(7Q21.3) MUTATED      13  35  37  66
  AMP PEAK  9(7Q21.3) WILD-TYPE    37 102  63 107
D9V4, multiclass
       clus
vv      AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  T0+T1                          13                            37
  T2                             35                           102
  T3                             37                            63
  T4                             66                           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  9(7Q21.3) MUTATED    58  19  56   5
  AMP PEAK  9(7Q21.3) WILD-TYPE 121  49 112   3
D9V5, multiclass
    clus
vv   AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  N0                          58                           121
  N1                          19                            49
  N2                          56                           112
  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"
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(7Q21.3) MUTATED    52   0
  AMP PEAK  9(7Q21.3) WILD-TYPE 138   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED     52    0
  AMP PEAK  9(7Q21.3) WILD-TYPE  138    1
   clus
vv  AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  0                          52                           138
  1                           0                             1
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(7Q21.3) MUTATED    43 126
  AMP PEAK  9(7Q21.3) WILD-TYPE  97 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED     43  126
  AMP PEAK  9(7Q21.3) WILD-TYPE   97  256
        clus
vv       AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  FEMALE                          43                            97
  MALE                           126                           256
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(7Q21.3) MUTATED    48  95
  AMP PEAK  9(7Q21.3) WILD-TYPE 114 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED     48   95
  AMP PEAK  9(7Q21.3) WILD-TYPE  114  206
     clus
vv    AMP PEAK  9(7Q21.3) MUTATED AMP PEAK  9(7Q21.3) WILD-TYPE
  NO                           48                           114
  YES                          95                           206
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(7Q21.3) MUTATED                                   167
  AMP PEAK  9(7Q21.3) WILD-TYPE                                 344
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK  9(7Q21.3) MUTATED                                                   1
  AMP PEAK  9(7Q21.3) WILD-TYPE                                                 9
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK  9(7Q21.3) MUTATED                                                           1
  AMP PEAK  9(7Q21.3) WILD-TYPE                                                         0
D9V9, multiclass
                                                           clus
vv                                                          AMP PEAK  9(7Q21.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               167
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          AMP PEAK  9(7Q21.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 344
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, continuous
D9V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(7Q21.3) MUTATED                                  1     1
  AMP PEAK  9(7Q21.3) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(7Q21.3) MUTATED                          27   138
  AMP PEAK  9(7Q21.3) WILD-TYPE                        21   308
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(7Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    138
                                  clus
vv                                 AMP PEAK  9(7Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      308
[1] 4 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(7Q21.3) MUTATED    10 149
  AMP PEAK  9(7Q21.3) WILD-TYPE  16 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7Q21.3) MUTATED     10  149
  AMP PEAK  9(7Q21.3) WILD-TYPE   16  310
                        clus
vv                       AMP PEAK  9(7Q21.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         149
                        clus
vv                       AMP PEAK  9(7Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           310
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(8P11.23) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(8P11.23) MUTATED    98  63
  AMP PEAK 10(8P11.23) WILD-TYPE 203 156
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                           161                            359 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                            63                            156 
$`AMP PEAK 10(8P11.23) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6022 TCGA-CN-6992 
        9.30        68.48         3.55        28.11         9.24        35.05 
TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-BA-5152 
       43.04         6.02         0.36        30.94        14.04        42.35 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DL 
       15.52        14.83        41.85        20.45         2.27        20.48 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
        6.15       105.90         9.14         4.80        18.38        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 
       36.72        50.20        66.28        24.66        71.05        20.52 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4739 
       48.76        38.04        56.68        12.89        32.81        45.83 
TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6012 
       27.58        42.02        46.32        12.39        50.07        48.00 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63V 
       19.07         6.74        38.89        23.57         7.40        22.32 
TCGA-CQ-5324 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       52.37        13.25        38.76        41.88        23.24        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6474 
       14.14        31.23        84.23        58.42        50.01        18.54 
TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       16.90        11.34         7.69        47.18        39.16        47.34 
TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 
        3.45         0.99        34.06        26.17        12.89        49.58 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-6003 
        5.95       139.43        17.16       107.51        76.50        54.74 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6945 
       21.07         9.60         2.14         5.46         4.73        12.03 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
       53.95        65.82       172.67       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7253 
        7.99         9.01        10.75        36.00        31.36        11.87 
TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 
       47.97        18.41        35.54         0.46        25.08         0.07 
TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45P TCGA-CV-A45R 
       34.09        16.27       153.86        22.19        21.01       180.16 
TCGA-CV-A45T TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A468 
      159.65        45.96         6.51        48.20        67.86        15.25 
TCGA-CV-A6JE TCGA-CV-A6K0 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-8568 
       35.34        19.92        18.84        25.41        11.44        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EP TCGA-DQ-5624 TCGA-DQ-5631 
       17.72        12.36        28.77        13.94        58.45        18.02 
TCGA-F7-A50J TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7917 
       31.13        20.25        12.43        20.94        28.47        27.48 
TCGA-HD-A634 TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67G 
        4.27        13.84        15.48        14.37         1.84         6.25 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-QK-A6VC TCGA-QK-A8Z8 
        7.13        17.98        15.78        51.25        19.73         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T3-A92M TCGA-TN-A7HI 
       17.82        15.32         8.32         6.87        13.71        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        55.43        29.46 
TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       22.36        20.55        14.56        13.35        18.15 

$`AMP PEAK 10(8P11.23) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
       37.28        20.48        30.18        25.71        51.29         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       52.08        11.08        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 
       32.88        70.13        16.73        11.61        34.52        34.36 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       46.32        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
        2.96         3.35        15.19        13.64         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 
       23.74        57.93        17.10        23.84        65.59        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
       12.62         4.01        29.42        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP 
        5.69        14.47         7.82        11.05        13.38        16.41 
TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A5HZ 
        4.41        33.70        44.98        38.40        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4726 
       12.92         8.81         6.28        12.69        55.86         4.67 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       26.86        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 
       73.61        13.05         8.58        71.31         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        52.08 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       56.94        30.67        23.90        47.44        28.04        34.13 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       10.45        32.22         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W 
       25.41        17.29        29.72        21.21        31.69        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       19.53        21.50         2.93        54.58        70.45        62.37 
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-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        56.58         4.24        14.99        64.87        53.52 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
       43.10        77.56        44.48        29.36        33.60        12.46 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 
       11.77        54.67        37.87        26.27        39.52        36.99 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.90        10.22        11.64        12.46        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        9.27        40.93        35.84         3.09        24.95        29.23 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
       31.96         9.17        19.92        17.13        32.78        47.01 
TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       27.06        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 
       24.79         5.13        35.41        29.95        48.39       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 
      108.95        76.24        19.20        17.95        94.88        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-6436 TCGA-CV-6933 TCGA-CV-6935 
       60.49         7.07        43.23        62.43        90.12         9.70 
TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
       20.52        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6955 TCGA-CV-6956 
       42.38        15.09        30.08         6.08        10.98         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7101 
        8.42        28.34         2.50         4.14        64.83         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 
        1.84        52.31        12.92        21.80        71.21       130.88 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
       77.16         4.73        89.65        26.20        18.97        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7409 
       95.34         4.96         2.10        49.71        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7423 
      210.97        89.33         9.67        22.85        25.94       100.57 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 
       14.89        56.48       156.49        54.94         3.52        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45Q 
       19.76         7.17        16.64         6.38        27.98       169.38 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 
       35.47         1.05        88.87        60.43         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        7.07         5.98         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
        3.62        21.24        23.47        22.52        10.42        10.55 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       51.12        13.25         9.60        23.05         2.53        16.14 
TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ 
       18.67        25.32         7.63        22.59        24.95        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
       12.79        23.34        37.25        33.86        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        40.04        39.12        41.59        37.18        32.71 
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        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
       17.85        11.80        13.38        15.16        15.06        33.76 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         0.36 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       13.84         3.65         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       14.50        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
        5.29        13.68        19.04        19.27        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        71.74 
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 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO 
       27.39        21.07        12.89        14.76        12.20        12.72 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HL 
       16.96        15.91         7.10        32.45         3.12        20.35 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
       64.80         2.83        49.51        49.45        74.47        24.30 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW 
       18.05        13.94        20.75        32.65        17.03 

  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE 
                         20.55                          21.21 
[1] "0.1 - 180.2 (20.6)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 10(8P11.23) MUTATED         8       29        29        68         0
  AMP PEAK 10(8P11.23) WILD-TYPE      19       47        53       184        12
                                vv
clus                             STAGE IVC
  AMP PEAK 10(8P11.23) MUTATED           1
  AMP PEAK 10(8P11.23) WILD-TYPE         0
D10V3, multiclass
           clus
vv          AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  STAGE I                              8                             19
  STAGE II                            29                             47
  STAGE III                           29                             53
  STAGE IVA                           68                            184
  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 10(8P11.23) MUTATED      16  52  28  43
  AMP PEAK 10(8P11.23) WILD-TYPE    34  85  72 130
D10V4, multiclass
       clus
vv      AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  T0+T1                           16                             34
  T2                              52                             85
  T3                              28                             72
  T4                              43                            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 10(8P11.23) MUTATED    55  23  46   0
  AMP PEAK 10(8P11.23) WILD-TYPE 124  45 122   8
D10V5, multiclass
    clus
vv   AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  N0                           55                            124
  N1                           23                             45
  N2                           46                            122
  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"
D10V6, binary
                                cls
clus                               0   1
  AMP PEAK 10(8P11.23) MUTATED    56   1
  AMP PEAK 10(8P11.23) WILD-TYPE 134   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED     56    1
  AMP PEAK 10(8P11.23) WILD-TYPE  134    0
   clus
vv  AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  0                           56                            134
  1                            1                              0
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(8P11.23) MUTATED    41 120
  AMP PEAK 10(8P11.23) WILD-TYPE  99 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED     41  120
  AMP PEAK 10(8P11.23) WILD-TYPE   99  262
        clus
vv       AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  FEMALE                           41                             99
  MALE                            120                            262
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(8P11.23) MUTATED    52  92
  AMP PEAK 10(8P11.23) WILD-TYPE 110 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED     52   92
  AMP PEAK 10(8P11.23) WILD-TYPE  110  209
     clus
vv    AMP PEAK 10(8P11.23) MUTATED AMP PEAK 10(8P11.23) WILD-TYPE
  NO                            52                            110
  YES                           92                            209
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(8P11.23) MUTATED                                   155
  AMP PEAK 10(8P11.23) WILD-TYPE                                 356
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 10(8P11.23) MUTATED                                                   5
  AMP PEAK 10(8P11.23) WILD-TYPE                                                 5
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 10(8P11.23) MUTATED                                                           1
  AMP PEAK 10(8P11.23) WILD-TYPE                                                         0
D10V9, multiclass
                                                           clus
vv                                                          AMP PEAK 10(8P11.23) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                155
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          AMP PEAK 10(8P11.23) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  356
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
D10V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(8P11.23) MUTATED                                  0     0
  AMP PEAK 10(8P11.23) WILD-TYPE                                2    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(8P11.23) MUTATED                          22   134
  AMP PEAK 10(8P11.23) WILD-TYPE                        26   312
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     134
                                  clus
vv                                 AMP PEAK 10(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    26
  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"
D10V14, binary
                                cls
clus                               0   1
  AMP PEAK 10(8P11.23) MUTATED     8 139
  AMP PEAK 10(8P11.23) WILD-TYPE  18 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8P11.23) MUTATED      8  139
  AMP PEAK 10(8P11.23) WILD-TYPE   18  320
                        clus
vv                       AMP PEAK 10(8P11.23) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          139
                        clus
vv                       AMP PEAK 10(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            320
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(8Q11.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(8Q11.21) MUTATED   178 131
  AMP PEAK 11(8Q11.21) WILD-TYPE 123  88
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                           309                            211 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                           131                             88 
$`AMP PEAK 11(8Q11.21) MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CQ-7063 TCGA-CQ-7067 
       25.71         9.24        11.08        35.05        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        11.61         6.02         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J 
       14.04        46.32        12.66        22.85         2.96         3.35 
TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
       26.50        17.10        65.59        15.52        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL 
        4.01        41.85        20.45         2.27        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       16.41         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 
       18.38        22.42        33.70        50.20        66.28        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       71.05        20.52        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-4728 
       12.69        48.76        55.86        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       12.89        32.81        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 
       27.58        13.05        42.02        46.32        12.39         8.32 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 
       11.84        11.57         8.52        52.08        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       47.44         6.74        38.89         3.68        17.42        11.74 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
       25.41        23.57        17.29        29.72         7.40        22.32 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 
       12.39         4.41         2.70        52.37        21.50        70.45 
TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 
       62.37        56.58        13.25         4.24        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       53.52        41.88        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 
       29.49        14.14        31.23        84.23        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       39.52        36.99        16.90        11.34        11.64         7.69 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
       12.46         9.27        39.16        47.34        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       24.95        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7399 
       17.13        47.01        27.06        12.89        49.58         5.95 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
       35.41       139.43       129.21        76.24        19.20       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 
       94.88        76.50        80.12        17.92        86.83        48.59 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 
       60.49        54.74        21.07        62.43        90.12         2.14 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        5.46        20.52         4.73        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       53.95         8.42        28.34         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 
      111.16        18.81        12.66        12.92        71.21        10.75 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        89.65        31.36        26.20        18.97 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7416 
       47.97         2.10        18.41        35.54        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-7438 
        0.07       100.57        14.89        54.94         7.17         6.38 
TCGA-CV-7440 TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45W 
       22.19        21.01       180.16       159.65        35.47        45.96 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
        6.51        48.20        67.86        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        28.01 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       23.47        19.92        18.84        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        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       22.59        24.95        13.94        12.10        12.79        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       37.25        33.86        37.58        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A623 
       20.25         3.02        31.13        18.94        17.85        20.25 
TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7831 
       12.43        15.16        15.06        20.94        33.76        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 
       27.48        27.48        14.66         4.27        34.75        15.95 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.71        37.41        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       19.04        14.37         7.96         6.25        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T7 
       17.98        71.74        51.25        18.97        29.00        16.01 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.07        21.21         7.30        21.47         9.34        12.72 
TCGA-QK-A6VB TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ 
       21.07        17.82         8.32        12.72         6.87        15.91 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.71        13.55        13.25        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

$`AMP PEAK 11(8Q11.21) WILD-TYPE`
TCGA-BA-4077 TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A6V1 
       37.28        51.29         9.07        52.08        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CR-6472 TCGA-DQ-7593 TCGA-H7-A6C5 
       24.39        48.20        32.88        34.52        40.24        21.11 
TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
       48.03        15.19        13.64         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-4730 TCGA-CN-4733 TCGA-CN-4735 
       44.98        24.66        12.92        26.86        52.14        57.11 
TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5369 
       73.61         8.58        71.31        16.21        11.54        12.49 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       56.94        50.07        30.67        28.04        19.07        34.13 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A497 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y 
       10.45        32.22        35.01        21.21        31.69        16.57 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5327 
       12.07        23.44        20.88        19.53         2.93        54.58 
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-6228 TCGA-CQ-7071 TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5247 
       46.95        14.99        43.10        33.60        12.46        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 
       54.67        37.87        26.27        18.54        11.90        10.22 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 
       22.78        15.75        47.18        40.93         3.09        29.23 
TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        0.99        32.78        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
       30.58        24.79         5.13        29.95        48.39        17.16 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 
      108.95        17.95        91.53        13.35        23.05         7.07 
TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6954 TCGA-CV-6955 
       43.23         9.60         9.70        21.90        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        7.13         2.50         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 
       52.31        21.80       130.88        36.00        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
        4.96        11.87        49.71        57.47        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7425 
       89.33         9.67         0.46        25.94        34.09        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
      156.49         3.52        16.27        84.49        19.76       153.86 
TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A460 
       16.64        27.98       169.38         1.05        88.87        60.43 
TCGA-CV-A463 TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
        0.76         3.62        21.24        22.52        10.42        10.55 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EM 
       51.12        13.25         2.53        16.14        18.67         7.63 
TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 
       23.34        18.02        46.45        20.45        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-H7-7774 TCGA-HD-7753 
       41.59        24.95         0.46        11.80        13.38        28.47 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 
       25.74        22.03         0.36        13.84         3.65         6.90 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A6SH TCGA-KU-A6H7 
       38.53        14.50        11.84         0.07        15.48        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       10.75        30.05         1.84        12.62        16.08        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       15.78        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A6VC 
        2.04        12.99        13.15        23.15        27.39        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TP 
       12.89         5.62        14.76        12.20        15.32        16.96 
TCGA-T2-A6X0 TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A71B TCGA-UF-A7JT TCGA-UP-A6WW 
        7.10         3.12        20.35        49.51        32.65        17.03 
TCGA-WA-A7GZ 
       20.55 

  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE 
                         21.07                          21.11 
[1] "0.1 - 180.2 (21.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 11(8Q11.21) MUTATED        18       45        59       143         7
  AMP PEAK 11(8Q11.21) WILD-TYPE       9       31        23       109         5
                                vv
clus                             STAGE IVC
  AMP PEAK 11(8Q11.21) MUTATED           0
  AMP PEAK 11(8Q11.21) WILD-TYPE         1
D11V3, multiclass
           clus
vv          AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  STAGE I                             18                              9
  STAGE II                            45                             31
  STAGE III                           59                             23
  STAGE IVA                          143                            109
  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 11(8Q11.21) MUTATED      32 78 67 99
  AMP PEAK 11(8Q11.21) WILD-TYPE    18 59 33 74
D11V4, multiclass
       clus
vv      AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  T0+T1                           32                             18
  T2                              78                             59
  T3                              67                             33
  T4                              99                             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 11(8Q11.21) MUTATED   105  46  99   4
  AMP PEAK 11(8Q11.21) WILD-TYPE  74  22  69   4
D11V5, multiclass
    clus
vv   AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  N0                          105                             74
  N1                           46                             22
  N2                           99                             69
  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"
D11V6, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q11.21) MUTATED   123   0
  AMP PEAK 11(8Q11.21) WILD-TYPE  67   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED    123    0
  AMP PEAK 11(8Q11.21) WILD-TYPE   67    1
   clus
vv  AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  0                          123                             67
  1                            0                              1
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q11.21) MUTATED    82 228
  AMP PEAK 11(8Q11.21) WILD-TYPE  58 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED     82  228
  AMP PEAK 11(8Q11.21) WILD-TYPE   58  154
        clus
vv       AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  FEMALE                           82                             58
  MALE                            228                            154
[1] 2 2
[1] FALSE
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(8Q11.21) MUTATED   105 172
  AMP PEAK 11(8Q11.21) WILD-TYPE  57 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED    105  172
  AMP PEAK 11(8Q11.21) WILD-TYPE   57  129
     clus
vv    AMP PEAK 11(8Q11.21) MUTATED AMP PEAK 11(8Q11.21) WILD-TYPE
  NO                           105                             57
  YES                          172                            129
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(8Q11.21) MUTATED                                   304
  AMP PEAK 11(8Q11.21) WILD-TYPE                                 207
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 11(8Q11.21) MUTATED                                                   5
  AMP PEAK 11(8Q11.21) WILD-TYPE                                                 5
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 11(8Q11.21) MUTATED                                                           1
  AMP PEAK 11(8Q11.21) WILD-TYPE                                                         0
D11V9, multiclass
                                                           clus
vv                                                          AMP PEAK 11(8Q11.21) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                304
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          AMP PEAK 11(8Q11.21) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  207
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, continuous
D11V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(8Q11.21) MUTATED                                  1     7
  AMP PEAK 11(8Q11.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8Q11.21) MUTATED                          24   266
  AMP PEAK 11(8Q11.21) WILD-TYPE                        24   180
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(8Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     266
                                  clus
vv                                 AMP PEAK 11(8Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       180
[1] 4 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(8Q11.21) MUTATED    18 267
  AMP PEAK 11(8Q11.21) WILD-TYPE   8 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q11.21) MUTATED     18  267
  AMP PEAK 11(8Q11.21) WILD-TYPE    8  192
                        clus
vv                       AMP PEAK 11(8Q11.21) MUTATED
  HISPANIC OR LATINO                               18
  NOT HISPANIC OR LATINO                          267
                        clus
vv                       AMP PEAK 11(8Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED   213 172
  AMP PEAK 12(8Q24.21) WILD-TYPE  88  47
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           385                            135 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                           172                             47 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       25.71        51.29         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 
       32.48        24.39        70.13        16.73        43.04        11.61 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
        6.02         0.36        34.36        30.94        14.04        46.32 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 
       12.66        22.85        48.03         2.96         3.35        13.64 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
       26.50        23.74        42.35        17.10        65.59        15.52 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
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-7863 
      105.90         9.14         4.80         4.41        18.38        33.70 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       50.20        66.28        38.40        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       27.19         8.81         6.28        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 
       38.04         4.67        56.68        12.89        32.81        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 
       20.55        14.33        45.83        27.58        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       46.32        12.39         8.32        16.21        11.54        11.84 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       11.57         8.52        52.08        48.00        23.90        47.44 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
        6.74        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        25.41        23.57        17.29        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-5324 
       31.69        22.32        12.39         4.41         2.70        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50         2.93        70.45        62.37        45.99        10.42 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
        4.24        41.19        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        64.87        53.52        41.88        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI 
       23.24        29.36        33.60        29.49        14.14        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       84.23        11.77        58.42        50.01        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       18.54        16.90        11.34        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
       22.78         9.27        39.16        47.34        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       26.17        17.13        47.01        27.06        12.89        49.58 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
       24.79         5.95        35.41        48.39       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
      129.21       108.95        76.24        19.20       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 
       76.50        80.12        17.92        13.35        48.59        60.49 
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-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 
        2.14         9.70         5.46        20.52         4.73        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       11.24       140.78        19.79        12.03        42.38        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 
       30.08         6.08        53.95         7.13         8.42         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 
        1.84        52.31        12.92        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        89.65        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 
       18.97        17.13        47.97         2.10        18.41        35.54 
TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       17.85         0.46        22.85        25.08        25.94         0.07 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7434 
      100.57        14.89       156.49        54.94        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45P TCGA-CV-A45Q 
      153.86        16.64         6.38        22.19        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y 
      180.16       159.65        35.47        45.96         6.51        88.87 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
       48.20        67.86        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        28.01         3.62 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6517 
       23.47        19.92        18.84        51.12        25.41         9.60 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       23.05         2.53        11.44        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        28.77        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.79        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       37.58        37.18        32.71        21.63         3.02        31.13 
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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        28.47        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ 
       27.48        27.48        14.66        22.03         4.27         3.65 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61K TCGA-IQ-A61L 
       34.75        15.95        37.71        11.84         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X 
       13.84        19.04        15.48        19.27        14.37         7.96 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
        1.84         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 
       15.78        71.74        51.25        19.00        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        21.21 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
        7.30        21.47         9.34        12.72        21.07        19.73 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.76        17.82         8.32        12.72         6.87        15.91 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A718 
       32.45        13.71         3.12        13.55        13.25        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-BA-4077 TCGA-CN-6021 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CR-6472 
       37.28         9.07        19.82        48.20        32.88        34.52 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5556 
       40.24        21.11        15.19         9.07        57.93        23.84 
TCGA-BA-6869 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-A6UM 
       21.17        22.42        36.72        44.98        24.66        12.92 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5360 
       26.86        52.14        57.11        73.61         8.58        71.31 
TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 
       12.49        56.94        50.07        30.67        28.04        19.07 
TCGA-CN-6019 TCGA-CN-A497 TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY 
       34.13        35.01        21.21        16.57        12.07        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5327 TCGA-CQ-5333 TCGA-CQ-6220 TCGA-CQ-6223 
       20.88        19.53        54.58        11.21        32.38        46.95 
TCGA-CQ-7071 TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6480 
       43.10        12.46        54.67        37.87        26.27        11.90 
TCGA-CR-6481 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 
       10.22        15.75        47.18        40.93         3.09        29.23 
TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       32.78        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 
        5.13        29.95        17.95        91.53        23.05        86.83 
TCGA-CV-6441 TCGA-CV-6939 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6961 
        9.60        21.90        65.82        10.98        28.34         2.50 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
        9.01         5.26        21.80        95.34         4.96        11.87 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7422 
       49.71        57.47       210.97        89.33         9.67        34.09 
TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-A45O TCGA-CV-A45V 
       56.48         3.52        16.27        84.49        27.98         1.05 
TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       60.43         0.76        21.24        22.52        10.42        10.55 
TCGA-D6-6515 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EM TCGA-DQ-7590 TCGA-DQ-7591 
       13.25        16.14        18.67         7.63        46.45        20.45 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A50G TCGA-F7-A61V TCGA-H7-7774 
       40.04        39.12        41.59        20.25        24.95        13.38 
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        38.53        14.50 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
       37.41         0.07        33.57        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        23.15 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TP 
       27.39        12.89         5.62        12.20        15.32        16.96 
TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UP-A6WW 
        7.10        20.35        17.03 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         20.48                          23.44 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (23.4)"
[1] "hr=" "1.4"
D12V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 12(8Q24.21) MUTATED        20       51        61       195        11
  AMP PEAK 12(8Q24.21) WILD-TYPE       7       25        21        57         1
                                vv
clus                             STAGE IVC
  AMP PEAK 12(8Q24.21) MUTATED           0
  AMP PEAK 12(8Q24.21) WILD-TYPE         1
D12V3, multiclass
           clus
vv          AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  STAGE I                             20                              7
  STAGE II                            51                             25
  STAGE III                           61                             21
  STAGE IVA                          195                             57
  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 12(8Q24.21) MUTATED      35  95  79 135
  AMP PEAK 12(8Q24.21) WILD-TYPE    15  42  21  38
D12V4, multiclass
       clus
vv      AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  T0+T1                           35                             15
  T2                              95                             42
  T3                              79                             21
  T4                             135                             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 12(8Q24.21) MUTATED   124  49 136   7
  AMP PEAK 12(8Q24.21) WILD-TYPE  55  19  32   1
D12V5, multiclass
    clus
vv   AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  N0                          124                             55
  N1                           49                             19
  N2                          136                             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"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED   150   0
  AMP PEAK 12(8Q24.21) WILD-TYPE  40   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED    150    0
  AMP PEAK 12(8Q24.21) WILD-TYPE   40    1
   clus
vv  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  0                          150                             40
  1                            0                              1
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED   104 282
  AMP PEAK 12(8Q24.21) WILD-TYPE  36 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED    104  282
  AMP PEAK 12(8Q24.21) WILD-TYPE   36  100
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                          104                             36
  MALE                            282                            100
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED   121 220
  AMP PEAK 12(8Q24.21) WILD-TYPE  41  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED    121  220
  AMP PEAK 12(8Q24.21) WILD-TYPE   41   81
     clus
vv    AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  NO                           121                             41
  YES                          220                             81
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8Q24.21) MUTATED                                   379
  AMP PEAK 12(8Q24.21) WILD-TYPE                                 132
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 12(8Q24.21) MUTATED                                                   6
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                 4
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 12(8Q24.21) MUTATED                                                           1
  AMP PEAK 12(8Q24.21) WILD-TYPE                                                         0
D12V9, multiclass
                                                           clus
vv                                                          AMP PEAK 12(8Q24.21) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                379
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          AMP PEAK 12(8Q24.21) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  132
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
D12V11, continuous
D12V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(8Q24.21) MUTATED                                  2     9
  AMP PEAK 12(8Q24.21) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED                          37   325
  AMP PEAK 12(8Q24.21) WILD-TYPE                        11   121
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  37
  WHITE                                                     325
                                  clus
vv                                 AMP PEAK 12(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"
D12V14, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED    22 334
  AMP PEAK 12(8Q24.21) WILD-TYPE   4 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     22  334
  AMP PEAK 12(8Q24.21) WILD-TYPE    4  125
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                               22
  NOT HISPANIC OR LATINO                          334
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            125
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(9P24.1) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(9P24.1) MUTATED    65  61
  AMP PEAK 13(9P24.1) WILD-TYPE 236 158
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                          126                           394 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                           61                           158 
$`AMP PEAK 13(9P24.1) MUTATED`
TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-6023 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       20.48        68.48        52.08        70.13        43.04        11.61 
TCGA-CR-6478 TCGA-HD-8634 TCGA-UF-A7JV TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-A6DA 
        6.02        12.66         2.96        23.84         4.01        11.54 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-7870 TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       11.05        13.38        66.28        27.19         8.81         6.28 
TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
       42.02         8.32         8.52        52.08        50.07        30.67 
TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A640 
       19.07        38.89        17.42        23.57        21.21         4.41 
TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 
        2.70        20.88        21.50        70.45        62.37        46.95 
TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6493 
       38.76        44.48        33.60        58.42         7.69         9.27 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7382 TCGA-CR-7389 
       47.34         3.45         3.09        29.23        26.17        12.89 
TCGA-CR-7395 TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 
       30.58         5.95        17.16       108.95       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 
       76.50        91.53        17.92        60.49        21.07        62.43 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6952 
        4.73        21.90        26.43        11.24       140.78         6.08 
TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7104 TCGA-CV-7178 
        7.13         4.14        64.83         7.99        12.92        71.21 
TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7416 
       18.97        47.97        35.54        17.85        22.85        25.08 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-A45Q 
       56.48       156.49        54.94         3.52         7.17       169.38 
TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-D6-6516 
        0.76         5.98        29.79         6.48        23.47        25.41 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-DQ-5625 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A622 
        7.63        22.59        37.25        20.25        18.94        11.80 
TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 
       13.38        15.06        33.76        27.48         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 
       34.75        37.71        37.41         5.29        13.68        19.27 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW 
       14.37        30.05        12.62         6.25        16.08        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K 
       75.55        29.00        16.01        14.76        12.20         8.32 
TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A7JT 
       12.72         6.87         3.12        13.55        20.35        32.65 

$`AMP PEAK 13(9P24.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6472 
       19.82        24.39        48.20        32.88        16.73        34.52 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
        0.36        34.36        30.94        14.04        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       21.11        22.85        48.03         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       65.59        15.52        21.17        14.83        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       29.42        20.45        27.95         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        20.48        16.41         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.80         4.41        18.38        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-A5HY TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       20.52        10.55        12.92        12.69        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       52.14        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        13.05        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       71.31        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       56.94        48.00        23.90        47.44        28.04        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 
        6.74        10.45        32.22         3.68        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       25.41        17.29        29.72         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
       12.39        16.57        12.07        23.44        19.53        52.37 
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-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       41.19        32.38        56.58        13.25         4.24        14.99 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 
       64.87        53.52        41.88        43.10        77.56        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        29.49        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
       11.64        12.46        22.78        15.75        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       40.93        35.84        24.95         0.99        31.96         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-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 
       49.58        30.02        46.85        32.65        44.25        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.13        35.41        29.95        48.39       139.43       129.21 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
       76.24        19.20        17.95        80.12        13.35        23.05 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
       86.83        48.59         7.07        43.23        54.74         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6943 
       90.12         2.14         9.70         5.46        20.52        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 
       12.03        42.38        15.09        30.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
       10.98         8.42        28.34         2.50       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       18.81        12.66         9.01         5.26         1.84        52.31 
TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       21.80        10.75       130.88        77.16         4.73        89.65 
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-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 
       11.87         2.10        49.71        18.41        57.47       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
       89.33         9.67         0.46        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
      100.57        14.89        16.27        84.49        19.76       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R 
       16.64         6.38        22.19        27.98        21.01       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-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        60.43        67.86        56.61         7.07        15.25 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 
       35.34         6.38        28.01         3.62        21.24        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        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        28.77        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 
       13.94        12.10        12.79        23.34        58.45        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        46.45        20.45        37.58        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        32.71        21.63         3.02        31.13 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 
       24.95         0.46        17.85        20.25        12.43        15.16 
TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       20.94        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 
       22.03         0.36        13.84         3.65        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG 
       14.50        11.84         0.07        33.57        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI 
       15.48        10.75         7.96         1.84        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 
       47.01        19.00        18.97         2.04        12.99        13.15 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       17.82        15.32        16.96        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.71        13.25        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW 
       29.46        18.05        13.94        20.75        22.36        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                         0.76                          0.07 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                       169.38                        210.97 
  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE 
                        20.68                         21.19 
[1] "0.8 - 169.4 (20.7)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 13(9P24.1) MUTATED         8       19        18        63         4
  AMP PEAK 13(9P24.1) WILD-TYPE      19       57        64       189         8
                               vv
clus                            STAGE IVC
  AMP PEAK 13(9P24.1) MUTATED           0
  AMP PEAK 13(9P24.1) WILD-TYPE         1
D13V3, multiclass
           clus
vv          AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  STAGE I                             8                            19
  STAGE II                           19                            57
  STAGE III                          18                            64
  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 13(9P24.1) MUTATED      10  32  28  43
  AMP PEAK 13(9P24.1) WILD-TYPE    40 105  72 130
D13V4, multiclass
       clus
vv      AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  T0+T1                          10                            40
  T2                             32                           105
  T3                             28                            72
  T4                             43                           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 13(9P24.1) MUTATED    37  17  44   4
  AMP PEAK 13(9P24.1) WILD-TYPE 142  51 124   4
D13V5, multiclass
    clus
vv   AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  N0                          37                           142
  N1                          17                            51
  N2                          44                           124
  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(9P24.1) MUTATED    40   0
  AMP PEAK 13(9P24.1) WILD-TYPE 150   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     40    0
  AMP PEAK 13(9P24.1) WILD-TYPE  150    1
   clus
vv  AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  0                          40                           150
  1                           0                             1
[1] 2 2
[1] FALSE
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED    51  75
  AMP PEAK 13(9P24.1) WILD-TYPE  89 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     51   75
  AMP PEAK 13(9P24.1) WILD-TYPE   89  307
        clus
vv       AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  FEMALE                          51                            89
  MALE                            75                           307
[1] 2 2
[1] FALSE
D13V8, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED    45  67
  AMP PEAK 13(9P24.1) WILD-TYPE 117 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED     45   67
  AMP PEAK 13(9P24.1) WILD-TYPE  117  234
     clus
vv    AMP PEAK 13(9P24.1) MUTATED AMP PEAK 13(9P24.1) WILD-TYPE
  NO                           45                           117
  YES                          67                           234
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(9P24.1) MUTATED                                   125
  AMP PEAK 13(9P24.1) WILD-TYPE                                 386
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 13(9P24.1) MUTATED                                                   1
  AMP PEAK 13(9P24.1) WILD-TYPE                                                 9
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 13(9P24.1) MUTATED                                                           0
  AMP PEAK 13(9P24.1) WILD-TYPE                                                         1
D13V9, multiclass
                                                           clus
vv                                                          AMP PEAK 13(9P24.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               125
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          AMP PEAK 13(9P24.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 386
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
D13V11, continuous
D13V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(9P24.1) MUTATED                                  0     3
  AMP PEAK 13(9P24.1) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(9P24.1) MUTATED                          12   110
  AMP PEAK 13(9P24.1) WILD-TYPE                        36   336
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(9P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    110
                                  clus
vv                                 AMP PEAK 13(9P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                               cls
clus                              0   1
  AMP PEAK 13(9P24.1) MUTATED     9 113
  AMP PEAK 13(9P24.1) WILD-TYPE  17 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(9P24.1) MUTATED      9  113
  AMP PEAK 13(9P24.1) WILD-TYPE   17  346
                        clus
vv                       AMP PEAK 13(9P24.1) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         113
                        clus
vv                       AMP PEAK 13(9P24.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           346
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(9P23) MUTATION ANALYSIS
D14V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 14(9P23) MUTATED    63  61
  AMP PEAK 14(9P23) WILD-TYPE 238 158
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                        124                         396 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                         61                         158 
$`AMP PEAK 14(9P23) MUTATED`
TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-6023 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 
       20.48        68.48        52.08        70.13        43.04        11.61 
TCGA-CR-6478 TCGA-DQ-7589 TCGA-HD-8634 TCGA-UF-A7JV TCGA-BA-5556 TCGA-BA-6873 
        6.02        46.32        12.66         2.96        23.84         4.01 
TCGA-BA-A6DA TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       11.54        11.05        13.38        27.19         8.81         6.28 
TCGA-CN-4725 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5370 
       38.04        42.02        12.39         8.32        11.57         8.52 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 
       50.07        30.67        19.07        38.89        17.42        23.57 
TCGA-CN-A49C TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5329 
       21.21         4.41         2.70        20.88        21.50        70.45 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CD 
       62.37        46.95        56.58        38.76        44.48        33.60 
TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7382 
       58.42         7.69         9.27         3.45         3.09        26.17 
TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 
       12.89        30.58         5.95       139.43        17.16       108.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 
      107.51        94.88        76.50        17.92        60.49        21.07 
TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6952 
       62.43         4.73        21.90        26.43        11.24         6.08 
TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
        7.13         4.14        64.83       172.67        12.66         7.99 
TCGA-CV-7102 TCGA-CV-7243 TCGA-CV-7254 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7416 
        1.84        31.36        47.97        35.54        17.85        25.08 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-A45Q 
       56.48       156.49        54.94         3.52         7.17       169.38 
TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-D6-6516 TCGA-D6-A6EM 
        0.76         5.98         6.48        23.47        25.41         7.63 
TCGA-D6-A6EN TCGA-DQ-5625 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 
       22.59        37.25        20.25        18.94        11.80        13.38 
TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61E 
       15.06        27.48         4.27         6.90        34.75        37.71 
TCGA-IQ-A61H TCGA-IQ-A61K TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
       37.41         5.29        14.37        30.05        12.62         6.25 
TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A6IF 
       16.08        36.82        75.55        29.00        16.01        23.15 
TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX 
        7.30        12.72        14.76         8.32        12.72         6.87 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A7JT 
        3.12        13.55        20.35        32.65 

$`AMP PEAK 14(9P23) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
       51.29         9.07         9.24        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6472 
       19.82        24.39        48.20        32.88        16.73        34.52 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 
        0.36        34.36        30.94        14.04        40.24        21.11 
TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       22.85        48.03         3.35        15.19        13.64         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        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       15.52        21.17        14.83        12.62        41.85        29.42 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        27.95         7.10         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         4.41        18.38        22.42        36.72        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-8601 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
       20.52        10.55        12.92        12.69        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 
       73.61        13.05        46.32         8.58        71.31        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 
       11.54        11.84        12.49        52.08        56.94        48.00 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       23.90        47.44        28.04        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       32.22         3.68        11.74        35.01        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       29.72         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 
       12.07        23.44        19.53        52.37         2.93        54.58 
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-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
       13.25         4.24        14.99        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
       43.10        77.56        23.24        29.36        29.49        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-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
       26.27        50.01        39.52        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        22.78 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75        47.18        39.16        47.34        40.93        35.84 
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-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
       19.92        17.13        32.78        47.01        27.06        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 
       30.02        46.85        32.65        44.25        24.79         5.13 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
       35.41        29.95        48.39       129.21        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
       17.95        91.53        80.12        13.35        23.05        86.83 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 
       48.59         7.07        43.23        54.74         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6942 TCGA-CV-6943 
        2.14         9.70         5.46        20.52       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 
       12.03        42.38        15.09        30.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
       10.98         8.42        28.34         2.50       111.16        18.81 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        9.01         5.26        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
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-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
        2.10        49.71        18.41        57.47       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
        9.67         0.46        22.85        25.94         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
      100.57        14.89        16.27        84.49        19.76       153.86 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R 
       16.64         6.38        22.19        27.98        21.01       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-A464 TCGA-CV-A465 TCGA-CV-A468 
       48.20        60.43        67.86        56.61         7.07        15.25 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
       35.34         6.38        29.79        28.01         3.62        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
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        28.77 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       39.12        41.59        37.18        32.71        21.63         3.02 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       31.13        24.95         0.46        17.85        20.25        12.43 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.16        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       27.48        14.66        22.03         0.36        13.84         3.65 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        38.53        14.50        11.84         0.07        33.57 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        7.96         1.84        15.42         7.13        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        71.74        51.25        10.85        47.01        19.00 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
       18.97         2.04        12.99        13.15        21.07        21.21 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WZ 
        5.62        12.20        17.82        15.32        16.96        15.91 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
        7.10        32.45        13.71        13.25        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       22.36        17.03        20.55        14.56        13.35        18.15 

  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                       0.76                        0.07 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                     172.67                      210.97 
  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE 
                     20.300                      21.355 
[1] "0.8 - 172.7 (20.3)" "0.1 - 211.0 (21.4)"
[1] "hr=" "1.3"
D14V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 14(9P23) MUTATED         7       20        19        60         4
  AMP PEAK 14(9P23) WILD-TYPE      20       56        63       192         8
                             vv
clus                          STAGE IVC
  AMP PEAK 14(9P23) MUTATED           0
  AMP PEAK 14(9P23) WILD-TYPE         1
D14V3, multiclass
           clus
vv          AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  STAGE I                           7                          20
  STAGE II                         20                          56
  STAGE III                        19                          63
  STAGE IVA                        60                         192
  STAGE IVB                         4                           8
  STAGE IVC                         0                           1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T0+T1  T2  T3  T4
  AMP PEAK 14(9P23) MUTATED       9  34  27  40
  AMP PEAK 14(9P23) WILD-TYPE    41 103  73 133
D14V4, multiclass
       clus
vv      AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  T0+T1                         9                          41
  T2                           34                         103
  T3                           27                          73
  T4                           40                         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
  AMP PEAK 14(9P23) MUTATED    32  18  44   4
  AMP PEAK 14(9P23) WILD-TYPE 147  50 124   4
D14V5, multiclass
    clus
vv   AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  N0                        32                         147
  N1                        18                          50
  N2                        44                         124
  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(9P23) MUTATED    40   0
  AMP PEAK 14(9P23) WILD-TYPE 150   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED     40    0
  AMP PEAK 14(9P23) WILD-TYPE  150    1
   clus
vv  AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  0                        40                         150
  1                         0                           1
[1] 2 2
[1] FALSE
D14V7, binary
                             cls
clus                            0   1
  AMP PEAK 14(9P23) MUTATED    47  77
  AMP PEAK 14(9P23) WILD-TYPE  93 305
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED     47   77
  AMP PEAK 14(9P23) WILD-TYPE   93  305
        clus
vv       AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  FEMALE                        47                          93
  MALE                          77                         305
[1] 2 2
[1] FALSE
D14V8, binary
                             cls
clus                            0   1
  AMP PEAK 14(9P23) MUTATED    45  66
  AMP PEAK 14(9P23) WILD-TYPE 117 235
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED     45   66
  AMP PEAK 14(9P23) WILD-TYPE  117  235
     clus
vv    AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  NO                         45                         117
  YES                        66                         235
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P23) MUTATED                                   123
  AMP PEAK 14(9P23) WILD-TYPE                                 388
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 14(9P23) MUTATED                                                   1
  AMP PEAK 14(9P23) WILD-TYPE                                                 9
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 14(9P23) MUTATED                                                           0
  AMP PEAK 14(9P23) WILD-TYPE                                                         1
D14V9, multiclass
                                                           clus
vv                                                          AMP PEAK 14(9P23) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                             123
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                         0
                                                           clus
vv                                                          AMP PEAK 14(9P23) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               388
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
D14V11, continuous
D14V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(9P23) MUTATED                                  0     3
  AMP PEAK 14(9P23) WILD-TYPE                                2     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(9P23) MUTATED                          10   110
  AMP PEAK 14(9P23) WILD-TYPE                        38   336
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               10
  WHITE                                                  110
                                  clus
vv                                 AMP PEAK 14(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 38
  WHITE                                                    336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                             cls
clus                            0   1
  AMP PEAK 14(9P23) MUTATED     8 112
  AMP PEAK 14(9P23) WILD-TYPE  18 347
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 14(9P23) MUTATED      8  112
  AMP PEAK 14(9P23) WILD-TYPE   18  347
                        clus
vv                       AMP PEAK 14(9P23) MUTATED AMP PEAK 14(9P23) WILD-TYPE
  HISPANIC OR LATINO                             8                          18
  NOT HISPANIC OR LATINO                       112                         347
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(9P13.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(9P13.3) MUTATED    77  61
  AMP PEAK 15(9P13.3) WILD-TYPE 224 158
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                          138                           382 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                           61                           158 
$`AMP PEAK 15(9P13.3) MUTATED`
TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V3 TCGA-CQ-7063 
       20.48        68.48        52.08        11.08        24.39        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CX-7219 TCGA-DQ-5629 TCGA-HD-8634 TCGA-UF-A71D 
       43.04        11.61        34.36        30.94        12.66        48.03 
TCGA-BA-5556 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DJ TCGA-BA-A6DL 
       23.84        12.62         4.01        11.54        13.38        20.48 
TCGA-BB-4224 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-5355 
        9.14        66.28        27.19        56.68        20.55        42.02 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       12.39         8.32         8.52        50.07        30.67        48.00 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A640 
       38.89         3.68        17.42        23.57         7.40         4.41 
TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-6229 
        2.70        20.88        70.45        62.37        56.58        38.76 
TCGA-CQ-A4C6 TCGA-CQ-A4CI TCGA-CR-6467 TCGA-CR-6488 TCGA-CR-7368 TCGA-CR-7370 
       44.48        31.23        58.42        12.46        40.93         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7380 TCGA-CR-7390 
        3.09        24.95        29.23        31.96        19.92        49.58 
TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       30.58         5.95        35.41        17.16       129.21       108.95 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
       17.95       107.51        94.88        76.50        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 
       13.35        60.49        21.07        62.43         4.73        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7095 
       26.43        11.24         6.08         4.14        64.83        18.81 
TCGA-CV-7099 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7247 
        7.99        12.92        10.75        77.16        89.65        18.97 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7425 
       47.97         2.10        18.41        35.54        17.85        56.48 
TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A463 TCGA-CV-A468 
      156.49         3.52         7.17       169.38         0.76        15.25 
TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-D6-6516 TCGA-D6-A6EM TCGA-D6-A6EN 
        5.98         6.48        23.47        25.41         7.63        22.59 
TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S 
       12.10        37.25        32.71        20.25         3.02        18.94 
TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A634 
       11.80        13.38        15.06        27.48        14.66         4.27 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
        6.90        15.95        13.68        14.37         7.96        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-QK-A64Z 
       12.62         6.25        36.82        75.55        29.00        21.07 
TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO 
        7.30        12.89        14.76        12.20         8.32        12.72 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A7JT TCGA-WA-A7H4 
        6.87        15.91        13.55        13.25        32.65        14.56 

$`AMP PEAK 15(9P13.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
       51.29         9.07         9.24        35.05        32.48        19.82 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       48.20        32.88        16.73        34.52         6.02         0.36 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A7JV 
       14.04        46.32        40.24        21.11        22.85         2.96 
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-5558 TCGA-BA-6868 TCGA-BA-6869 
       42.35        57.93        17.10        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB 
       14.83        41.85        29.42        20.45        27.95         7.10 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A8YP 
        5.69        14.47         7.82         2.27        11.05        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        6.15       105.90         4.80         4.41        18.38        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-4729 
       12.69        48.76        55.86        38.04         4.67        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
       26.86        32.81        52.14        57.11        12.99        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        46.32         8.58 
TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       71.31        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       52.08        56.94        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A497 
       34.13         6.74        10.45        32.22        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       25.41        17.29        29.72        21.21        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
       12.39        16.57        12.07        23.44        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       21.50         2.93        54.58        45.99        10.42        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        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       14.99        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.34        11.64         7.69        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7374 TCGA-CR-7377 
       47.18        39.16        47.34        35.84         0.99         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-7397 
       12.89        30.02        46.85        32.65        44.25        24.79 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5436 
        5.13        29.95        48.39       139.43        76.24        19.20 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
       91.53        23.05        86.83        48.59         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-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       20.52       140.78        19.79        12.03        42.38        15.09 
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-7097 TCGA-CV-7100 
       28.34         2.50       172.67       111.16        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 
        5.26         1.84        52.31        21.80        71.21       130.88 
TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        4.73        36.00        31.36        26.20        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
        4.96        11.87        49.71        57.47       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-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
       34.09       100.57        14.89        54.94        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       19.76       153.86        16.64         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
       21.01       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-A465 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU 
        7.07        35.34         6.38        29.79        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       21.24        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       51.12        13.25         9.60        23.05         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-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       28.77        24.95        13.94        12.79        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61V 
       39.12        41.59        37.18        21.63        31.13        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A76A 
        0.46        17.85        20.25        12.43        15.16        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8314 
       33.76        28.47        25.74        21.93        27.48        22.03 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
        0.36        13.84         3.65        34.75        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D 
       13.84        19.04        15.48        19.27        10.75         1.84 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 
       71.74        51.25        10.85        47.01        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF 
        2.04        12.99        16.01        13.15        21.21        23.15 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-T2-A6X2 
        5.62        17.82        15.32        16.96         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.71         3.12        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S TCGA-KU-A66T 
       17.03        20.55        13.35        18.15 

  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                         0.76                          0.07 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                       169.38                        210.97 
  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE 
                       19.445                        21.715 
[1] "0.8 - 169.4 (19.4)" "0.1 - 211.0 (21.7)"
[1] "hr=" "1.1"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 15(9P13.3) MUTATED         8       25        18        72         5
  AMP PEAK 15(9P13.3) WILD-TYPE      19       51        64       180         7
                               vv
clus                            STAGE IVC
  AMP PEAK 15(9P13.3) MUTATED           0
  AMP PEAK 15(9P13.3) WILD-TYPE         1
D15V3, multiclass
           clus
vv          AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  STAGE I                             8                            19
  STAGE II                           25                            51
  STAGE III                          18                            64
  STAGE IVA                          72                           180
  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 15(9P13.3) MUTATED      12  40  29  50
  AMP PEAK 15(9P13.3) WILD-TYPE    38  97  71 123
D15V4, multiclass
       clus
vv      AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  T0+T1                          12                            38
  T2                             40                            97
  T3                             29                            71
  T4                             50                           123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 15(9P13.3) MUTATED    45  20  49   4
  AMP PEAK 15(9P13.3) WILD-TYPE 134  48 119   4
D15V5, multiclass
    clus
vv   AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  N0                          45                           134
  N1                          20                            48
  N2                          49                           119
  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"
D15V6, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P13.3) MUTATED    52   0
  AMP PEAK 15(9P13.3) WILD-TYPE 138   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED     52    0
  AMP PEAK 15(9P13.3) WILD-TYPE  138    1
   clus
vv  AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  0                          52                           138
  1                           0                             1
[1] 2 2
[1] FALSE
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P13.3) MUTATED    45  94
  AMP PEAK 15(9P13.3) WILD-TYPE  95 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED     45   94
  AMP PEAK 15(9P13.3) WILD-TYPE   95  288
        clus
vv       AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  FEMALE                          45                            95
  MALE                            94                           288
[1] 2 2
[1] FALSE
D15V8, binary
                               cls
clus                              0   1
  AMP PEAK 15(9P13.3) MUTATED    46  78
  AMP PEAK 15(9P13.3) WILD-TYPE 116 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED     46   78
  AMP PEAK 15(9P13.3) WILD-TYPE  116  223
     clus
vv    AMP PEAK 15(9P13.3) MUTATED AMP PEAK 15(9P13.3) WILD-TYPE
  NO                           46                           116
  YES                          78                           223
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(9P13.3) MUTATED                                   136
  AMP PEAK 15(9P13.3) WILD-TYPE                                 375
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 15(9P13.3) MUTATED                                                   3
  AMP PEAK 15(9P13.3) WILD-TYPE                                                 7
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 15(9P13.3) MUTATED                                                           0
  AMP PEAK 15(9P13.3) WILD-TYPE                                                         1
D15V9, multiclass
                                                           clus
vv                                                          AMP PEAK 15(9P13.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               136
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          AMP PEAK 15(9P13.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 375
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
D15V11, continuous
D15V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(9P13.3) MUTATED                                  0     2
  AMP PEAK 15(9P13.3) WILD-TYPE                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(9P13.3) MUTATED                          11   122
  AMP PEAK 15(9P13.3) WILD-TYPE                        37   324
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(9P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    122
                                  clus
vv                                 AMP PEAK 15(9P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      324
[1] 4 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(9P13.3) MUTATED    10 122
  AMP PEAK 15(9P13.3) WILD-TYPE  16 337
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(9P13.3) MUTATED     10  122
  AMP PEAK 15(9P13.3) WILD-TYPE   16  337
                        clus
vv                       AMP PEAK 15(9P13.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         122
                        clus
vv                       AMP PEAK 15(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           337
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(9Q34.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(9Q34.3) MUTATED    89  88
  AMP PEAK 16(9Q34.3) WILD-TYPE 212 131
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                          177                           343 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                           88                           131 
$`AMP PEAK 16(9Q34.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-4727 TCGA-CN-6021 
        9.30        37.28        20.48        68.48        51.29         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       52.08        11.08        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7589 TCGA-BA-5149 
       43.04        11.61         0.36        34.36        46.32        26.50 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A6DA TCGA-BA-A6DD 
       17.10        23.84        14.83         4.01        11.54         5.69 
TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4723 
       13.38         9.14        38.40        20.52        10.55        55.86 
TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 
       56.68        32.81        73.61        42.02        12.39         8.32 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6994 
       16.21        11.84        11.57        50.07        30.67        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
        3.68        17.42        23.57        17.29        21.21         7.40 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5330 
       12.39         4.41         2.70        20.88        21.50        62.37 
TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CD 
       10.42        46.95        13.25        38.76        44.48        33.60 
TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
       58.42        16.90        22.78        39.16        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7402 TCGA-CV-5432 
        3.45        29.23        34.06        19.92        29.95       129.21 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
      108.95        19.20        17.95       107.51        76.50        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
       17.92        13.35        60.49         7.07        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6950 
        9.60        90.12         4.73        21.90        26.43        15.09 
TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7177 
        6.08         4.14        64.83         7.99         9.01        21.80 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7261 
       10.75        77.16         4.73        26.20        18.97        49.71 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7415 TCGA-CV-7422 
       18.41        35.54        17.85       210.97        22.85        34.09 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
       56.48       156.49         3.52        16.27        84.49         7.17 
TCGA-CV-A45Q TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A468 
      169.38        48.20        67.86         0.76         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 
        5.98        23.47        51.12        25.41        23.05        25.32 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 
        7.63        22.59        13.94        12.10        23.34        37.25 
TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7832 
       18.94        11.80        13.38        15.06        33.76        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       27.48        14.66        22.03         4.27         3.65         6.90 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
       33.57        13.68        14.37        30.05         1.84         6.25 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T8 
       17.98        15.78        36.82        75.55        29.00        13.15 
TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-AA3K 
       21.07         7.30         9.34        19.73        14.76         8.32 
TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92N TCGA-TN-A7HI 
       12.72         6.87        15.91         7.10         3.12        13.55 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH 
       49.45        44.65        74.47        17.95        55.43        29.46 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW 
       22.36        32.65        17.03 

$`AMP PEAK 16(9Q34.3) WILD-TYPE`
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6992 
        3.55        28.11        30.18        25.71         9.24        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-7067 TCGA-CR-6472 TCGA-CR-6478 TCGA-DQ-5629 
       32.48        19.82        16.73        34.52         6.02        30.94 
TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       14.04        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
        2.96         3.35        15.19        13.64         9.07        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 
       42.35        57.93        65.59        15.52        21.17        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
       41.85        29.42        20.45        27.95         7.10        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
        7.82         2.27        11.05        20.48        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         4.80         4.41        18.38        22.42        36.72 
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-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        48.76 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 
       38.04         4.67        12.89        26.86        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
       12.99        20.55        14.33        45.83        27.58        13.05 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5370 
       46.32         8.58        71.31        11.54        12.49         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       52.08        56.94        48.00        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6998 
       19.07        34.13         6.74        10.45        32.22        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       35.01        25.41        29.72        31.69        22.32        16.57 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 
       12.07        23.44        19.53        52.37         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       70.45        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
       56.58         4.24        14.99        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
       43.10        77.56        23.24        29.36        29.49        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-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       26.27        50.01        39.52        36.99        18.54        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 
       10.22        11.34        11.64         7.69        12.46        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
        9.27        47.18        47.34         3.09        24.95         0.99 
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-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5443 
       48.39       139.43        17.16        76.24        94.88        91.53 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6934 
       23.05        86.83        48.59        43.23        54.74         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        9.70         5.46        20.52        11.24       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       12.03        42.38        30.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        7.13         8.42        28.34         2.50       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
       18.81        12.66         5.26         1.84        52.31        12.92 
TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 
       71.21       130.88        89.65        36.00        31.36        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7406 
       95.34         4.96        11.87        47.97         2.10        57.47 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67         0.46        25.08        25.94         0.07 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 
      100.57        14.89        54.94        19.76       153.86        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T 
        6.38        22.19        27.98        21.01       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 
       35.47         1.05        45.96         6.51        88.87        60.43 
TCGA-CV-A464 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
       56.61        35.34         6.38        29.79         6.48        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
        3.62        21.24        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       18.84        13.25         9.60         2.53        16.14        11.44 
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        28.77        24.95 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       12.79        58.45        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
       21.63        20.25         3.02        31.13        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7753 
       17.85        20.25        12.43        15.16        20.94        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HL-7533 TCGA-IQ-7630 
       25.74        21.93         0.36        13.84        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
        5.29        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51X TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
        7.96        12.62        15.42         7.13        16.08        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 
       71.74        51.25        10.85        47.01        19.00        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
        2.04        12.99        16.01        21.21        23.15        21.47 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       12.72        27.39        21.07        12.89         5.62        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ 
       17.82        15.32        16.96        32.45        13.71        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JD 
       20.35        64.80        54.67         2.83        49.51        24.30 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       18.05        13.94        20.75        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                         0.36                          0.07 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                       210.97                        180.16 
  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE 
                        21.07                         21.17 
[1] "0.4 - 211.0 (21.1)" "0.1 - 180.2 (21.2)"
[1] "hr=" "1.3"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 16(9Q34.3) MUTATED         7       23        24        99         7
  AMP PEAK 16(9Q34.3) WILD-TYPE      20       53        58       153         5
                               vv
clus                            STAGE IVC
  AMP PEAK 16(9Q34.3) MUTATED           0
  AMP PEAK 16(9Q34.3) WILD-TYPE         1
D16V3, multiclass
           clus
vv          AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  STAGE I                             7                            20
  STAGE II                           23                            53
  STAGE III                          24                            58
  STAGE IVA                          99                           153
  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 16(9Q34.3) MUTATED      11 39 37 75
  AMP PEAK 16(9Q34.3) WILD-TYPE    39 98 63 98
D16V4, multiclass
       clus
vv      AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  T0+T1                          11                            39
  T2                             39                            98
  T3                             37                            63
  T4                             75                            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 16(9Q34.3) MUTATED    57  23  64   5
  AMP PEAK 16(9Q34.3) WILD-TYPE 122  45 104   3
D16V5, multiclass
    clus
vv   AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  N0                          57                           122
  N1                          23                            45
  N2                          64                           104
  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"
D16V6, binary
                               cls
clus                              0   1
  AMP PEAK 16(9Q34.3) MUTATED    61   0
  AMP PEAK 16(9Q34.3) WILD-TYPE 129   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED     61    0
  AMP PEAK 16(9Q34.3) WILD-TYPE  129    1
   clus
vv  AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  0                          61                           129
  1                           0                             1
[1] 2 2
[1] FALSE
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(9Q34.3) MUTATED    48 129
  AMP PEAK 16(9Q34.3) WILD-TYPE  92 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED     48  129
  AMP PEAK 16(9Q34.3) WILD-TYPE   92  253
        clus
vv       AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  FEMALE                          48                            92
  MALE                           129                           253
[1] 2 2
[1] FALSE
D16V8, binary
                               cls
clus                              0   1
  AMP PEAK 16(9Q34.3) MUTATED    52 101
  AMP PEAK 16(9Q34.3) WILD-TYPE 110 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED     52  101
  AMP PEAK 16(9Q34.3) WILD-TYPE  110  200
     clus
vv    AMP PEAK 16(9Q34.3) MUTATED AMP PEAK 16(9Q34.3) WILD-TYPE
  NO                           52                           110
  YES                         101                           200
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(9Q34.3) MUTATED                                   174
  AMP PEAK 16(9Q34.3) WILD-TYPE                                 337
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 16(9Q34.3) MUTATED                                                   3
  AMP PEAK 16(9Q34.3) WILD-TYPE                                                 7
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 16(9Q34.3) MUTATED                                                           0
  AMP PEAK 16(9Q34.3) WILD-TYPE                                                         1
D16V9, multiclass
                                                           clus
vv                                                          AMP PEAK 16(9Q34.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               174
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          AMP PEAK 16(9Q34.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 337
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
D16V11, continuous
D16V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(9Q34.3) MUTATED                                  0     3
  AMP PEAK 16(9Q34.3) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(9Q34.3) MUTATED                          19   152
  AMP PEAK 16(9Q34.3) WILD-TYPE                        29   294
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    152
                                  clus
vv                                 AMP PEAK 16(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      294
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                               cls
clus                              0   1
  AMP PEAK 16(9Q34.3) MUTATED    12 153
  AMP PEAK 16(9Q34.3) WILD-TYPE  14 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(9Q34.3) MUTATED     12  153
  AMP PEAK 16(9Q34.3) WILD-TYPE   14  306
                        clus
vv                       AMP PEAK 16(9Q34.3) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         153
                        clus
vv                       AMP PEAK 16(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           306
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(11P13) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(11P13) MUTATED    57  45
  AMP PEAK 17(11P13) WILD-TYPE 244 174
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                         102                          418 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                          45                          174 
$`AMP PEAK 17(11P13) MUTATED`
TCGA-BA-4075 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-A4C7 TCGA-CX-7219 
        9.30        48.20        32.88        70.13        11.61        34.36 
TCGA-DQ-7588 TCGA-UF-A7JV TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 
       14.04         2.96        23.84        15.52        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP 
       41.85        27.95         5.69        11.05        20.48        16.41 
TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 
        4.80        22.42        10.55         6.28        55.86        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-6018 
       20.55        14.33        13.05        42.02         8.32        19.07 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5333 
       38.89         3.68         7.40         2.93        70.45        11.21 
TCGA-CQ-5334 TCGA-CQ-6225 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
        4.24        13.25        53.52        41.88        44.48        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 
       29.49        14.14        11.64        12.46        39.16        47.34 
TCGA-CR-7370 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7392 TCGA-CV-5430 TCGA-CV-5440 
        3.45        19.92        26.17        46.85       139.43       107.51 
TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6937 TCGA-CV-6939 
       13.35        60.49        54.74        21.07        20.52        21.90 
TCGA-CV-6942 TCGA-CV-6950 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7247 TCGA-CV-7254 
      140.78        15.09         8.42         4.14        18.97        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7409 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-A460 
        2.10        49.71        17.85       100.57         3.52        60.43 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6827 TCGA-D6-8569 
       21.24        23.47        51.12         9.60        18.67        25.32 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5624 TCGA-F7-A50J TCGA-F7-A622 TCGA-IQ-7630 
       13.94        23.34        58.45        31.13        11.80        15.95 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67D TCGA-P3-A5Q6 
        5.29        13.68        19.04        15.48         1.84        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       71.74        10.85        36.82        75.55        18.97         2.04 
TCGA-P3-A6T6 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-T2-A6WX TCGA-WA-A7GZ 
       12.99         7.30        12.72        21.07         6.87        20.55 

$`AMP PEAK 17(11P13) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-7067 TCGA-CQ-7068 
       35.05        32.48        19.82        24.39        16.73        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 
       34.52         6.02         0.36        30.94        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4074 
       21.11        12.66        22.85        48.03         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       13.64         9.07        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A4IH 
       17.10        65.59        21.17        14.83        29.42        20.45 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ 
       11.54         7.10        14.47         7.82         2.27        13.38 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
        6.15       105.90         9.14         4.41        18.38        36.72 
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-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-4728 TCGA-CN-4729 TCGA-CN-4730 
       48.76        38.04         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       32.81        52.14        57.11        45.83        27.58        73.61 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       46.32         8.58        12.39        71.31        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        52.08        56.94 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       50.07        30.67        48.00        23.90        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 
       34.13         6.74        10.45        32.22        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       54.58        62.37        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 
       46.95        56.58         4.24        14.99        38.76        64.87 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI 
       43.10        77.56        29.36        33.60        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        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        22.78        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
       47.18        40.93        35.84         3.09        24.95        29.23 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 
        0.99        31.96         9.17        34.06        17.13        32.78 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 
       47.01        27.06        12.89        49.58        30.02        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.95        48.39        17.16       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-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-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-6938 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
        4.73        26.43        11.24        19.79        12.03        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-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
       28.34         2.50        64.83       172.67       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-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-7248 
        4.73        89.65        36.00        31.36        26.20        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       95.34         4.96        11.87        18.41        57.47        35.54 
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-7424 TCGA-CV-7425 TCGA-CV-7427 
       25.94         0.07        34.09        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94        16.27        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        21.01       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-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       88.87        48.20        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-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       28.01         3.62        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       18.84        13.25        25.41        23.05         2.53        16.14 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       11.44        24.95        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 
       22.59        24.95        12.10        12.79        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        46.45        20.45        37.58        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
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-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
       38.53        14.50        37.71        11.84        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       33.57        13.84        19.27        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 
       30.05        12.62         6.25        15.42         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T5 
       17.98        29.92        51.25        47.01        19.00        29.00 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       16.01        13.15        21.07        21.21        23.15        21.47 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        9.34        27.39        19.73        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       12.20        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
       15.91         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       13.25        20.35        64.80        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.45        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        14.56        13.35        18.15 

  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                        1.84                         0.07 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                      140.78                       210.97 
  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE 
                       18.97                        22.11 
[1] "1.8 - 140.8 (19.0)" "0.1 - 211.0 (22.1)"
[1] "hr=" "1.2"
D17V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 17(11P13) MUTATED         4       19        19        43         5
  AMP PEAK 17(11P13) WILD-TYPE      23       57        63       209         7
                              vv
clus                           STAGE IVC
  AMP PEAK 17(11P13) MUTATED           0
  AMP PEAK 17(11P13) WILD-TYPE         1
D17V3, multiclass
           clus
vv          AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  STAGE I                            4                           23
  STAGE II                          19                           57
  STAGE III                         19                           63
  STAGE IVA                         43                          209
  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 17(11P13) MUTATED       8  30  21  35
  AMP PEAK 17(11P13) WILD-TYPE    42 107  79 138
D17V4, multiclass
       clus
vv      AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  T0+T1                          8                           42
  T2                            30                          107
  T3                            21                           79
  T4                            35                          138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 17(11P13) MUTATED    40  11  29   4
  AMP PEAK 17(11P13) WILD-TYPE 139  57 139   4
D17V5, multiclass
    clus
vv   AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  N0                         40                          139
  N1                         11                           57
  N2                         29                          139
  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(11P13) MUTATED    42   0
  AMP PEAK 17(11P13) WILD-TYPE 148   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED     42    0
  AMP PEAK 17(11P13) WILD-TYPE  148    1
   clus
vv  AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  0                         42                          148
  1                          0                            1
[1] 2 2
[1] FALSE
D17V7, binary
                              cls
clus                             0   1
  AMP PEAK 17(11P13) MUTATED    25  77
  AMP PEAK 17(11P13) WILD-TYPE 115 305
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED     25   77
  AMP PEAK 17(11P13) WILD-TYPE  115  305
        clus
vv       AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  FEMALE                         25                          115
  MALE                           77                          305
[1] 2 2
[1] FALSE
D17V8, binary
                              cls
clus                             0   1
  AMP PEAK 17(11P13) MUTATED    40  54
  AMP PEAK 17(11P13) WILD-TYPE 122 247
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED     40   54
  AMP PEAK 17(11P13) WILD-TYPE  122  247
     clus
vv    AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
  NO                          40                          122
  YES                         54                          247
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(11P13) MUTATED                                   101
  AMP PEAK 17(11P13) WILD-TYPE                                 410
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 17(11P13) MUTATED                                                   1
  AMP PEAK 17(11P13) WILD-TYPE                                                 9
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 17(11P13) MUTATED                                                           0
  AMP PEAK 17(11P13) WILD-TYPE                                                         1
D17V9, multiclass
                                                           clus
vv                                                          AMP PEAK 17(11P13) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                              101
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                          0
                                                           clus
vv                                                          AMP PEAK 17(11P13) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                410
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
D17V11, continuous
D17V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(11P13) MUTATED                                  0     4
  AMP PEAK 17(11P13) WILD-TYPE                                2     7
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(11P13) MUTATED                          11    84
  AMP PEAK 17(11P13) WILD-TYPE                        37   362
D17V13, multiclass
                                  clus
vv                                 AMP PEAK 17(11P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                11
  WHITE                                                    84
                                  clus
vv                                 AMP PEAK 17(11P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  37
  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"
D17V14, binary
                              cls
clus                             0   1
  AMP PEAK 17(11P13) MUTATED     8  88
  AMP PEAK 17(11P13) WILD-TYPE  18 371
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(11P13) MUTATED      8   88
  AMP PEAK 17(11P13) WILD-TYPE   18  371
                        clus
vv                       AMP PEAK 17(11P13) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         88
                        clus
vv                       AMP PEAK 17(11P13) WILD-TYPE
  HISPANIC OR LATINO                               18
  NOT HISPANIC OR LATINO                          371
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(11Q13.3) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(11Q13.3) MUTATED   120 108
  AMP PEAK 18(11Q13.3) WILD-TYPE 181 111
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           228                            292 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                           108                            111 
$`AMP PEAK 18(11Q13.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
        9.30        37.28         3.55        30.18        25.71        51.29 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       35.05        32.48        48.20        32.88        70.13        16.73 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 
       11.61         6.02         0.36        34.36        14.04        46.32 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
       48.03         2.96        15.19        13.64         9.07        26.50 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
       17.10        23.84        65.59        15.52        14.83        12.62 
TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP 
       41.85        11.54         5.69         2.27        20.48        16.41 
TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7870 TCGA-BB-7871 
        6.15         4.80         4.41        22.42        66.28        24.66 
TCGA-BB-8596 TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4728 TCGA-CN-4731 
       71.05         8.81         6.28        55.86        56.68        32.81 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 
       57.11        20.55        14.33        45.83        13.05        42.02 
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-6018 
       52.08        50.07        30.67        48.00        23.90        19.07 
TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A498 TCGA-CN-A49A 
        6.74        32.22        38.89         3.68        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5329 
       29.72        21.21        31.69        19.53         2.93        70.45 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       11.21         4.24        13.25         4.24        14.99        38.76 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       53.52        41.88        44.48        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 
       14.14        11.77        54.67        18.54        16.90        12.46 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
       22.78         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        49.58         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        49.71        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-7086 TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6517 
       21.24        23.47        18.84        51.12        25.41         9.60 
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-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-8298 
       13.94        12.79        37.25        18.02        37.18        32.71 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A622 TCGA-H7-8502 TCGA-HD-7229 
        3.02        31.13        24.95        11.80        15.06        33.76 
TCGA-HD-7753 TCGA-HD-7831 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61G TCGA-IQ-A61H 
       28.47        21.93        15.95        38.53        11.84        37.41 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H8 
       33.57         5.29        13.68        19.04        15.48        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       14.37         7.96         1.84        17.98        15.78        71.74 
TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A6IG 
       47.01        18.97         2.04        29.00        16.01         7.30 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K 
       21.47        12.72        14.76        12.20        15.32         8.32 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E 
       15.91        13.71        64.80        54.67        49.51        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-KU-A66T 
       74.47        17.95        24.30        18.05        22.36        18.15 

$`AMP PEAK 18(11Q13.3) WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       20.48        68.48        28.11         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-7068 TCGA-CR-6472 TCGA-DQ-5629 
       11.08        19.82        24.39        43.04        34.52        30.94 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-5151 
       40.24        21.11        12.66        22.85         3.35        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH 
       42.35        57.93        21.17         4.01        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BA-A6DJ 
       27.95         7.10        14.47         7.82        11.05        13.38 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
      105.90         9.14        18.38        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       44.98        38.40        20.52        10.55        27.19        12.92 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
       12.69        48.76        38.04         4.67        12.89        26.86 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 
       52.14        12.99        27.58        73.61        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 
       12.39        71.31        12.49        56.94        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 
       34.13        10.45        17.42        11.74        35.01        23.57 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
        2.70        23.44        20.88        52.37        21.50        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       62.37        45.99        10.42        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CH 
       56.58        64.87        43.10        77.56        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-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-7364 TCGA-CR-7368 TCGA-CR-7373 TCGA-CR-7374 
        7.69        15.75        47.18        40.93        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 
       31.96        26.17        32.78        47.01        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       46.85        32.65        44.25        30.58        24.79         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-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       19.20        17.95        76.50        91.53        80.12        17.92 
TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6938 
       23.05        21.07        62.43         9.60         2.14         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 
       21.90        11.24       140.78        19.79        42.38         6.08 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
       53.95        65.82        10.98         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 
      172.67         7.99         9.01         5.26        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       21.80        10.75       130.88         4.73        89.65        36.00 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       26.20        17.13        95.34         4.96        11.87        47.97 
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-7421 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
        0.07        14.89        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
       16.27         7.17        16.64         6.38        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
      169.38       159.65         1.05        88.87        48.20        67.86 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO 
        0.76        56.61         7.07        15.25         5.98         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       28.01         3.62        19.92        22.52        10.42        10.55 
TCGA-D6-6515 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM 
       13.25        23.05         2.53        25.32        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 
       22.59        24.95        12.10        23.34        58.45        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
       21.63        20.25        18.94         0.46        17.85        20.25 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7832 
       12.43        13.38        15.16        20.94        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I 
        3.65         6.90        34.75        14.50        37.71         0.07 
TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       13.84        19.27        30.05        12.62         6.25        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        21.21 
TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       23.15         9.34        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        5.62        17.82        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71A 
       32.45         3.12        13.55        13.25        20.35         2.83 
TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT 
       44.65        55.43        29.46        13.94        20.75        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       17.03        20.55        14.56        13.35 

  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                          0.36                           0.07 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                        180.16                         210.97 
  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE 
                        20.535                         21.140 
[1] "0.4 - 180.2 (20.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.3"
D18V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 18(11Q13.3) MUTATED        15       30        34       116         7
  AMP PEAK 18(11Q13.3) WILD-TYPE      12       46        48       136         5
                                vv
clus                             STAGE IVC
  AMP PEAK 18(11Q13.3) MUTATED           0
  AMP PEAK 18(11Q13.3) WILD-TYPE         1
D18V3, multiclass
           clus
vv          AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  STAGE I                             15                             12
  STAGE II                            30                             46
  STAGE III                           34                             48
  STAGE IVA                          116                            136
  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 18(11Q13.3) MUTATED      21 55 47 83
  AMP PEAK 18(11Q13.3) WILD-TYPE    29 82 53 90
D18V4, multiclass
       clus
vv      AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  T0+T1                           21                             29
  T2                              55                             82
  T3                              47                             53
  T4                              83                             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 18(11Q13.3) MUTATED    78  26  87   4
  AMP PEAK 18(11Q13.3) WILD-TYPE 101  42  81   4
D18V5, multiclass
    clus
vv   AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  N0                           78                            101
  N1                           26                             42
  N2                           87                             81
  N3                            4                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    86   0
  AMP PEAK 18(11Q13.3) WILD-TYPE 104   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     86    0
  AMP PEAK 18(11Q13.3) WILD-TYPE  104    1
   clus
vv  AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  0                           86                            104
  1                            0                              1
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    57 172
  AMP PEAK 18(11Q13.3) WILD-TYPE  83 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     57  172
  AMP PEAK 18(11Q13.3) WILD-TYPE   83  210
        clus
vv       AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  FEMALE                           57                             83
  MALE                            172                            210
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    71 134
  AMP PEAK 18(11Q13.3) WILD-TYPE  91 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     71  134
  AMP PEAK 18(11Q13.3) WILD-TYPE   91  167
     clus
vv    AMP PEAK 18(11Q13.3) MUTATED AMP PEAK 18(11Q13.3) WILD-TYPE
  NO                            71                             91
  YES                          134                            167
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(11Q13.3) MUTATED                                   227
  AMP PEAK 18(11Q13.3) WILD-TYPE                                 284
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 18(11Q13.3) MUTATED                                                   2
  AMP PEAK 18(11Q13.3) WILD-TYPE                                                 8
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 18(11Q13.3) MUTATED                                                           0
  AMP PEAK 18(11Q13.3) WILD-TYPE                                                         1
D18V9, multiclass
                                                           clus
vv                                                          AMP PEAK 18(11Q13.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                227
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          AMP PEAK 18(11Q13.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  284
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
D18V11, continuous
D18V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(11Q13.3) MUTATED                                  0     3
  AMP PEAK 18(11Q13.3) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(11Q13.3) MUTATED                          25   193
  AMP PEAK 18(11Q13.3) WILD-TYPE                        23   253
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     193
                                  clus
vv                                 AMP PEAK 18(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    23
  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"
D18V14, binary
                                cls
clus                               0   1
  AMP PEAK 18(11Q13.3) MUTATED    11 200
  AMP PEAK 18(11Q13.3) WILD-TYPE  15 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(11Q13.3) MUTATED     11  200
  AMP PEAK 18(11Q13.3) WILD-TYPE   15  259
                        clus
vv                       AMP PEAK 18(11Q13.3) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          200
                        clus
vv                       AMP PEAK 18(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            259
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(12P13.33) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(12P13.33) MUTATED    94  73
  AMP PEAK 19(12P13.33) WILD-TYPE 207 146
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                            167                             353 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                             73                             146 
$`AMP PEAK 19(12P13.33) MUTATED`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6023 TCGA-CN-6024 
       37.28        68.48         3.55        28.11        52.08        11.08 
TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       32.88        16.73        34.36        30.94        14.04        46.32 
TCGA-4P-AA8J TCGA-BA-5555 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DI 
        3.35        17.10         4.01        29.42        20.45        11.05 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 
       20.48        16.41       105.90         9.14         4.80        36.72 
TCGA-BB-7870 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
       66.28        10.55         6.28        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5363 
       12.89        20.55        14.33        45.83        12.39         8.32 
TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6989 
       11.84        48.00        23.90        19.07        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       38.89         3.68        35.01        17.29        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A6V6 TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6223 
       31.69        20.88        70.45        10.42        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6487 
       56.58        29.49        84.23        11.77        58.42         7.69 
TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 
       12.46        47.18        39.16        24.95         9.17        34.06 
TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 
       17.13        49.58        24.79         5.13         5.95       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5973 TCGA-CV-5978 
       17.16       129.21       108.95       107.51        86.83         7.07 
TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 
       54.74        90.12        20.52        26.43        11.24        12.03 
TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7102 TCGA-CV-7103 
       30.08         8.42         4.14       111.16         1.84        52.31 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       21.80        71.21        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 
       17.13        47.97        49.71        57.47        35.54        17.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7434 
       25.08        25.94         0.07        34.09        16.27         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W 
      153.86        16.64        22.19       180.16        35.47        45.96 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JM TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6823 
       48.20        60.43         6.38        18.84        13.25        23.05 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7591 TCGA-DQ-7592 
       13.94        12.79        23.34        58.45        20.45        37.58 
TCGA-F7-7848 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 TCGA-HD-7753 
       37.18        31.13        18.94        12.43        13.38        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A6HZ TCGA-IQ-A6SG 
       25.74        21.93        27.48        22.03         3.65        19.04 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
       15.48        14.37         7.96        30.05         1.84         6.25 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF 
       17.98        15.78        75.55        13.15        21.07        23.15 
TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T3-A92N 
        7.30        21.07        14.76        12.20        12.72         3.12 
TCGA-TN-A7HI TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
       13.55         2.83        49.51        49.45        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-KU-A66T 
       24.30        55.43        29.46        13.94        18.15 

$`AMP PEAK 19(12P13.33) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
        9.30        20.48        30.18        25.71        51.29         9.07 
TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
        9.24        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 
       70.13        43.04        11.61        34.52         6.02         0.36 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
       57.93        23.84        65.59        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       12.62        41.85        27.95        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4227 
       14.47         7.82         2.27        13.38         6.15         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       18.38        22.42        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-4723 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       12.69        48.76        55.86        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       57.11        12.99        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 
       46.32         8.58        71.31        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        52.08        56.94        50.07        30.67 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6996 TCGA-CN-6998 
       47.44        28.04        34.13         6.74        17.42        11.74 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       25.41        23.57        21.21        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41        12.07         2.70        23.44        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50         2.93        54.58        62.37        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-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       64.87        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       23.24        29.36        33.60        14.14        12.46        31.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        50.01        39.52        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-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       22.78        15.75         9.27        47.34        40.93        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7380 
        3.45         3.09        29.23         0.99        31.96        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-7401 TCGA-CR-7402 
       46.85        32.65        44.25        30.58        35.41        29.95 
TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
       48.39        76.24        19.20        17.95        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-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       60.49        43.23        21.07        62.43         9.60         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 
        9.70         5.46         4.73        21.90       140.78        19.79 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       42.38        15.09         6.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 
        7.13        28.34         2.50        64.83       172.67        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7104 TCGA-CV-7180 
       12.66         7.99         9.01         5.26        12.92        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7252 
      130.88        77.16         4.73        89.65        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       11.87         2.10        18.41       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 
        0.46        22.85       100.57        14.89        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-A45O 
       54.94         3.52        84.49        19.76         6.38        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
       21.01       169.38       159.65         1.05         6.51        88.87 
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        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ 
       23.47        19.92        22.52        10.42        10.55        51.12 
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-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       22.59        24.95        12.10        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       46.45        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       20.25         3.02        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7832 
       20.25        15.16        15.06        20.94        33.76        27.48 
TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       14.66         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        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 
        0.07        33.57         5.29        13.68        13.84        19.27 
TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       10.75        12.62        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 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 
       18.97         2.04        29.00        12.99        16.01        21.21 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 
       21.47         9.34        12.72        27.39        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX 
        5.62        17.82        15.32         8.32        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-TN-A7HL 
       15.91         7.10        32.45        13.71        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS 
       64.80        54.67        74.47        18.05        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        20.55        14.56        13.35 

  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                         180.16                          210.97 
  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE 
                          21.93                           21.01 
[1] "0.1 - 180.2 (21.9)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1"  
D19V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 19(12P13.33) MUTATED         8       22        27        85
  AMP PEAK 19(12P13.33) WILD-TYPE      19       54        55       167
                                 vv
clus                              STAGE IVB STAGE IVC
  AMP PEAK 19(12P13.33) MUTATED           5         0
  AMP PEAK 19(12P13.33) WILD-TYPE         7         1
D19V3, multiclass
           clus
vv          AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  STAGE I                               8                              19
  STAGE II                             22                              54
  STAGE III                            27                              55
  STAGE IVA                            85                             167
  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 19(12P13.33) MUTATED      16  44  33  59
  AMP PEAK 19(12P13.33) WILD-TYPE    34  93  67 114
D19V4, multiclass
       clus
vv      AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  T0+T1                            16                              34
  T2                               44                              93
  T3                               33                              67
  T4                               59                             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
  AMP PEAK 19(12P13.33) MUTATED    57  20  60   4
  AMP PEAK 19(12P13.33) WILD-TYPE 122  48 108   4
D19V5, multiclass
    clus
vv   AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  N0                            57                             122
  N1                            20                              48
  N2                            60                             108
  N3                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                                 cls
clus                                0   1
  AMP PEAK 19(12P13.33) MUTATED    58   0
  AMP PEAK 19(12P13.33) WILD-TYPE 132   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED     58    0
  AMP PEAK 19(12P13.33) WILD-TYPE  132    1
   clus
vv  AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  0                            58                             132
  1                             0                               1
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(12P13.33) MUTATED    36 131
  AMP PEAK 19(12P13.33) WILD-TYPE 104 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED     36  131
  AMP PEAK 19(12P13.33) WILD-TYPE  104  251
        clus
vv       AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  FEMALE                            36                             104
  MALE                             131                             251
[1] 2 2
[1] FALSE
D19V8, binary
                                 cls
clus                                0   1
  AMP PEAK 19(12P13.33) MUTATED    48  93
  AMP PEAK 19(12P13.33) WILD-TYPE 114 208
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED     48   93
  AMP PEAK 19(12P13.33) WILD-TYPE  114  208
     clus
vv    AMP PEAK 19(12P13.33) MUTATED AMP PEAK 19(12P13.33) WILD-TYPE
  NO                             48                             114
  YES                            93                             208
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(12P13.33) MUTATED                                   164
  AMP PEAK 19(12P13.33) WILD-TYPE                                 347
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 19(12P13.33) MUTATED                                                   3
  AMP PEAK 19(12P13.33) WILD-TYPE                                                 7
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 19(12P13.33) MUTATED                                                           0
  AMP PEAK 19(12P13.33) WILD-TYPE                                                         1
D19V9, multiclass
                                                           clus
vv                                                          AMP PEAK 19(12P13.33) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 164
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
                                                           clus
vv                                                          AMP PEAK 19(12P13.33) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   347
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
D19V11, continuous
D19V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(12P13.33) MUTATED                                  1     1
  AMP PEAK 19(12P13.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(12P13.33) MUTATED                          19   141
  AMP PEAK 19(12P13.33) WILD-TYPE                        29   305
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      141
                                  clus
vv                                 AMP PEAK 19(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     29
  WHITE                                                        305
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                                 cls
clus                                0   1
  AMP PEAK 19(12P13.33) MUTATED     7 148
  AMP PEAK 19(12P13.33) WILD-TYPE  19 311
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(12P13.33) MUTATED      7  148
  AMP PEAK 19(12P13.33) WILD-TYPE   19  311
                        clus
vv                       AMP PEAK 19(12P13.33) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           148
                        clus
vv                       AMP PEAK 19(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                  19
  NOT HISPANIC OR LATINO                             311
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(12Q15) MUTATION ANALYSIS
D20V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 20(12Q15) MUTATED    58  44
  AMP PEAK 20(12Q15) WILD-TYPE 243 175
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                         102                          418 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                          44                          175 
$`AMP PEAK 20(12Q15) MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6024 TCGA-CQ-7067 
       68.48         3.55        51.29        52.08        11.08        16.73 
TCGA-CR-6478 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-6870 TCGA-BA-A6D8 TCGA-BA-A6DL 
        6.02        14.04        46.32        14.83        27.95        20.48 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HY TCGA-C9-A47Z 
      105.90         4.80        66.28        38.40        10.55         6.28 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-6010 
       38.04        56.68        20.55        45.83        46.32        50.07 
TCGA-CN-6012 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-A499 TCGA-CN-A49A 
       48.00        10.45        32.22         3.68        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A6V6 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-A4CE 
       29.72         7.40        20.88        32.38        56.58        29.49 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7390 
       11.77        58.42        39.16        34.06        17.13        49.58 
TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6959 
      139.43       108.95         9.70        26.43        42.38         8.42 
TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
      111.16         5.26         1.84        36.00        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 
       18.97        17.13        35.54        25.08         0.07        34.09 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45R 
       54.94        16.27        16.64         6.38        22.19       180.16 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 
        6.51        88.87        48.20        13.25        25.41        23.05 
TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A74Q TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A50J 
       11.44        12.36        23.34        37.58        40.04        31.13 
TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 TCGA-HD-7753 TCGA-HD-A6HZ TCGA-IQ-A6SH 
       18.94        12.43        13.38        28.47         3.65        15.48 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6T4 TCGA-QK-A6IF 
       14.37        30.05         1.84         6.25         2.04        23.15 
TCGA-QK-A6VB TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T2-A6X0 TCGA-T3-A92N TCGA-TN-A7HI 
       21.07        12.20        12.72         7.10         3.12        13.55 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JH TCGA-UF-A7JO TCGA-KU-A66T 
        2.83        49.45        44.65        29.46        20.75        18.15 

$`AMP PEAK 20(12Q15) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        20.48        28.11        30.18        25.71 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.07         9.24        35.05        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       48.20        32.88        70.13        43.04        11.61        34.52 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        0.36        34.36        30.94        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       23.84        65.59        15.52        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        20.45        11.54         7.10         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP 
       14.47         7.82         2.27        11.05        13.38        16.41 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        6.15         9.14         4.41        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 
       33.70        50.20        44.98        24.66        71.05        20.52 
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        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        4.67        12.89        26.86        32.81        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       12.99        14.33        27.58        73.61        13.05        42.02 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         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        52.08        56.94 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
        6.74        38.89        17.42        11.74        35.01        25.41 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
       12.07         2.70        23.44        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
       11.21         4.24        41.19        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       77.56        44.48        23.24        29.36        33.60        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-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        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        22.78 
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-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-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        9.17        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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       24.79         5.13         5.95        35.41        29.95        48.39 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       129.21        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-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        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-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       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82        10.98         7.13        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       172.67        18.81        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-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       77.16         4.73        89.65        95.34         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
       47.97         2.10        49.71        18.41        57.47        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-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7432 
      100.57        14.89        56.48       156.49         3.52        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
       19.76         7.17       153.86        27.98        21.01       169.38 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A461 
      159.65        35.47         1.05        45.96        60.43        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        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       51.12         9.60         2.53        16.14        18.67        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        28.77         7.63        22.59        24.95 
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        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       18.02        46.45        20.45        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W 
       32.71        21.63        20.25         3.02        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       17.85        11.80        20.25        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       33.76        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         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        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI 
       19.27        10.75         7.96        12.62        15.42         7.13 
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        71.74        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        21.21 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC 
        7.30        21.47         9.34        12.72        27.39        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       12.89         5.62        14.76        17.82        15.32         8.32 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ 
       16.96         6.87        15.91        32.45        13.71        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC 
       20.35        64.80        54.67        49.51        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       24.30        55.43        18.05        13.94        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       17.03        20.55        14.56        13.35 

  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                      180.16                       210.97 
  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE 
                       22.62                        21.07 
[1] "0.1 - 180.2 (22.6)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D20V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 20(12Q15) MUTATED         9       14        15        49         2
  AMP PEAK 20(12Q15) WILD-TYPE      18       62        67       203        10
                              vv
clus                           STAGE IVC
  AMP PEAK 20(12Q15) MUTATED           0
  AMP PEAK 20(12Q15) WILD-TYPE         1
D20V3, multiclass
           clus
vv          AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  STAGE I                            9                           18
  STAGE II                          14                           62
  STAGE III                         15                           67
  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 20(12Q15) MUTATED      12  28  16  35
  AMP PEAK 20(12Q15) WILD-TYPE    38 109  84 138
D20V4, multiclass
       clus
vv      AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  T0+T1                         12                           38
  T2                            28                          109
  T3                            16                           84
  T4                            35                          138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2  N3
  AMP PEAK 20(12Q15) MUTATED    44  10  29   1
  AMP PEAK 20(12Q15) WILD-TYPE 135  58 139   7
D20V5, multiclass
    clus
vv   AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  N0                         44                          135
  N1                         10                           58
  N2                         29                          139
  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"
D20V6, binary
                              cls
clus                             0   1
  AMP PEAK 20(12Q15) MUTATED    35   0
  AMP PEAK 20(12Q15) WILD-TYPE 155   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED     35    0
  AMP PEAK 20(12Q15) WILD-TYPE  155    1
   clus
vv  AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  0                         35                          155
  1                          0                            1
[1] 2 2
[1] FALSE
D20V7, binary
                              cls
clus                             0   1
  AMP PEAK 20(12Q15) MUTATED    28  75
  AMP PEAK 20(12Q15) WILD-TYPE 112 307
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED     28   75
  AMP PEAK 20(12Q15) WILD-TYPE  112  307
        clus
vv       AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  FEMALE                         28                          112
  MALE                           75                          307
[1] 2 2
[1] FALSE
D20V8, binary
                              cls
clus                             0   1
  AMP PEAK 20(12Q15) MUTATED    29  57
  AMP PEAK 20(12Q15) WILD-TYPE 133 244
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED     29   57
  AMP PEAK 20(12Q15) WILD-TYPE  133  244
     clus
vv    AMP PEAK 20(12Q15) MUTATED AMP PEAK 20(12Q15) WILD-TYPE
  NO                          29                          133
  YES                         57                          244
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(12Q15) MUTATED                                   102
  AMP PEAK 20(12Q15) WILD-TYPE                                 409
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 20(12Q15) MUTATED                                                   1
  AMP PEAK 20(12Q15) WILD-TYPE                                                 9
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 20(12Q15) MUTATED                                                           0
  AMP PEAK 20(12Q15) WILD-TYPE                                                         1
D20V9, multiclass
                                                           clus
vv                                                          AMP PEAK 20(12Q15) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                              102
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                          0
                                                           clus
vv                                                          AMP PEAK 20(12Q15) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                409
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
D20V11, continuous
D20V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(12Q15) MUTATED                                  2     2
  AMP PEAK 20(12Q15) WILD-TYPE                                0     9
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(12Q15) MUTATED                          10    86
  AMP PEAK 20(12Q15) WILD-TYPE                        38   360
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                    86
                                  clus
vv                                 AMP PEAK 20(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  38
  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"
D20V14, binary
                              cls
clus                             0   1
  AMP PEAK 20(12Q15) MUTATED     4  89
  AMP PEAK 20(12Q15) WILD-TYPE  22 370
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 20(12Q15) MUTATED      4   89
  AMP PEAK 20(12Q15) WILD-TYPE   22  370
                        clus
vv                       AMP PEAK 20(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         89
                        clus
vv                       AMP PEAK 20(12Q15) WILD-TYPE
  HISPANIC OR LATINO                               22
  NOT HISPANIC OR LATINO                          370
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(13Q22.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(13Q22.1) MUTATED    51  54
  AMP PEAK 21(13Q22.1) WILD-TYPE 250 165
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                           105                            415 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                            54                            165 
$`AMP PEAK 21(13Q22.1) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CN-6997 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-5629 
        9.30         3.55        32.48        34.52        34.36        30.94 
TCGA-DQ-7588 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       14.04        14.83        29.42         9.14         4.80         4.41 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 
        4.67        56.68        12.89        12.99        20.55        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6989 TCGA-CN-6996 
       73.61        13.05         8.52        23.90        32.22        17.42 
TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-6220 
       29.72        31.69        22.32        12.39        16.57        32.38 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4CH TCGA-CR-5247 
       13.25         4.24        53.52        77.56        12.46        11.77 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
       11.64        12.46        39.16        47.34        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7380 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 
       24.95         0.99        19.92        49.58       139.43        17.16 
TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6939 TCGA-CV-6956 
      107.51        54.74         9.60        90.12        21.90         7.13 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 
      172.67        18.81        12.66         9.01         1.84        71.21 
TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7255 
       10.75        31.36        18.97        17.13        11.87         2.10 
TCGA-CV-7261 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7437 TCGA-CV-7440 
       49.71        25.08       100.57        14.89        16.64        22.19 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A463 TCGA-CV-A6JM TCGA-D6-6823 TCGA-D6-8569 
       45.96         6.51         0.76         6.38        23.05        25.32 
TCGA-D6-A4Z9 TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       17.72        12.10        58.45        18.02        20.45        37.58 
TCGA-F7-A50J TCGA-HD-7753 TCGA-HD-7832 TCGA-IQ-A61G TCGA-IQ-A61K TCGA-MT-A51W 
       31.13        28.47        27.48        11.84         5.29        14.37 
TCGA-MT-A51X TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-QK-A6VB 
        7.96        18.97         2.04        29.00        21.47        21.07 
TCGA-QK-A8Z7 TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A7JA TCGA-UF-A7JC 
       12.89        15.91        13.25        54.67        74.47        17.95 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7GZ 
       29.46        13.94        20.55 

$`AMP PEAK 21(13Q22.1) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       51.29         9.07         9.24        52.08        11.08        35.05 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7589 TCGA-DQ-7593 
       43.04        11.61         6.02         0.36        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62         4.01        41.85        20.45        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       105.90        18.38 
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-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        10.55        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        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 
       38.04        26.86        32.81        52.14        57.11        14.33 
TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       45.83        42.02        46.32         8.58        12.39        71.31 
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-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
       52.08        56.94        50.07        30.67        48.00        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 
       28.04        19.07        34.13         6.74        10.45        38.89 
TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
        3.68        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       21.21         7.40         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       70.45        62.37        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       41.19        46.95        56.58        14.99        38.76        64.87 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       41.88        43.10        44.48        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       29.49        14.14        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 
       16.90        11.90        10.22        11.34         7.69        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 
       15.75         9.27        47.18        40.93         3.09        29.23 
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-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        27.06        12.89        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       29.95        48.39       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95        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-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
       43.23        21.07        62.43         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       140.78        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-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82        10.98         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 
       64.83       111.16         7.99         5.26        52.31        12.92 
TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       21.80       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7406 
       26.20        95.34         4.96        47.97        18.41        57.47 
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-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 
       22.85        25.94         0.07        34.09        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-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
      153.86         6.38        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
      159.65        35.47         1.05        88.87        48.20        60.43 
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-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
       29.79         6.48        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60         2.53        16.14        11.44 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       18.67        24.95        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 
       24.95        13.94        12.79        23.34        37.25        33.86 
TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       46.45        40.04        39.12        41.59        37.18        32.71 
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        24.95         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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7917 
       15.06        20.94        33.76        25.74        21.93        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         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        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41         0.07        33.57        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       15.48        19.27        10.75        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       19.00        75.55        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15         7.30         9.34        12.72        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73         5.62        14.76        12.20        17.82        15.32 
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-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
       13.71         3.12        13.55        20.35        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
       49.51        49.45        44.65        24.30        55.43        18.05 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        17.03        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                          0.76                           0.07 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                        172.67                         210.97 
  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE 
                         18.97                          21.63 
[1] "0.8 - 172.7 (19.0)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.4"
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 21(13Q22.1) MUTATED         3       16        14        52         2
  AMP PEAK 21(13Q22.1) WILD-TYPE      24       60        68       200        10
                                vv
clus                             STAGE IVC
  AMP PEAK 21(13Q22.1) MUTATED           0
  AMP PEAK 21(13Q22.1) WILD-TYPE         1
D21V3, multiclass
           clus
vv          AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  STAGE I                              3                             24
  STAGE II                            16                             60
  STAGE III                           14                             68
  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 21(13Q22.1) MUTATED       5  25  24  36
  AMP PEAK 21(13Q22.1) WILD-TYPE    45 112  76 137
D21V4, multiclass
       clus
vv      AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  T0+T1                            5                             45
  T2                              25                            112
  T3                              24                             76
  T4                              36                            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 21(13Q22.1) MUTATED    33  12  36   0
  AMP PEAK 21(13Q22.1) WILD-TYPE 146  56 132   8
D21V5, multiclass
    clus
vv   AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  N0                           33                            146
  N1                           12                             56
  N2                           36                            132
  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(13Q22.1) MUTATED    32   0
  AMP PEAK 21(13Q22.1) WILD-TYPE 158   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED     32    0
  AMP PEAK 21(13Q22.1) WILD-TYPE  158    1
   clus
vv  AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  0                           32                            158
  1                            0                              1
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(13Q22.1) MUTATED    25  80
  AMP PEAK 21(13Q22.1) WILD-TYPE 115 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED     25   80
  AMP PEAK 21(13Q22.1) WILD-TYPE  115  302
        clus
vv       AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  FEMALE                           25                            115
  MALE                             80                            302
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(13Q22.1) MUTATED    32  59
  AMP PEAK 21(13Q22.1) WILD-TYPE 130 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED     32   59
  AMP PEAK 21(13Q22.1) WILD-TYPE  130  242
     clus
vv    AMP PEAK 21(13Q22.1) MUTATED AMP PEAK 21(13Q22.1) WILD-TYPE
  NO                            32                            130
  YES                           59                            242
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(13Q22.1) MUTATED                                   104
  AMP PEAK 21(13Q22.1) WILD-TYPE                                 407
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 21(13Q22.1) MUTATED                                                   1
  AMP PEAK 21(13Q22.1) WILD-TYPE                                                 9
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 21(13Q22.1) MUTATED                                                           0
  AMP PEAK 21(13Q22.1) WILD-TYPE                                                         1
D21V9, multiclass
                                                           clus
vv                                                          AMP PEAK 21(13Q22.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                104
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          AMP PEAK 21(13Q22.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  407
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
D21V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(13Q22.1) MUTATED                                  1     4
  AMP PEAK 21(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(13Q22.1) MUTATED                           9    87
  AMP PEAK 21(13Q22.1) WILD-TYPE                        39   359
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      87
                                  clus
vv                                 AMP PEAK 21(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       359
[1] 4 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(13Q22.1) MUTATED     7  88
  AMP PEAK 21(13Q22.1) WILD-TYPE  19 371
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(13Q22.1) MUTATED      7   88
  AMP PEAK 21(13Q22.1) WILD-TYPE   19  371
                        clus
vv                       AMP PEAK 21(13Q22.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       AMP PEAK 21(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            371
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(13Q34) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(13Q34) MUTATED    51  54
  AMP PEAK 22(13Q34) WILD-TYPE 250 165
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                         105                          415 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                          54                          165 
$`AMP PEAK 22(13Q34) MUTATED`
TCGA-BA-4075 TCGA-CN-6997 TCGA-CQ-A4C7 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
        9.30        32.48        11.61        34.36        30.94        14.04 
TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-A5HY 
       14.83        29.42        20.48         9.14         4.80        10.55 
TCGA-BB-A5HZ TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4742 
       27.19         4.67        56.68        12.89        20.55        13.05 
TCGA-CN-5358 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6996 
        8.58         8.52        23.90         6.74        32.22        17.42 
TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V6 TCGA-CQ-5329 
       29.72        22.32        12.39        16.57        20.88        70.45 
TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CH 
       32.38        13.25        14.99        77.56        23.24        12.46 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 
       31.23        11.77        54.67        58.42        11.64        12.46 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7380 TCGA-CR-7388 
       39.16        47.34         3.45        24.95        19.92        27.06 
TCGA-CR-7390 TCGA-CR-7392 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5966 TCGA-CV-6003 
       49.58        46.85        17.16       107.51        17.92        54.74 
TCGA-CV-6933 TCGA-CV-6950 TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 
       90.12        15.09         7.13         2.50       172.67        18.81 
TCGA-CV-7097 TCGA-CV-7178 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7255 TCGA-CV-7414 
       12.66        71.21        31.36        18.97         2.10         0.46 
TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45R 
       25.08       100.57        14.89        16.64        22.19       180.16 
TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A6JM TCGA-D6-6517 
       35.47         6.51         0.76         7.07         6.38         9.60 
TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5631 TCGA-F7-A50J 
       23.05        25.32        12.10        12.79        18.02        31.13 
TCGA-HD-7832 TCGA-HD-8314 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X 
       27.48        22.03        15.95        11.84        14.37         7.96 
TCGA-P3-A5Q6 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-QK-A6VC 
       15.78        18.97         2.04        29.00        21.47        19.73 
TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 
       12.20        12.72        16.96        15.91        13.25        54.67 
TCGA-UF-A7JC TCGA-UF-A7JH TCGA-WA-A7GZ 
       17.95        29.46        20.55 

$`AMP PEAK 22(13Q34) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       35.05        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7589 
       16.73        43.04        34.52         6.02         0.36        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       40.24        21.11        12.66        22.85        48.03         2.96 
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-5558 TCGA-BA-6868 
       42.35        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 
       21.17        12.62         4.01        41.85        20.45        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       105.90         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        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-A6UM 
       66.28        24.66        38.40        71.05        20.52        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        48.76        55.86        38.04 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
       26.86        32.81        52.14        57.11        12.99        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 
       45.83        27.58        73.61        42.02        46.32        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       12.49        52.08        56.94        50.07        30.67        48.00 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6994 
       47.44        28.04        19.07        34.13        10.45        38.89 
TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
        3.68        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       21.21         7.40        31.69         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       23.44        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       46.95        56.58         4.24        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       41.88        43.10        44.48        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
       14.14        84.23        37.87        26.27        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        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        22.78        15.75         9.27        47.18        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
       35.84         3.09        29.23         0.99        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
       34.06        26.17        17.13        32.78        47.01        12.89 
TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
       30.02        32.65        44.25        30.58        24.79         5.13 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.95        35.41        29.95        48.39       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20        17.95        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
       91.53        80.12        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-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         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       140.78        19.79        12.03        42.38 
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-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 
       28.34         4.14        64.83       111.16         7.99         9.01 
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-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
      130.88        77.16         4.73        89.65        36.00        26.20 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       17.13        95.34         4.96        11.87        47.97        49.71 
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-7413 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7425 
        9.67        22.85        25.94         0.07        34.09        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-7435 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17       153.86         6.38        27.98        21.01       169.38 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
      159.65         1.05        45.96        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
       67.86        56.61        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        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
       25.41         2.53        16.14        11.44        18.67        24.95 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 
       13.94        23.34        58.45        37.25        33.86        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        37.58        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63        20.25         3.02        18.94        24.95 
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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       21.93        27.48        14.66         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        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D 
       19.04        15.48        19.27        10.75        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       12.62         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       29.92        71.74        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       19.00        75.55        12.99        16.01        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15         7.30         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       21.07        12.89         5.62        14.76        17.82        15.32 
TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        8.32         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.55        20.35        64.80         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       44.65        74.47        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        17.03        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                        0.46                         0.07 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                      180.16                       210.97 
  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE 
                       18.02                        21.93 
[1] "0.5 - 180.2 (18.0)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1.4"
D22V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 22(13Q34) MUTATED         2       19        21        47         2
  AMP PEAK 22(13Q34) WILD-TYPE      25       57        61       205        10
                              vv
clus                           STAGE IVC
  AMP PEAK 22(13Q34) MUTATED           0
  AMP PEAK 22(13Q34) WILD-TYPE         1
D22V3, multiclass
           clus
vv          AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  STAGE I                            2                           25
  STAGE II                          19                           57
  STAGE III                         21                           61
  STAGE IVA                         47                          205
  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 22(13Q34) MUTATED       6  33  25  31
  AMP PEAK 22(13Q34) WILD-TYPE    44 104  75 142
D22V4, multiclass
       clus
vv      AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  T0+T1                          6                           44
  T2                            33                          104
  T3                            25                           75
  T4                            31                          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 22(13Q34) MUTATED    34  20  34   0
  AMP PEAK 22(13Q34) WILD-TYPE 145  48 134   8
D22V5, multiclass
    clus
vv   AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  N0                         34                          145
  N1                         20                           48
  N2                         34                          134
  N3                          0                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                              cls
clus                             0   1
  AMP PEAK 22(13Q34) MUTATED    39   0
  AMP PEAK 22(13Q34) WILD-TYPE 151   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED     39    0
  AMP PEAK 22(13Q34) WILD-TYPE  151    1
   clus
vv  AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  0                         39                          151
  1                          0                            1
[1] 2 2
[1] FALSE
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(13Q34) MUTATED    24  82
  AMP PEAK 22(13Q34) WILD-TYPE 116 300
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED     24   82
  AMP PEAK 22(13Q34) WILD-TYPE  116  300
        clus
vv       AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  FEMALE                         24                          116
  MALE                           82                          300
[1] 2 2
[1] FALSE
D22V8, binary
                              cls
clus                             0   1
  AMP PEAK 22(13Q34) MUTATED    32  64
  AMP PEAK 22(13Q34) WILD-TYPE 130 237
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED     32   64
  AMP PEAK 22(13Q34) WILD-TYPE  130  237
     clus
vv    AMP PEAK 22(13Q34) MUTATED AMP PEAK 22(13Q34) WILD-TYPE
  NO                          32                          130
  YES                         64                          237
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(13Q34) MUTATED                                   104
  AMP PEAK 22(13Q34) WILD-TYPE                                 407
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 22(13Q34) MUTATED                                                   2
  AMP PEAK 22(13Q34) WILD-TYPE                                                 8
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 22(13Q34) MUTATED                                                           0
  AMP PEAK 22(13Q34) WILD-TYPE                                                         1
D22V9, multiclass
                                                           clus
vv                                                          AMP PEAK 22(13Q34) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                              104
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                          0
                                                           clus
vv                                                          AMP PEAK 22(13Q34) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                407
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
D22V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(13Q34) MUTATED                                  0     3
  AMP PEAK 22(13Q34) WILD-TYPE                                2     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(13Q34) MUTATED                           8    90
  AMP PEAK 22(13Q34) WILD-TYPE                        40   356
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                    90
                                  clus
vv                                 AMP PEAK 22(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  40
  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"
D22V14, binary
                              cls
clus                             0   1
  AMP PEAK 22(13Q34) MUTATED     8  92
  AMP PEAK 22(13Q34) WILD-TYPE  18 367
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(13Q34) MUTATED      8   92
  AMP PEAK 22(13Q34) WILD-TYPE   18  367
                        clus
vv                       AMP PEAK 22(13Q34) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                         92
                        clus
vv                       AMP PEAK 22(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               18
  NOT HISPANIC OR LATINO                          367
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(15Q26.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(15Q26.3) MUTATED    54  51
  AMP PEAK 23(15Q26.3) WILD-TYPE 247 168
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                           105                            415 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                            51                            168 
$`AMP PEAK 23(15Q26.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-6871 TCGA-CN-6022 TCGA-CN-6992 TCGA-CQ-7067 
        9.30        37.28         3.55         9.24        35.05        16.73 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A6D8 
       30.94        14.04        46.32        14.83         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        56.68        12.89 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5365 
       20.55        45.83        27.58        46.32        12.39        11.54 
TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6995 TCGA-CQ-6225 TCGA-CQ-6228 
       11.84        50.07        23.90         3.68        13.25        14.99 
TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 
       41.88        23.24        31.23        11.77        18.54        16.90 
TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7374 
       11.64        22.78        47.18        39.16         3.45         0.99 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6955 
       34.06        19.92        49.58        54.74         2.14        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7178 
        7.13         8.42         4.14       172.67         5.26        71.21 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7413 
       77.16        36.00        47.97         2.10        49.71         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7427 
       22.85        25.08        25.94         0.07        14.89       156.49 
TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-A45X TCGA-CV-A6JD TCGA-CV-A6JM 
        3.52        19.76        16.64         6.51         5.98         6.38 
TCGA-CV-A6K2 TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5631 
       10.42        51.12        25.41        25.32         7.63        18.02 
TCGA-F7-7848 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A633 
       37.18        15.16        28.47        27.48        14.66        13.84 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A6SH TCGA-MT-A67A 
        3.65         6.90        14.50        37.41        15.48        30.05 
TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A6IH TCGA-QK-A8Z7 
        6.25        71.74        12.99        16.01        21.47        12.89 
TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HJ TCGA-UF-A71E TCGA-UF-A7JF 
       15.32        15.91         7.10        13.25        49.45        55.43 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-WA-A7GZ 
       29.46        13.94        20.55 

$`AMP PEAK 23(15Q26.3) WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
       20.48        68.48        28.11        30.18        25.71        51.29 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.07        52.08        11.08        32.48        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       48.20        32.88        70.13        43.04        11.61        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        6.02         0.36        34.36        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
        9.07        26.50        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 
       23.84        65.59        15.52        21.17        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       29.42        20.45        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
      105.90         9.14         4.80         4.41        18.38        36.72 
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-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       20.52        10.55        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 
       48.76        55.86        38.04         4.67        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
       52.14        57.11        12.99        14.33        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5367 
       42.02         8.58        71.31         8.32        16.21        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
       12.49         8.52        52.08        56.94        30.67        48.00 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       47.44        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       32.22        38.89        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        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        46.95        56.58         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        64.87        53.52        43.10        77.56        44.48 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
       29.36        33.60        29.49        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       36.99        11.90        10.22        11.34         7.69        12.46 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       15.75         9.27        47.34        40.93        35.84         3.09 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 
       24.95        29.23        31.96         9.17        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        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
       32.65        44.25        30.58        24.79         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-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-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-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60        90.12         9.70         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       140.78        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-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 
       65.82        28.34         2.50        64.83       111.16        18.81 
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-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
       21.80        10.75       130.88         4.73        89.65        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-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-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7428 TCGA-CV-7430 
        0.46        34.09       100.57        56.48        54.94        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O 
       84.49         7.17       153.86         6.38        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V 
       21.01       169.38       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-A465 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61         7.07        15.25        35.34        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       10.55        18.84        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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       37.58        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8314 
       20.94        33.76        25.74        21.93        27.48        22.03 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E 
        0.36         4.27        34.75        15.95        38.53        37.71 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       11.84         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       19.04        19.27        10.75        14.37         7.96         1.84 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       12.62        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       15.78        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z 
       75.55        18.97         2.04        29.00        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15         7.30         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       21.07        19.73         5.62        14.76        12.20        17.82 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M 
        8.32        12.72        16.96         6.87        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        3.12        13.55        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ 
       49.51        44.65        74.47        17.95        24.30        18.05 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        17.03        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                        172.67                         210.97 
  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE 
                         16.73                          21.80 
[1] "0.1 - 172.7 (16.7)" "0.1 - 211.0 (21.8)"
[1] "hr=" "1.4"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 23(15Q26.3) MUTATED         6       13        15        52         4
  AMP PEAK 23(15Q26.3) WILD-TYPE      21       63        67       200         8
                                vv
clus                             STAGE IVC
  AMP PEAK 23(15Q26.3) MUTATED           0
  AMP PEAK 23(15Q26.3) WILD-TYPE         1
D23V3, multiclass
           clus
vv          AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  STAGE I                              6                             21
  STAGE II                            13                             63
  STAGE III                           15                             67
  STAGE IVA                           52                            200
  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 23(15Q26.3) MUTATED       9  27  13  43
  AMP PEAK 23(15Q26.3) WILD-TYPE    41 110  87 130
D23V4, multiclass
       clus
vv      AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  T0+T1                            9                             41
  T2                              27                            110
  T3                              13                             87
  T4                              43                            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 23(15Q26.3) MUTATED    33  14  32   2
  AMP PEAK 23(15Q26.3) WILD-TYPE 146  54 136   6
D23V5, multiclass
    clus
vv   AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  N0                           33                            146
  N1                           14                             54
  N2                           32                            136
  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"
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(15Q26.3) MUTATED    38   0
  AMP PEAK 23(15Q26.3) WILD-TYPE 152   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED     38    0
  AMP PEAK 23(15Q26.3) WILD-TYPE  152    1
   clus
vv  AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  0                           38                            152
  1                            0                              1
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(15Q26.3) MUTATED    29  76
  AMP PEAK 23(15Q26.3) WILD-TYPE 111 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED     29   76
  AMP PEAK 23(15Q26.3) WILD-TYPE  111  306
        clus
vv       AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  FEMALE                           29                            111
  MALE                             76                            306
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(15Q26.3) MUTATED    29  64
  AMP PEAK 23(15Q26.3) WILD-TYPE 133 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED     29   64
  AMP PEAK 23(15Q26.3) WILD-TYPE  133  237
     clus
vv    AMP PEAK 23(15Q26.3) MUTATED AMP PEAK 23(15Q26.3) WILD-TYPE
  NO                            29                            133
  YES                           64                            237
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(15Q26.3) MUTATED                                   101
  AMP PEAK 23(15Q26.3) WILD-TYPE                                 410
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 23(15Q26.3) MUTATED                                                   4
  AMP PEAK 23(15Q26.3) WILD-TYPE                                                 6
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 23(15Q26.3) MUTATED                                                           0
  AMP PEAK 23(15Q26.3) WILD-TYPE                                                         1
D23V9, multiclass
                                                           clus
vv                                                          AMP PEAK 23(15Q26.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                101
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          AMP PEAK 23(15Q26.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  410
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
D23V11, continuous
D23V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(15Q26.3) MUTATED                                  0     3
  AMP PEAK 23(15Q26.3) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(15Q26.3) MUTATED                          12    86
  AMP PEAK 23(15Q26.3) WILD-TYPE                        36   360
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      86
                                  clus
vv                                 AMP PEAK 23(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    36
  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"
D23V14, binary
                                cls
clus                               0   1
  AMP PEAK 23(15Q26.3) MUTATED     4  91
  AMP PEAK 23(15Q26.3) WILD-TYPE  22 368
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(15Q26.3) MUTATED      4   91
  AMP PEAK 23(15Q26.3) WILD-TYPE   22  368
                        clus
vv                       AMP PEAK 23(15Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       AMP PEAK 23(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            368
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(17Q12) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(17Q12) MUTATED    47  44
  AMP PEAK 24(17Q12) WILD-TYPE 254 175
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          91                          429 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                          44                          175 
$`AMP PEAK 24(17Q12) MUTATED`
TCGA-CN-6023 TCGA-CR-6478 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-BA-6872 
       52.08         6.02        30.94        14.04        46.32        12.62 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-8601 
       41.85        29.42        11.05         4.80         4.41        20.52 
TCGA-C9-A47Z TCGA-CN-5356 TCGA-CN-5366 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
        6.28        46.32        11.84        10.45        32.22        38.89 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6228 
       21.21        31.69        12.39        32.38        13.25        14.99 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 
       41.88        77.56        23.24        29.49        11.77        58.42 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7399 
       12.46        39.16         3.45        17.13        49.58         5.95 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 
      139.43        17.16       129.21       107.51        13.35        60.49 
TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 
       54.74        90.12        26.43        11.24        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7248 TCGA-CV-7250 
       30.08         4.14         5.26         1.84        17.13        95.34 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7424 
       47.97        49.71         0.46        22.85         0.07        14.89 
TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JZ 
      180.16        35.47        45.96         7.07         6.38        23.47 
TCGA-CX-A4AQ TCGA-D6-8569 TCGA-D6-A6EP TCGA-D6-A6ES TCGA-F7-8298 TCGA-HD-7753 
       51.12        25.32        13.94        12.79        32.71        28.47 
TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-MT-A67D 
       27.48         3.65        13.68        13.84        19.04         1.84 
TCGA-P3-A6T7 TCGA-QK-A6IG TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       16.01         7.30        21.07        19.73        12.89         5.62 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JH 
        8.32        12.72        54.67         2.83        49.45        29.46 
TCGA-UF-A7JO 
       20.75 

$`AMP PEAK 24(17Q12) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
       30.18        25.71        51.29         9.07         9.24        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 
       70.13        16.73        43.04        11.61        34.52         0.36 
TCGA-CX-7219 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       34.36        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
        2.96         3.35        15.19        13.64         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 
       15.52        21.17        14.83         4.01        20.45        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       105.90         9.14 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
       18.38        22.42        36.72        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HY TCGA-BB-A5HZ 
       66.28        24.66        38.40        71.05        10.55        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
       12.92         8.81        12.69        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       57.11        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       73.61        13.05        42.02         8.58        12.39        71.31 
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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6995 
       47.44        28.04        19.07        34.13         6.74         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       29.72         7.40        22.32        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
       11.21         4.24        41.19        46.95        56.58         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       38.76        64.87        53.52        43.10        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
       33.60        14.14        12.46        31.23        84.23        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       37.87        26.27        50.01        39.52        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
       16.90        11.90        10.22        11.34        11.64         7.69 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
       22.78        15.75         9.27        47.18        47.34        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-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        9.17        34.06        19.92        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        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       30.58        24.79         5.13        35.41        29.95        48.39 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
      108.95        76.24        19.20        17.95        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-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        7.07        43.23        21.07        62.43         9.60         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 
        9.70         5.46        20.52         4.73        21.90       140.78 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       19.79        42.38         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       172.67 
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-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        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
        4.96        11.87         2.10        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 
       17.85       210.97        89.33         9.67        25.08        25.94 
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-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-A45T 
        6.38        22.19        27.98        21.01       169.38       159.65 
TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1.05         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-A6JN 
        0.76        56.61        15.25         5.98        35.34        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01         3.62        21.24        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        10.55        18.84        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-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.10        23.34        58.45        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
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        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       13.38        15.16        15.06        20.94        33.76        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        14.66        22.03         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        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        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         6.25        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        71.74        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-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
       12.99        13.15        21.07        21.21        23.15        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
        9.34        12.72        27.39        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       15.32        16.96         6.87        15.91         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        44.65        74.47        17.95        24.30        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       18.05        13.94        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                      180.16                       210.97 
  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE 
                       19.73                        21.24 
[1] "0.1 - 180.2 (19.7)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D24V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 24(17Q12) MUTATED         3       13        19        43         0
  AMP PEAK 24(17Q12) WILD-TYPE      24       63        63       209        12
                              vv
clus                           STAGE IVC
  AMP PEAK 24(17Q12) MUTATED           1
  AMP PEAK 24(17Q12) WILD-TYPE         0
D24V3, multiclass
           clus
vv          AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  STAGE I                            3                           24
  STAGE II                          13                           63
  STAGE III                         19                           63
  STAGE IVA                         43                          209
  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 24(17Q12) MUTATED       4  24  22  29
  AMP PEAK 24(17Q12) WILD-TYPE    46 113  78 144
D24V4, multiclass
       clus
vv      AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  T0+T1                          4                           46
  T2                            24                          113
  T3                            22                           78
  T4                            29                          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
  AMP PEAK 24(17Q12) MUTATED    33  13  30   0
  AMP PEAK 24(17Q12) WILD-TYPE 146  55 138   8
D24V5, multiclass
    clus
vv   AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  N0                         33                          146
  N1                         13                           55
  N2                         30                          138
  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"
D24V6, binary
                              cls
clus                             0   1
  AMP PEAK 24(17Q12) MUTATED    36   1
  AMP PEAK 24(17Q12) WILD-TYPE 154   0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED     36    1
  AMP PEAK 24(17Q12) WILD-TYPE  154    0
   clus
vv  AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  0                         36                          154
  1                          1                            0
[1] 2 2
[1] FALSE
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(17Q12) MUTATED    21  70
  AMP PEAK 24(17Q12) WILD-TYPE 119 312
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED     21   70
  AMP PEAK 24(17Q12) WILD-TYPE  119  312
        clus
vv       AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  FEMALE                         21                          119
  MALE                           70                          312
[1] 2 2
[1] FALSE
D24V8, binary
                              cls
clus                             0   1
  AMP PEAK 24(17Q12) MUTATED    29  52
  AMP PEAK 24(17Q12) WILD-TYPE 133 249
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED     29   52
  AMP PEAK 24(17Q12) WILD-TYPE  133  249
     clus
vv    AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
  NO                          29                          133
  YES                         52                          249
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(17Q12) MUTATED                                    88
  AMP PEAK 24(17Q12) WILD-TYPE                                 423
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 24(17Q12) MUTATED                                                   2
  AMP PEAK 24(17Q12) WILD-TYPE                                                 8
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 24(17Q12) MUTATED                                                           1
  AMP PEAK 24(17Q12) WILD-TYPE                                                         0
D24V9, multiclass
                                                           clus
vv                                                          AMP PEAK 24(17Q12) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               88
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                          1
                                                           clus
vv                                                          AMP PEAK 24(17Q12) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                423
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
D24V11, continuous
D24V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(17Q12) MUTATED                                  0     2
  AMP PEAK 24(17Q12) WILD-TYPE                                2     9
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(17Q12) MUTATED                          10    76
  AMP PEAK 24(17Q12) WILD-TYPE                        38   370
D24V13, multiclass
                                  clus
vv                                 AMP PEAK 24(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                    76
                                  clus
vv                                 AMP PEAK 24(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       9
  BLACK OR AFRICAN AMERICAN                                  38
  WHITE                                                     370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                              cls
clus                             0   1
  AMP PEAK 24(17Q12) MUTATED     9  75
  AMP PEAK 24(17Q12) WILD-TYPE  17 384
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(17Q12) MUTATED      9   75
  AMP PEAK 24(17Q12) WILD-TYPE   17  384
                        clus
vv                       AMP PEAK 24(17Q12) MUTATED
  HISPANIC OR LATINO                              9
  NOT HISPANIC OR LATINO                         75
                        clus
vv                       AMP PEAK 24(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               17
  NOT HISPANIC OR LATINO                          384
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(18P11.31) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(18P11.31) MUTATED    85  71
  AMP PEAK 25(18P11.31) WILD-TYPE 216 148
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                            156                             364 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                             71                             148 
$`AMP PEAK 25(18P11.31) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-4727 
        9.30        68.48         3.55        28.11        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CR-6478 TCGA-DQ-7588 TCGA-H7-A6C5 
        9.24        11.08        16.73         6.02        14.04        21.11 
TCGA-UF-A71D TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6869 
       48.03        13.64        23.74        17.10        65.59        21.17 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       12.62         4.01        20.48       105.90         9.14         4.80 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A5HY 
       18.38        22.42        36.72        66.28        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 
       27.19         8.81         6.28        38.04        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
       26.86        12.99        20.55         8.32        11.84        11.57 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A63T TCGA-CN-A63U 
       48.00         6.74        10.45        35.01         7.40        31.69 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-6227 
       12.39        12.07        23.44        10.42        13.25         4.24 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 
       77.56        23.24        14.14        11.77        58.42        18.54 
TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 
       11.34         9.27        47.18        39.16         3.45        24.95 
TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 
       49.58         5.95        35.41        29.95        48.39       129.21 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 
      108.95        17.95       107.51        94.88        17.92        86.83 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6937 
       60.49        43.23        21.07         9.60         9.70        20.52 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6962 
       11.24        12.03        15.09        30.08        53.95         4.14 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 
        5.26         1.84        10.75        77.16        31.36        26.20 
TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7418 
       18.97        11.87         2.10        17.85        22.85        25.94 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 
        0.07        34.09         7.17       153.86        16.64        22.19 
TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM TCGA-CX-7086 TCGA-CX-A4AQ 
       45.96        48.20        67.86         6.38        18.84        51.12 
TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q 
       23.05        24.95        25.32        24.95        13.94        23.34 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7595 TCGA-F7-8298 TCGA-F7-A623 TCGA-H7-8502 
       18.02        46.45        39.12        32.71        20.25        15.06 
TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ 
       20.94        25.74        21.93        22.03         4.27         3.65 
TCGA-IQ-A61G TCGA-IQ-A61K TCGA-IQ-A6SH TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T3 
       11.84         5.29        15.48        17.98        15.78        18.97 
TCGA-P3-A6T6 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-RS-A6TO 
       12.99        12.89         5.62        12.20        17.82        12.72 
TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JA 
       15.91        32.45        54.67         2.83        49.45        74.47 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JS TCGA-KU-A66S TCGA-KU-A66T 
       24.30        55.43        13.94        22.36        13.35        18.15 

$`AMP PEAK 25(18P11.31) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 
       37.28        20.48        30.18         9.07        52.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        11.61        34.52         0.36        34.36        30.94 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J 
       46.32        40.24        12.66        22.85         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
       15.19         9.07        26.50        42.35        57.93        23.84 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       15.52        14.83        41.85        29.42        20.45        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-4227 TCGA-BB-7863 
       11.05        13.38        16.41         6.15         4.41        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A6UM 
       50.20        44.98        24.66        38.40        71.05        12.92 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4731 TCGA-CN-4733 
       12.69        48.76        55.86         4.67        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       57.11        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5364 
       42.02        46.32         8.58        12.39        71.31        16.21 
TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.54        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
       32.22        38.89         3.68        17.42        11.74        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y 
       23.57        17.29        29.72        21.21        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        4.41         2.70        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
        4.24        41.19        32.38        46.95        56.58        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       38.76        64.87        53.52        41.88        43.10        44.48 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        33.60        29.49        12.46        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        50.01        39.52        36.99 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
       16.90        11.90        10.22        11.64         7.69        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
       22.78        15.75        47.34        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-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        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 
        5.13       139.43        17.16        76.24        19.20        76.50 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 
       91.53        80.12        13.35        23.05        48.59         7.07 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6938 
       54.74        62.43        90.12         2.14         5.46         4.73 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 
       21.90        26.43       140.78        19.79        42.38         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-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       111.16        18.81        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 
        9.01        52.31        12.92        21.80        71.21       130.88 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
        4.73        89.65        36.00        17.13        95.34         4.96 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
       47.97        49.71        18.41        57.47        35.54       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-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-A45R 
       19.76         6.38        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 
      159.65        35.47         1.05         6.51        88.87        60.43 
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        28.01         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-D6-6825 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-A6EN TCGA-D6-A6EQ TCGA-D6-A6ES 
       12.36        28.77         7.63        22.59        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       58.45        37.25        33.86        20.45        37.58        40.04 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7832 TCGA-HD-7917 
       13.38        15.16        33.76        28.47        27.48        27.48 
TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       14.66         0.36        13.84         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        37.71        37.41         0.07        33.57 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.68        13.84        19.04        19.27        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         6.25        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        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        19.00        75.55         2.04        29.00 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       21.47         9.34        12.72        27.39        21.07        19.73 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       14.76        15.32         8.32        16.96         6.87         7.10 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO 
       49.51        44.65        17.95        29.46        18.05        20.75 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 
       32.65        17.03        20.55        14.56 

  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                         153.86                          210.97 
  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE 
                          18.97                           22.11 
[1] "0.1 - 153.9 (19.0)" "0.1 - 211.0 (22.1)"
[1] "hr=" "1.3"
D25V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 25(18P11.31) MUTATED         4       16        29        80
  AMP PEAK 25(18P11.31) WILD-TYPE      23       60        53       172
                                 vv
clus                              STAGE IVB STAGE IVC
  AMP PEAK 25(18P11.31) MUTATED           2         1
  AMP PEAK 25(18P11.31) WILD-TYPE        10         0
D25V3, multiclass
           clus
vv          AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  STAGE I                               4                              23
  STAGE II                             16                              60
  STAGE III                            29                              53
  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 25(18P11.31) MUTATED      13  32  40  52
  AMP PEAK 25(18P11.31) WILD-TYPE    37 105  60 121
D25V4, multiclass
       clus
vv      AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  T0+T1                            13                              37
  T2                               32                             105
  T3                               40                              60
  T4                               52                             121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 25(18P11.31) MUTATED    45  23  59   2
  AMP PEAK 25(18P11.31) WILD-TYPE 134  45 109   6
D25V5, multiclass
    clus
vv   AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  N0                            45                             134
  N1                            23                              45
  N2                            59                             109
  N3                             2                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                                 cls
clus                                0   1
  AMP PEAK 25(18P11.31) MUTATED    49   1
  AMP PEAK 25(18P11.31) WILD-TYPE 141   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED     49    1
  AMP PEAK 25(18P11.31) WILD-TYPE  141    0
   clus
vv  AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  0                            49                             141
  1                             1                               0
[1] 2 2
[1] FALSE
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(18P11.31) MUTATED    25 131
  AMP PEAK 25(18P11.31) WILD-TYPE 115 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED     25  131
  AMP PEAK 25(18P11.31) WILD-TYPE  115  251
        clus
vv       AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  FEMALE                            25                             115
  MALE                             131                             251
[1] 2 2
[1] FALSE
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(18P11.31) MUTATED    42  95
  AMP PEAK 25(18P11.31) WILD-TYPE 120 206
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED     42   95
  AMP PEAK 25(18P11.31) WILD-TYPE  120  206
     clus
vv    AMP PEAK 25(18P11.31) MUTATED AMP PEAK 25(18P11.31) WILD-TYPE
  NO                             42                             120
  YES                            95                             206
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(18P11.31) MUTATED                                   152
  AMP PEAK 25(18P11.31) WILD-TYPE                                 359
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 25(18P11.31) MUTATED                                                   4
  AMP PEAK 25(18P11.31) WILD-TYPE                                                 6
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 25(18P11.31) MUTATED                                                           0
  AMP PEAK 25(18P11.31) WILD-TYPE                                                         1
D25V9, multiclass
                                                           clus
vv                                                          AMP PEAK 25(18P11.31) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 152
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
                                                           clus
vv                                                          AMP PEAK 25(18P11.31) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   359
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
D25V11, continuous
D25V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(18P11.31) MUTATED                                  0     1
  AMP PEAK 25(18P11.31) WILD-TYPE                                2    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(18P11.31) MUTATED                          18   131
  AMP PEAK 25(18P11.31) WILD-TYPE                        30   315
D25V13, multiclass
                                  clus
vv                                 AMP PEAK 25(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   18
  WHITE                                                      131
                                  clus
vv                                 AMP PEAK 25(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     30
  WHITE                                                        315
[1] 4 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(18P11.31) MUTATED     5 139
  AMP PEAK 25(18P11.31) WILD-TYPE  21 320
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(18P11.31) MUTATED      5  139
  AMP PEAK 25(18P11.31) WILD-TYPE   21  320
                        clus
vv                       AMP PEAK 25(18P11.31) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           139
                        clus
vv                       AMP PEAK 25(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                  21
  NOT HISPANIC OR LATINO                             320
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(18Q11.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(18Q11.2) MUTATED    59  47
  AMP PEAK 26(18Q11.2) WILD-TYPE 242 172
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                           106                            414 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                            47                            172 
$`AMP PEAK 26(18Q11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6022 TCGA-CN-6024 
        9.30        68.48        28.11        30.18         9.24        11.08 
TCGA-CQ-7067 TCGA-CX-7219 TCGA-DQ-7589 TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       16.73        34.36        46.32         3.35        15.19        13.64 
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP 
       23.74        17.10        65.59        29.42        20.48        16.41 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-CN-4723 
      105.90         9.14         4.80        18.38        22.42        55.86 
TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6020 
       26.86        12.99        20.55        11.57        48.00         6.74 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY TCGA-CQ-5326 TCGA-CQ-7064 TCGA-CQ-7065 
       12.39        12.07        23.44         2.93        64.87        53.52 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6482 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 
       11.77        58.42        11.34        47.34         3.45        24.95 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
        0.99        17.13        49.58         5.13         5.95        35.41 
TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5977 
       48.39       129.21       108.95        17.95       107.51        60.49 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 
       43.23        21.07        20.52        11.24        15.09        30.08 
TCGA-CV-6954 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 
       65.82         4.14       172.67        12.66         5.26        52.31 
TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7415 
       12.92        10.75        11.87         2.10        57.47        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7437 TCGA-CV-A45W TCGA-CV-A45Z 
       25.08        25.94         0.07        16.64        45.96        48.20 
TCGA-CV-A461 TCGA-CV-A6JM TCGA-CX-A4AQ TCGA-D6-A6EO TCGA-D6-A6ES TCGA-DQ-7590 
       67.86         6.38        51.12        24.95        12.79        46.45 
TCGA-H7-A76A TCGA-HD-7917 TCGA-HD-A634 TCGA-IQ-7630 TCGA-IQ-A61O TCGA-IQ-A6SH 
       20.94        27.48         4.27        15.95        13.84        15.48 
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        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-UF-A71B TCGA-UF-A71E 
        5.62        12.20        15.91        32.45        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-KU-A66S TCGA-KU-A66T 
       44.65        74.47        13.35        18.15 

$`AMP PEAK 26(18Q11.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
       37.28        20.48         3.55        25.71        51.29         9.07 
TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       52.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        0.36        30.94        14.04        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 
       22.85        48.03         2.96         9.07        26.50        42.35 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       57.93        23.84        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        41.85        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-A5HY 
       66.28        24.66        38.40        71.05        20.52        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        48.76 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        12.89        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       57.11        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       42.02        46.32         8.58        12.39        71.31         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        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       56.94        50.07        30.67        23.90        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       19.07        34.13        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        4.41         2.70        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
        4.24        41.19        32.38        46.95        56.58        13.25 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        4.24        14.99        38.76        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        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-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        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        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        9.27        47.18        39.16        40.93        35.84         3.09 
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-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        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7402 TCGA-CV-5430 
       32.65        44.25        30.58        24.79        29.95       139.43 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       17.16        76.24        19.20        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-5978 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
        7.07        54.74        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       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       19.79        12.03        42.38         6.08        53.95        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 
        7.13         8.42        28.34         2.50        64.83       111.16 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 
       18.81         7.99         9.01         1.84        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        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7254 
       26.20        18.97        17.13        95.34         4.96        47.97 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       49.71        18.41        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
        9.67         0.46        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-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17       153.86         6.38        22.19        27.98        21.01 
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-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
       88.87        60.43         0.76        56.61         7.07        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34        29.79         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
       16.14        11.44        18.67        24.95        25.32        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ 
       12.36        28.77         7.63        22.59        13.94        12.10 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        18.02        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       37.58        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       21.63        20.25         3.02        31.13        18.94        24.95 
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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.16        15.06        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       27.48        14.66        22.03         0.36        13.84         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG 
       37.41         0.07        33.57         5.29        13.68        19.04 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       19.27        10.75        14.37        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
        6.25         7.13        16.08        29.92        15.78        71.74 
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-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       21.07        19.73        14.76        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N 
       12.72        16.96         6.87         7.10        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.55        13.25        20.35        64.80        54.67         2.83 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
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 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                        172.67                         210.97 
  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE 
                        19.430                         21.485 
[1] "0.1 - 172.7 (19.4)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1.1"
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 26(18Q11.2) MUTATED         4       15        12        53         1
  AMP PEAK 26(18Q11.2) WILD-TYPE      23       61        70       199        11
                                vv
clus                             STAGE IVC
  AMP PEAK 26(18Q11.2) MUTATED           1
  AMP PEAK 26(18Q11.2) WILD-TYPE         0
D26V3, multiclass
           clus
vv          AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  STAGE I                              4                             23
  STAGE II                            15                             61
  STAGE III                           12                             70
  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 26(18Q11.2) MUTATED      11  29  17  33
  AMP PEAK 26(18Q11.2) WILD-TYPE    39 108  83 140
D26V4, multiclass
       clus
vv      AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  T0+T1                           11                             39
  T2                              29                            108
  T3                              17                             83
  T4                              33                            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"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 26(18Q11.2) MUTATED    31  12  35   1
  AMP PEAK 26(18Q11.2) WILD-TYPE 148  56 133   7
D26V5, multiclass
    clus
vv   AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  N0                           31                            148
  N1                           12                             56
  N2                           35                            133
  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"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(18Q11.2) MUTATED    31   1
  AMP PEAK 26(18Q11.2) WILD-TYPE 159   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED     31    1
  AMP PEAK 26(18Q11.2) WILD-TYPE  159    0
   clus
vv  AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  0                           31                            159
  1                            1                              0
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(18Q11.2) MUTATED    18  88
  AMP PEAK 26(18Q11.2) WILD-TYPE 122 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED     18   88
  AMP PEAK 26(18Q11.2) WILD-TYPE  122  294
        clus
vv       AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  FEMALE                           18                            122
  MALE                             88                            294
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  AMP PEAK 26(18Q11.2) MUTATED    28  65
  AMP PEAK 26(18Q11.2) WILD-TYPE 134 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED     28   65
  AMP PEAK 26(18Q11.2) WILD-TYPE  134  236
     clus
vv    AMP PEAK 26(18Q11.2) MUTATED AMP PEAK 26(18Q11.2) WILD-TYPE
  NO                            28                            134
  YES                           65                            236
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(18Q11.2) MUTATED                                   102
  AMP PEAK 26(18Q11.2) WILD-TYPE                                 409
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 26(18Q11.2) MUTATED                                                   3
  AMP PEAK 26(18Q11.2) WILD-TYPE                                                 7
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 26(18Q11.2) MUTATED                                                           1
  AMP PEAK 26(18Q11.2) WILD-TYPE                                                         0
D26V9, multiclass
                                                           clus
vv                                                          AMP PEAK 26(18Q11.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                102
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          AMP PEAK 26(18Q11.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  409
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
D26V11, continuous
D26V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(18Q11.2) MUTATED                                  0     1
  AMP PEAK 26(18Q11.2) WILD-TYPE                                2    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(18Q11.2) MUTATED                          16    88
  AMP PEAK 26(18Q11.2) WILD-TYPE                        32   358
D26V13, multiclass
                                  clus
vv                                 AMP PEAK 26(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      88
                                  clus
vv                                 AMP PEAK 26(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    32
  WHITE                                                       358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                                cls
clus                               0   1
  AMP PEAK 26(18Q11.2) MUTATED     3  96
  AMP PEAK 26(18Q11.2) WILD-TYPE  23 363
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(18Q11.2) MUTATED      3   96
  AMP PEAK 26(18Q11.2) WILD-TYPE   23  363
                        clus
vv                       AMP PEAK 26(18Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           96
                        clus
vv                       AMP PEAK 26(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 23
  NOT HISPANIC OR LATINO                            363
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20Q11.22) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(20Q11.22) MUTATED   134  93
  AMP PEAK 27(20Q11.22) WILD-TYPE 167 126
  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE 
                            227                             293 
  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE 
                             93                             126 
$`AMP PEAK 27(20Q11.22) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 
        9.30        68.48        25.71         9.24        52.08        35.05 
TCGA-CN-A6V3 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-DQ-7588 TCGA-DQ-7589 
       24.39        16.73        11.61         6.02        14.04        46.32 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 
       48.03         2.96         9.07        26.50        23.74        23.84 
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        41.85        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       105.90         9.14         4.80 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 
       18.38        22.42        36.72        50.20        44.98        38.40 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
       10.55         6.28        38.04        56.68        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
       52.14        12.99        20.55        14.33        45.83        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 
       73.61        13.05        46.32        12.39         8.32        11.84 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       56.94        30.67        23.90        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CQ-5329 
        3.68        17.29         7.40        31.69        23.44        70.45 
TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 
       62.37        32.38        46.95        56.58        13.25        38.76 
TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       64.87        41.88        77.56        44.48        23.24        29.49 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6474 
       14.14        84.23        11.77        58.42        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       16.90        11.64        12.46         9.27        47.18        39.16 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 
       47.34         3.45        24.95        29.23         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7397 TCGA-CR-7401 
       19.92        17.13        12.89        46.85        24.79        35.41 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       29.95       139.43       129.21       108.95        76.24        19.20 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 
       76.50        91.53        80.12        13.35        23.05        60.49 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 
        7.07        54.74        21.07        90.12         5.46        20.52 
TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6954 
       21.90        26.43        12.03        42.38        30.08        65.82 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7095 
        7.13         8.42        28.34         4.14       172.67        18.81 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       21.80        71.21        10.75        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7416 
       17.13        47.97         2.10        18.41        17.85        25.08 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45R 
        0.07       100.57         3.52        16.64         6.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A464 TCGA-CV-A465 
      159.65        35.47         6.51        48.20        56.61         7.07 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       35.34        29.79         3.62        21.24        23.47        19.92 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A6EP 
       18.84        25.41        23.05        16.14        25.32        13.94 
TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50J 
       58.45        18.02        20.45        37.58        32.71        31.13 
TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 
       18.94        20.25        15.16        28.47        21.93        27.48 
TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E 
       22.03         4.27         3.65        15.95        14.50        37.71 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MT-A51W 
        0.07         5.29        13.68        15.48        19.27        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05         1.84         6.25        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 
       17.98        15.78        71.74        19.00        18.97         2.04 
TCGA-P3-A6T5 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
       29.00        21.21         7.30        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T3-A92M 
       19.73        12.89        14.76        16.96        15.91        13.71 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       13.55        13.25         2.83        49.45        44.65        74.47 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-KU-A66T 
       55.43        18.05        13.94        20.55        18.15 

$`AMP PEAK 27(20Q11.22) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       37.28        20.48         3.55        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 
        9.07        11.08        32.48        19.82        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       70.13        43.04        34.52         0.36        34.36        30.94 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-4074 
       40.24        21.11        12.66        22.85         3.35        15.19 
TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6869 
       13.64        42.35        57.93        17.10        65.59        21.17 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        27.95        11.54         5.69        14.47         7.82 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7863 
       13.38        20.48        16.41         6.15         4.41        33.70 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM 
       66.28        24.66        71.05        20.52        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 
        8.81        12.69        48.76        55.86         4.67        12.89 
TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       57.11        42.02         8.58        71.31        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6012 
       11.57        12.49         8.52        52.08        50.07        48.00 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6996 
       47.44        28.04        19.07        34.13         6.74        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
       11.74        35.01        25.41        23.57        29.72        21.21 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6227 
       45.99        10.42        11.21         4.24        41.19         4.24 
TCGA-CQ-6228 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
       14.99        53.52        43.10        29.36        33.60        12.46 
TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
       31.23        54.67        37.87        26.27        50.01        39.52 
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        22.78        15.75 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 
       40.93        35.84         3.09         0.99        31.96        26.17 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 
       32.78        47.01        27.06        49.58        30.02        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 
       44.25        30.58         5.13         5.95        48.39        17.16 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 
       17.95       107.51        94.88        17.92        86.83        48.59 
TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 
       43.23        62.43         9.60         2.14         9.70         4.73 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 
       11.24       140.78        19.79        15.09         6.08        53.95 
TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
       10.98         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-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 
       77.16         4.73        89.65        18.97        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 
       11.87        49.71        57.47        35.54       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        9.67         0.46        22.85        25.94        34.09        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-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17       153.86        22.19        27.98        21.01       169.38 
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-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6K1 
       15.25         5.98         6.38         6.48        28.01        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 
       10.42        10.55        51.12        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        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       37.25        33.86        46.45        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W 
       37.18        21.63        20.25         3.02        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A76A 
       17.85        11.80        12.43        13.38        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 
       33.76        25.74        27.48        14.66         0.36        13.84 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
        6.90        34.75        38.53        11.84        37.41        33.57 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       13.84        19.04        10.75        12.62        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T6 
       51.25        10.85        36.82        47.01        75.55        12.99 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
       16.01        13.15        21.07        23.15        21.47         9.34 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
        5.62        12.20        17.82        15.32         8.32        12.72 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A718 
        6.87         7.10        32.45         3.12        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO 
       54.67        49.51        17.95        24.30        29.46        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        14.56        13.35 

  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE 
                           0.07                            0.36 
  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE 
                         180.16                          210.97 
  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE 
                          21.24                           21.01 
[1] "0.1 - 180.2 (21.2)" "0.4 - 211.0 (21.0)"
[1] "hr=" "1.1"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  AMP PEAK 27(20Q11.22) MUTATED        15       32        38       105
  AMP PEAK 27(20Q11.22) WILD-TYPE      12       44        44       147
                                 vv
clus                              STAGE IVB STAGE IVC
  AMP PEAK 27(20Q11.22) MUTATED           7         0
  AMP PEAK 27(20Q11.22) WILD-TYPE         5         1
D27V3, multiclass
           clus
vv          AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE
  STAGE I                              15                              12
  STAGE II                             32                              44
  STAGE III                            38                              44
  STAGE IVA                           105                             147
  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 27(20Q11.22) MUTATED      26 54 44 75
  AMP PEAK 27(20Q11.22) WILD-TYPE    24 83 56 98
D27V4, multiclass
       clus
vv      AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE
  T0+T1                            26                              24
  T2                               54                              83
  T3                               44                              56
  T4                               75                              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 27(20Q11.22) MUTATED    78  30  71   4
  AMP PEAK 27(20Q11.22) WILD-TYPE 101  38  97   4
D27V5, multiclass
    clus
vv   AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE
  N0                            78                             101
  N1                            30                              38
  N2                            71                              97
  N3                             4                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q11.22) MUTATED    88   0
  AMP PEAK 27(20Q11.22) WILD-TYPE 102   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q11.22) MUTATED     88    0
  AMP PEAK 27(20Q11.22) WILD-TYPE  102    1
   clus
vv  AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE
  0                            88                             102
  1                             0                               1
[1] 2 2
[1] FALSE
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q11.22) MUTATED    57 170
  AMP PEAK 27(20Q11.22) WILD-TYPE  83 212
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q11.22) MUTATED     57  170
  AMP PEAK 27(20Q11.22) WILD-TYPE   83  212
        clus
vv       AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE
  FEMALE                            57                              83
  MALE                             170                             212
[1] 2 2
[1] FALSE
D27V8, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q11.22) MUTATED    75 128
  AMP PEAK 27(20Q11.22) WILD-TYPE  87 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q11.22) MUTATED     75  128
  AMP PEAK 27(20Q11.22) WILD-TYPE   87  173
     clus
vv    AMP PEAK 27(20Q11.22) MUTATED AMP PEAK 27(20Q11.22) WILD-TYPE
  NO                             75                              87
  YES                           128                             173
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20Q11.22) MUTATED                                   224
  AMP PEAK 27(20Q11.22) WILD-TYPE                                 287
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 27(20Q11.22) MUTATED                                                   3
  AMP PEAK 27(20Q11.22) WILD-TYPE                                                 7
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 27(20Q11.22) MUTATED                                                           0
  AMP PEAK 27(20Q11.22) WILD-TYPE                                                         1
D27V9, multiclass
                                                           clus
vv                                                          AMP PEAK 27(20Q11.22) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 224
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
                                                           clus
vv                                                          AMP PEAK 27(20Q11.22) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   287
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
D27V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(20Q11.22) MUTATED                                  1     4
  AMP PEAK 27(20Q11.22) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q11.22) MUTATED                          25   189
  AMP PEAK 27(20Q11.22) WILD-TYPE                        23   257
D27V13, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      189
                                  clus
vv                                 AMP PEAK 27(20Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     23
  WHITE                                                        257
[1] 4 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(20Q11.22) MUTATED    13 195
  AMP PEAK 27(20Q11.22) WILD-TYPE  13 264
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q11.22) MUTATED     13  195
  AMP PEAK 27(20Q11.22) WILD-TYPE   13  264
                        clus
vv                       AMP PEAK 27(20Q11.22) MUTATED
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           195
                        clus
vv                       AMP PEAK 27(20Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             264
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(XQ28) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 28(XQ28) MUTATED    77  73
  AMP PEAK 28(XQ28) WILD-TYPE 224 146
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                        150                         370 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                         73                         146 
$`AMP PEAK 28(XQ28) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BB-A5HU TCGA-CN-6023 TCGA-CQ-7067 TCGA-CQ-A4C7 
        9.30        37.28        25.71        52.08        16.73        11.61 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-BA-5149 TCGA-BA-5558 
       30.94        14.04        21.11        22.85        26.50        65.59 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 
       12.62        41.85        11.54        20.48        16.41       105.90 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-8596 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
        4.80         4.41        71.05        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
        8.81        38.04        56.68        12.99        20.55        14.33 
TCGA-CN-4742 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6988 
       13.05        11.57        50.07        48.00        23.90        10.45 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63Y TCGA-CN-A6V6 TCGA-CQ-5327 
       32.22        17.42        29.72        16.57        20.88        54.58 
TCGA-CQ-5329 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7072 
       70.45        41.19        32.38         4.24        38.76        77.56 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6487 
       14.14        11.77        54.67        58.42        16.90         7.69 
TCGA-CR-6493 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 
        9.27        19.92        17.13        49.58        24.79         5.95 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
      139.43        17.16       129.21       108.95        76.24        17.95 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6433 
       76.50        80.12        13.35        48.59        60.49        21.07 
TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6951 TCGA-CV-6959 
       90.12         9.70         5.46        26.43        30.08         8.42 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7236 
       18.81         5.26         1.84        71.21        77.16         4.73 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7255 TCGA-CV-7407 
       31.36        26.20        18.97        95.34         2.10        35.54 
TCGA-CV-7409 TCGA-CV-7415 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7432 TCGA-CV-7437 
       17.85        22.85        14.89        56.48        84.49        16.64 
TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45X TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JM 
        6.38       169.38         6.51         7.07        35.34         6.38 
TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6827 TCGA-D6-8568 
       21.24        18.84        25.41        23.05        18.67        24.95 
TCGA-D6-A6EK TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50G 
       28.77        37.25        18.02        37.58        37.18        20.25 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61G 
       25.74        27.48        27.48         6.90        15.95        11.84 
TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A6I9 
        5.29        19.04        15.48         7.96        15.42        16.08 
TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
       15.78        51.25        18.97         2.04        29.00        12.99 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
        5.62        14.76        15.91        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JD 
       13.25        54.67         2.83        49.51        49.45        24.30 
TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       29.46        20.75        22.36        20.55        14.56        18.15 

$`AMP PEAK 28(XQ28) WILD-TYPE`
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       20.48        68.48         3.55        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07         9.24        11.08        35.05        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 
       24.39        48.20        32.88        70.13        43.04        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 
        6.02         0.36        34.36        46.32        40.24        12.66 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6868 
       23.74        42.35        57.93        17.10        23.84        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       21.17        14.83         4.01        29.42        20.45        27.95 
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-BB-4217 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
       13.38         6.15         9.14        18.38        22.42        36.72 
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-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
       20.52         6.28        12.69        48.76        55.86         4.67 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4739 
       12.89        26.86        32.81        52.14        57.11        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        42.02        46.32         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 
       71.31         8.32        16.21        11.54        11.84        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        56.94        30.67        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 
       19.07        34.13         6.74        38.89         3.68        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        17.29        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       31.69        22.32        12.39         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5330 
       23.44        19.53        52.37        21.50         2.93        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 
       45.99        10.42        11.21         4.24        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       13.25        14.99        64.87        53.52        41.88        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH 
       44.48        23.24        29.36        33.60        29.49        12.46 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
       31.23        84.23        37.87        26.27        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       36.99        18.54        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        22.78        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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
        0.99        31.96         9.17        34.06        26.17        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        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       44.25        30.58         5.13        35.41        29.95        48.39 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 
       19.20       107.51        94.88        91.53        17.92        23.05 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6441 
       86.83         7.07        43.23        54.74        62.43         9.60 
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       140.78 
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-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 
       65.82        10.98         7.13        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       172.67       111.16        12.66         7.99         9.01 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
       52.31        12.92        21.80        10.75       130.88        89.65 
TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       36.00        17.13         4.96        11.87        47.97        49.71 
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-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7427 
       25.08        25.94         0.07        34.09       100.57       156.49 
TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94         3.52        16.27        19.76         7.17       153.86 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
       22.19        27.98        21.01       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1.05        45.96        88.87        48.20        60.43        67.86 
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-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01         3.62        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       10.55        51.12        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-A6EN 
       11.44        25.32        17.72        12.36         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       33.86        46.45        20.45        40.04        39.12        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63         3.02        31.13        18.94        24.95 
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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        28.47        21.93 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         0.36        13.84         4.27         3.65 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I 
       34.75        38.53        14.50        37.71        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57        13.68        13.84        19.27        10.75        14.37 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 
       30.05         1.84        12.62         6.25         7.13        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       29.92        71.74        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       75.55        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       19.73        12.89        12.20        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HL 
       12.72        16.96         6.87         7.10        32.45        20.35 
TCGA-UF-A718 TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ 
       64.80        44.65        74.47        17.95        55.43        18.05 
TCGA-UF-A7JK TCGA-UF-A7JT TCGA-UP-A6WW TCGA-KU-A66S 
       13.94        32.65        17.03        13.35 

  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                       1.84                        0.07 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                     169.38                      210.97 
  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE 
                     20.515                      21.565 
[1] "1.8 - 169.4 (20.5)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.2"
D28V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  AMP PEAK 28(XQ28) MUTATED         6       19        23        79         3
  AMP PEAK 28(XQ28) WILD-TYPE      21       57        59       173         9
                             vv
clus                          STAGE IVC
  AMP PEAK 28(XQ28) MUTATED           1
  AMP PEAK 28(XQ28) WILD-TYPE         0
D28V3, multiclass
           clus
vv          AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  STAGE I                           6                          21
  STAGE II                         19                          57
  STAGE III                        23                          59
  STAGE IVA                        79                         173
  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 28(XQ28) MUTATED      11  34  38  51
  AMP PEAK 28(XQ28) WILD-TYPE    39 103  62 122
D28V4, multiclass
       clus
vv      AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  T0+T1                        11                          39
  T2                           34                         103
  T3                           38                          62
  T4                           51                         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 28(XQ28) MUTATED    45  19  59   2
  AMP PEAK 28(XQ28) WILD-TYPE 134  49 109   6
D28V5, multiclass
    clus
vv   AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  N0                        45                         134
  N1                        19                          49
  N2                        59                         109
  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"
D28V6, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED    46   1
  AMP PEAK 28(XQ28) WILD-TYPE 144   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     46    1
  AMP PEAK 28(XQ28) WILD-TYPE  144    0
   clus
vv  AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  0                        46                         144
  1                         1                           0
[1] 2 2
[1] FALSE
D28V7, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED    36 114
  AMP PEAK 28(XQ28) WILD-TYPE 104 268
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     36  114
  AMP PEAK 28(XQ28) WILD-TYPE  104  268
        clus
vv       AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  FEMALE                        36                         104
  MALE                         114                         268
[1] 2 2
[1] FALSE
D28V8, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED    46  86
  AMP PEAK 28(XQ28) WILD-TYPE 116 215
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED     46   86
  AMP PEAK 28(XQ28) WILD-TYPE  116  215
     clus
vv    AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  NO                         46                         116
  YES                        86                         215
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(XQ28) MUTATED                                   148
  AMP PEAK 28(XQ28) WILD-TYPE                                 363
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  AMP PEAK 28(XQ28) MUTATED                                                   2
  AMP PEAK 28(XQ28) WILD-TYPE                                                 8
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  AMP PEAK 28(XQ28) MUTATED                                                           0
  AMP PEAK 28(XQ28) WILD-TYPE                                                         1
D28V9, multiclass
                                                           clus
vv                                                          AMP PEAK 28(XQ28) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                             148
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                         0
                                                           clus
vv                                                          AMP PEAK 28(XQ28) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               363
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
D28V11, continuous
D28V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(XQ28) MUTATED                                  1     2
  AMP PEAK 28(XQ28) WILD-TYPE                                1     9
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(XQ28) MUTATED                          14   129
  AMP PEAK 28(XQ28) WILD-TYPE                        34   317
D28V13, multiclass
                                  clus
vv                                 AMP PEAK 28(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                               14
  WHITE                                                  129
                                  clus
vv                                 AMP PEAK 28(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 34
  WHITE                                                    317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                             cls
clus                            0   1
  AMP PEAK 28(XQ28) MUTATED     9 131
  AMP PEAK 28(XQ28) WILD-TYPE  17 328
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 28(XQ28) MUTATED      9  131
  AMP PEAK 28(XQ28) WILD-TYPE   17  328
                        clus
vv                       AMP PEAK 28(XQ28) MUTATED AMP PEAK 28(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             9                          17
  NOT HISPANIC OR LATINO                       131                         328
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  1(1P36.21) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.21) MUTATED    51  44
  DEL PEAK  1(1P36.21) WILD-TYPE 250 175
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            95                            425 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            44                            175 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
        9.30         3.55         9.07        11.08        35.05        32.48 
TCGA-CQ-6221 TCGA-CR-6472 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-8634 TCGA-UF-A71D 
       32.88        34.52        30.94        46.32        12.66        48.03 
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A6D8 
       15.19         9.07        15.52        14.83        41.85        27.95 
TCGA-BA-A6DL TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HY 
       20.48        18.38        36.72        24.66        20.52        10.55 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
       42.02        46.32        71.31        48.00        19.07        34.13 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-6225 
       32.22        38.89         3.68         7.40        10.42        13.25 
TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6470 TCGA-CR-6484 
       14.99        77.56        23.24        31.23        50.01        11.64 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       39.16         3.45         3.09        24.95        29.23         0.99 
TCGA-CR-7380 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
       19.92       129.21       108.95        76.24        17.95       107.51 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6948 TCGA-CV-6962 
        7.07        54.74        90.12         9.70        42.38         4.14 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
       18.81        12.66         5.26        47.97        49.71        57.47 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7430 TCGA-CV-7440 TCGA-CV-A6JE 
       25.94        14.89        56.48        16.27        22.19        35.34 
TCGA-D6-6516 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-7591 TCGA-DQ-7592 
       25.41         7.63        13.94        23.34        20.45        37.58 
TCGA-F7-8489 TCGA-HD-8314 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61L TCGA-IQ-A6SG 
       21.63        22.03         3.65        11.84        13.68        19.04 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-QK-A8Z7 TCGA-T2-A6X0 TCGA-UF-A71A TCGA-UF-A71E 
       15.48        14.37        12.89         7.10         2.83        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JO TCGA-WA-A7GZ TCGA-KU-A66S 
       44.65        24.30        20.75        20.55        13.35 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       51.29         9.24        52.08        19.82        24.39        48.20 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 
       70.13        16.73        43.04        11.61         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A7JV 
       34.36        14.04        40.24        21.11        22.85         2.96 
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
        3.35        13.64        26.50        23.74        42.35        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       17.10        23.84        65.59        21.17        12.62         4.01 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       29.42        20.45        11.54         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
        7.82         2.27        11.05        13.38        16.41         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7863 
      105.90         9.14         4.80         4.41        22.42        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HZ 
       50.20        44.98        66.28        38.40        71.05        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        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       38.04         4.67        56.68        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       52.14        57.11        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
       27.58        73.61        13.05         8.58        12.39         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-6013 TCGA-CN-6016 
       52.08        56.94        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       28.04         6.74        10.45        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
       25.41        23.57        17.29        29.72        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       23.44        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        62.37        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        46.95        56.58         4.24        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       64.87        53.52        41.88        43.10        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 
       33.60        29.49        14.14        12.46        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 
       54.67        37.87        26.27        58.42        39.52        36.99 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       18.54        16.90        11.90        10.22        11.34         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
       12.46        22.78        15.75         9.27        47.18        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
       40.93        35.84        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        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       17.16        19.20        94.88        76.50        91.53        80.12 
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-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
       43.23        21.07        62.43         9.60         2.14         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        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-7102 
       64.83       172.67       111.16         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        89.65        36.00        31.36        26.20 
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-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       18.41        35.54        17.85       210.97        89.33         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.08         0.07        34.09       100.57 
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-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
      153.86        16.64         6.38        27.98        21.01       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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
        7.07        15.25         5.98         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       10.42        10.55        18.84        51.12        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-A6EN TCGA-D6-A6EO 
       25.32        17.72        12.36        28.77        22.59        24.95 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.10        12.79        58.45        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
       46.45        40.04        39.12        41.59        37.18        32.71 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        27.48        14.66         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        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A6H7 
       37.41         0.07        33.57         5.29        13.84        19.27 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       10.75         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       15.42         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        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-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       13.15        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        27.39        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87        15.91        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       13.55        13.25        20.35        64.80        54.67        49.51 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        55.43        29.46        18.05        13.94 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66T 
       22.36        32.65        17.03        14.56        18.15 

  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 
                         20.75                          21.11 
[1] "1.0 - 129.2 (20.8)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.2"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.21) MUTATED         4       10        21        40         3
  DEL PEAK  1(1P36.21) WILD-TYPE      23       66        61       212         9
                                vv
clus                             STAGE IVC
  DEL PEAK  1(1P36.21) MUTATED           0
  DEL PEAK  1(1P36.21) WILD-TYPE         1
D29V3, multiclass
           clus
vv          DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  STAGE I                              4                             23
  STAGE II                            10                             66
  STAGE III                           21                             61
  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  20  22  31
  DEL PEAK  1(1P36.21) WILD-TYPE    42 117  78 142
D29V4, multiclass
       clus
vv      DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  T0+T1                            8                             42
  T2                              20                            117
  T3                              22                             78
  T4                              31                            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  1(1P36.21) MUTATED    32  13  25   2
  DEL PEAK  1(1P36.21) WILD-TYPE 147  55 143   6
D29V5, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  N0                           32                            147
  N1                           13                             55
  N2                           25                            143
  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
  DEL PEAK  1(1P36.21) MUTATED    31   0
  DEL PEAK  1(1P36.21) WILD-TYPE 159   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     31    0
  DEL PEAK  1(1P36.21) WILD-TYPE  159    1
   clus
vv  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  0                           31                            159
  1                            0                              1
[1] 2 2
[1] FALSE
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    23  72
  DEL PEAK  1(1P36.21) WILD-TYPE 117 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     23   72
  DEL PEAK  1(1P36.21) WILD-TYPE  117  310
        clus
vv       DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           23                            117
  MALE                             72                            310
[1] 2 2
[1] FALSE
D29V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    24  57
  DEL PEAK  1(1P36.21) WILD-TYPE 138 244
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     24   57
  DEL PEAK  1(1P36.21) WILD-TYPE  138  244
     clus
vv    DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  NO                            24                            138
  YES                           57                            244
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                    90
  DEL PEAK  1(1P36.21) WILD-TYPE                                 421
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  1(1P36.21) MUTATED                                                   5
  DEL PEAK  1(1P36.21) WILD-TYPE                                                 5
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  1(1P36.21) MUTATED                                                           0
  DEL PEAK  1(1P36.21) WILD-TYPE                                                         1
D29V9, multiclass
                                                           clus
vv                                                          DEL PEAK  1(1P36.21) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 90
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK  1(1P36.21) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  421
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, continuous
D29V12, 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                          11    78
  DEL PEAK  1(1P36.21) WILD-TYPE                        37   368
D29V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      78
                                  clus
vv                                 DEL PEAK  1(1P36.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       368
[1] 4 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
  DEL PEAK  1(1P36.21) MUTATED     5  81
  DEL PEAK  1(1P36.21) WILD-TYPE  21 378
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED      5   81
  DEL PEAK  1(1P36.21) WILD-TYPE   21  378
                        clus
vv                       DEL PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            378
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  2(1P13.2) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.2) MUTATED    68  64
  DEL PEAK  2(1P13.2) WILD-TYPE 233 155
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                          132                           388 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                           64                           155 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
        9.30         3.55         9.07         9.24        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-7067 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 
       32.48        24.39        16.73         6.02         0.36        30.94 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5152 
       12.66        22.85        48.03         3.35        13.64        42.35 
TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BB-7862 TCGA-BB-8601 
       14.83        41.85        14.47        11.05        36.72        20.52 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4729 
       10.55        27.19         8.81         6.28        55.86        12.89 
TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-6010 
       32.81        20.55        42.02        12.39        71.31        50.07 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A63T 
       48.00        19.07        38.89         3.68        11.74         7.40 
TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4CI 
       12.39        10.42        13.25        64.87        77.56        31.23 
TCGA-CR-6481 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 
       10.22        39.16         3.45         3.09        24.95         0.99 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        5.95       139.43       129.21       108.95        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 
       17.95       107.51        80.12        86.83        60.49         7.07 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 
       54.74        21.07         9.70         5.46        20.52        26.43 
TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
       11.24        42.38         4.14       111.16        18.81         5.26 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7254 
        1.84        52.31        10.75        36.00        26.20        47.97 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       49.71        35.54         0.46        25.08        25.94         0.07 
TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A45W TCGA-CV-A461 TCGA-CV-A6JT TCGA-D6-6516 
       14.89       153.86        45.96        67.86        28.01        25.41 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-F7-8489 
       12.36         7.63        24.95        13.94        23.34        21.63 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8314 
        3.02        18.94        20.25        28.47        21.93        22.03 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A6T5 
       37.41        13.68        15.48        15.78        51.25        29.00 
TCGA-P3-A6T8 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-T2-A6WZ 
       13.15        19.73         5.62        14.76        17.82        15.91 
TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E 
       13.71         3.12        64.80        54.67         2.83        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-KU-A66T 
       44.65        17.95        24.30        13.94        20.55        18.15 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       51.29        52.08        19.82        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 
       43.04        11.61        34.52        34.36        14.04        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 
       40.24        21.11         2.96        15.19         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       23.74        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       21.17        12.62         4.01        29.42        20.45        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-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       20.48        16.41         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.38        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A6UM TCGA-C9-A480 
       66.28        24.66        38.40        71.05        12.92        12.69 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 
       48.76        38.04         4.67        56.68        26.86        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       57.11        12.99        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       13.05        46.32         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-5374 
       11.84        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       30.67        23.90        47.44        28.04        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       10.45        32.22        17.42        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       17.29        29.72        21.21        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
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        46.95 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 
       56.58         4.24        14.99        38.76        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.10        44.48        23.24        29.36        33.60        29.49 
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-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-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 
       22.78        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 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
       24.79         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       140.78        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       172.67        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        89.65        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        21.01       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-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        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-A6EN TCGA-D6-A6EQ 
       24.95        25.32        17.72        28.77        22.59        12.10 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
       12.79        58.45        37.25        33.86        18.02        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        37.58        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       32.71        20.25        31.13        24.95         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 
       33.76        25.74        27.48        27.48        14.66         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-A61G TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        37.71        11.84         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
        5.29        13.84        19.04        19.27        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         6.25        15.42 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QF 
        7.13        16.08        17.98        29.92        71.74        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-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       12.99        16.01        21.07        21.21        23.15         7.30 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 
       21.47         9.34        12.72        27.39        21.07        12.89 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       12.20        15.32         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        20.35        49.51 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS 
       74.47        55.43        29.46        18.05        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        14.56        13.35 

  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 
                       20.385                        21.355 
[1] "0.1 - 153.9 (20.4)" "0.1 - 211.0 (21.4)"
[1] "hr=" "1.3"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  2(1P13.2) MUTATED         6       17        23        71         2
  DEL PEAK  2(1P13.2) WILD-TYPE      21       59        59       181        10
                               vv
clus                            STAGE IVC
  DEL PEAK  2(1P13.2) MUTATED           1
  DEL PEAK  2(1P13.2) WILD-TYPE         0
D30V3, multiclass
           clus
vv          DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  STAGE I                             6                            21
  STAGE II                           17                            59
  STAGE III                          23                            59
  STAGE IVA                          71                           181
  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  33  31  49
  DEL PEAK  2(1P13.2) WILD-TYPE    41 104  69 124
D30V4, multiclass
       clus
vv      DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  T0+T1                           9                            41
  T2                             33                           104
  T3                             31                            69
  T4                             49                           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  20  46   2
  DEL PEAK  2(1P13.2) WILD-TYPE 132  48 122   6
D30V5, multiclass
    clus
vv   DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                          47                           132
  N1                          20                            48
  N2                          46                           122
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    45   1
  DEL PEAK  2(1P13.2) WILD-TYPE 145   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     45    1
  DEL PEAK  2(1P13.2) WILD-TYPE  145    0
   clus
vv  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  0                          45                           145
  1                           1                             0
[1] 2 2
[1] FALSE
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    35  98
  DEL PEAK  2(1P13.2) WILD-TYPE 105 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     35   98
  DEL PEAK  2(1P13.2) WILD-TYPE  105  284
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                          35                           105
  MALE                            98                           284
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED    43  71
  DEL PEAK  2(1P13.2) WILD-TYPE 119 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED     43   71
  DEL PEAK  2(1P13.2) WILD-TYPE  119  230
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  NO                           43                           119
  YES                          71                           230
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.2) MUTATED                                   129
  DEL PEAK  2(1P13.2) WILD-TYPE                                 382
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  2(1P13.2) MUTATED                                                   4
  DEL PEAK  2(1P13.2) WILD-TYPE                                                 6
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  2(1P13.2) MUTATED                                                           0
  DEL PEAK  2(1P13.2) WILD-TYPE                                                         1
D30V9, multiclass
                                                           clus
vv                                                          DEL PEAK  2(1P13.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               129
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK  2(1P13.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 382
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
D30V11, continuous
D30V12, 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                          18   107
  DEL PEAK  2(1P13.2) WILD-TYPE                        30   339
D30V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 18
  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                                                      339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.2) MUTATED     7 114
  DEL PEAK  2(1P13.2) WILD-TYPE  19 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      7  114
  DEL PEAK  2(1P13.2) WILD-TYPE   19  345
                        clus
vv                       DEL PEAK  2(1P13.2) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       DEL PEAK  2(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           345
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  3(1Q44) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q44) MUTATED    24  24
  DEL PEAK  3(1Q44) WILD-TYPE 277 195
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         48                         472 
  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE 
                         24                         195 
$`DEL PEAK  3(1Q44) MUTATED`
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-HD-8634 TCGA-BA-4074 
       11.61         6.02        14.04        46.32        12.66        15.19 
TCGA-BA-5152 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-5355 
       42.35        20.52        27.19         6.28        12.99        42.02 
TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A640 
       19.07        38.89         3.68         7.40        12.39         4.41 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6227 TCGA-CR-7365 
       62.37        11.21        41.19        32.38         4.24        39.16 
TCGA-CR-7372 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-6945 TCGA-CV-6950 
       24.95        17.95        94.88        54.74        12.03        15.09 
TCGA-CV-7095 TCGA-CV-7416 TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JT 
       18.81        25.08         0.76         7.07        29.79        28.01 
TCGA-D6-6517 TCGA-D6-A4Z9 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A61W TCGA-IQ-A61L 
        9.60        17.72        21.63        18.94         0.46        13.68 
TCGA-KU-A6H7 TCGA-P3-A6T8 TCGA-T3-A92N TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-WA-A7GZ 
       19.27        13.15         3.12        44.65        17.95        20.55 

$`DEL PEAK  3(1Q44) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CX-7082 
       32.88        70.13        16.73        43.04        34.52         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D 
       34.36        30.94        40.24        21.11        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        2.96         3.35        13.64         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       57.93        17.10        23.84        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       14.83        12.62         4.01        41.85        29.42        20.45 
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 
      105.90         9.14         4.80         4.41        18.38        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-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       38.40        71.05        10.55        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       48.76        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.81        52.14        57.11        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         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-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       30.67        48.00        23.90        47.44        28.04        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
        6.74        10.45        32.22        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
       25.41        23.57        17.29        29.72        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       22.32        16.57        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       45.99        10.42         4.24        46.95        56.58        13.25 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        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-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        22.78        15.75         9.27        47.18 
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-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-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        5.13         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
       17.16       129.21       108.95        76.24        19.20       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-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-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-6940 TCGA-CV-6941 TCGA-CV-6942 
       20.52         4.73        21.90        26.43        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
       19.79        42.38        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-7097 TCGA-CV-7099 TCGA-CV-7100 
       64.83       172.67       111.16        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-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       31.36        26.20        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
       11.87        47.97         2.10        49.71        18.41        57.47 
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-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-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-A45R TCGA-CV-A45T TCGA-CV-A45U 
       27.98        21.01       169.38       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-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       67.86        56.61        15.25         5.98        35.34         6.38 
TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
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-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       33.86        18.02        46.45        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        41.59        37.18        32.71        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       31.13        24.95        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
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-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.84        19.04        15.48 
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 
        6.25        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
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-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         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-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       13.71        13.55        13.25        20.35        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
        2.83        49.51        49.45        74.47        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       29.46        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       17.03        14.56        13.35        18.15 

  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                       21.65 
[1] "0.5 - 94.9 (17.9)"  "0.1 - 211.0 (21.6)"
[1] "hr=" "1.6"
D31V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  3(1Q44) MUTATED         2        5         8        27         0
  DEL PEAK  3(1Q44) WILD-TYPE      25       71        74       225        12
                             vv
clus                          STAGE IVC
  DEL PEAK  3(1Q44) MUTATED           0
  DEL PEAK  3(1Q44) WILD-TYPE         1
D31V3, multiclass
           clus
vv          DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  STAGE I                           2                          25
  STAGE II                          5                          71
  STAGE III                         8                          74
  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
  DEL PEAK  3(1Q44) MUTATED       3  14  13  14
  DEL PEAK  3(1Q44) WILD-TYPE    47 123  87 159
D31V4, multiclass
       clus
vv      DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  T0+T1                         3                          47
  T2                           14                         123
  T3                           13                          87
  T4                           14                         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"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  3(1Q44) MUTATED    18   5  18   0
  DEL PEAK  3(1Q44) WILD-TYPE 161  63 150   8
D31V5, multiclass
    clus
vv   DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  N0                        18                         161
  N1                         5                          63
  N2                        18                         150
  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"
D31V6, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    18   0
  DEL PEAK  3(1Q44) WILD-TYPE 172   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     18    0
  DEL PEAK  3(1Q44) WILD-TYPE  172    1
   clus
vv  DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  0                        18                         172
  1                         0                           1
[1] 2 2
[1] FALSE
D31V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    15  33
  DEL PEAK  3(1Q44) WILD-TYPE 125 349
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     15   33
  DEL PEAK  3(1Q44) WILD-TYPE  125  349
        clus
vv       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  FEMALE                        15                         125
  MALE                          33                         349
[1] 2 2
[1] FALSE
D31V8, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q44) MUTATED    23  22
  DEL PEAK  3(1Q44) WILD-TYPE 139 279
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED     23   22
  DEL PEAK  3(1Q44) WILD-TYPE  139  279
     clus
vv    DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  NO                         23                         139
  YES                        22                         279
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(1Q44) MUTATED                                    48
  DEL PEAK  3(1Q44) WILD-TYPE                                 463
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  3(1Q44) MUTATED                                                   0
  DEL PEAK  3(1Q44) WILD-TYPE                                                10
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  3(1Q44) MUTATED                                                           0
  DEL PEAK  3(1Q44) WILD-TYPE                                                         1
D31V9, multiclass
                                                           clus
vv                                                          DEL PEAK  3(1Q44) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                              48
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                         0
                                                           clus
vv                                                          DEL PEAK  3(1Q44) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               463
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, continuous
D31V12, 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                           3    42
  DEL PEAK  3(1Q44) WILD-TYPE                        45   404
D31V13, multiclass
                                  clus
vv                                 DEL PEAK  3(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                3
  WHITE                                                   42
                                  clus
vv                                 DEL PEAK  3(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 45
  WHITE                                                    404
[1] 4 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  3(1Q44) MUTATED     4  42
  DEL PEAK  3(1Q44) WILD-TYPE  22 417
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q44) MUTATED      4   42
  DEL PEAK  3(1Q44) WILD-TYPE   22  417
                        clus
vv                       DEL PEAK  3(1Q44) MUTATED DEL PEAK  3(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             4                          22
  NOT HISPANIC OR LATINO                        42                         417
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  4(2Q21.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q21.2) MUTATED    48  30
  DEL PEAK  4(2Q21.2) WILD-TYPE 253 189
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           78                           442 
  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                           30                           189 
$`DEL PEAK  4(2Q21.2) MUTATED`
TCGA-CN-6024 TCGA-CN-A6V3 TCGA-CR-6472 TCGA-DQ-7593 TCGA-BA-4076 TCGA-BA-5151 
       11.08        24.39        34.52        40.24        13.64        23.74 
TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A6DF TCGA-BA-A8YP TCGA-BB-7861 
       42.35        15.52         4.01         7.82        16.41        22.42 
TCGA-BB-7862 TCGA-BB-7863 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-5359 
       36.72        33.70         6.28        55.86        12.99        12.39 
TCGA-CN-5363 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6994 
        8.32        52.08        56.94        30.67        19.07        38.89 
TCGA-CN-6995 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63V TCGA-CQ-5331 
        3.68        25.41        23.57        29.72        22.32        45.99 
TCGA-CQ-5334 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4CB TCGA-CR-6484 TCGA-CR-7395 
        4.24        64.87        41.88        29.36        11.64        30.58 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-7091 
        5.95        29.95        86.83        54.74        62.43       111.16 
TCGA-CV-7095 TCGA-CV-7235 TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7423 TCGA-CV-7425 
       18.81        77.16         4.96         2.10       100.57        56.48 
TCGA-CV-A45R TCGA-CV-A465 TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-D6-6826 TCGA-D6-A6EM 
      180.16         7.07        21.24        10.42        11.44         7.63 
TCGA-D6-A6EP TCGA-F7-A50J TCGA-F7-A620 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ 
       13.94        31.13        17.85        28.47        27.48         3.65 
TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-P3-A5Q6 TCGA-P3-A6T4 
       37.71        13.68        15.48        19.27        15.78         2.04 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO 
        7.30        21.47        12.89        12.20         8.32        12.72 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A71E TCGA-UF-A7JF TCGA-WA-A7GZ TCGA-KU-A66T 
       15.91        13.71        49.45        55.43        20.55        18.15 

$`DEL PEAK  4(2Q21.2) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       30.18        25.71        51.29         9.07         9.24        52.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       35.05        32.48        19.82        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       16.73        43.04        11.61         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        46.32        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 
       48.03         2.96         3.35        15.19         9.07        26.50 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       57.93        17.10        23.84        65.59        21.17        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62        41.85        29.42        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ 
        7.10         5.69        14.47         2.27        11.05        13.38 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
       20.48         6.15       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
       18.38        50.20        44.98        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       71.05        20.52        10.55        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       12.69        48.76        38.04         4.67        56.68        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.81        52.14        57.11        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        8.58        71.31        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       12.49         8.52        50.07        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 
       28.04        34.13         6.74        10.45        32.22        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       11.74        35.01        17.29        21.21         7.40        31.69 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 
       20.88        19.53        52.37        21.50         2.93        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6220 
       70.45        62.37        10.42        11.21        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD 
       53.52        43.10        77.56        44.48        23.24        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
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-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        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-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-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
       24.79         5.13        35.41        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-6433 
       23.05        48.59        60.49         7.07        43.23        21.07 
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-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        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-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       172.67        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-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       10.75       130.88         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 
       26.20        18.97        17.13        95.34        11.87        47.97 
TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       49.71        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-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
        0.07        34.09        14.89       156.49        54.94         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-A45T 
        6.38        22.19        27.98        21.01       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-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        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        28.01         3.62 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       23.47        19.92        22.52        10.55        18.84        51.12 
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-D6-6827 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        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       22.59        24.95        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       37.25        33.86        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       40.04        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 
       20.25         3.02        18.94        24.95         0.46        11.80 
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        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 
       33.76        25.74        21.93        27.48        14.66        22.03 
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-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       38.53        14.50        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
        5.29        13.84        19.04        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        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        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       36.82        47.01        19.00        75.55        18.97        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        21.21        23.15 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        27.39        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       14.76        17.82        15.32        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
       54.67         2.83        49.51        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       24.30        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        14.56        13.35 

  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE 
                         2.04                          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 
                       20.895                        21.090 
[1] "2.0 - 180.2 (20.9)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  4(2Q21.2) MUTATED         3        8        20        34         3
  DEL PEAK  4(2Q21.2) WILD-TYPE      24       68        62       218         9
                               vv
clus                            STAGE IVC
  DEL PEAK  4(2Q21.2) MUTATED           0
  DEL PEAK  4(2Q21.2) WILD-TYPE         1
D32V3, multiclass
           clus
vv          DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  STAGE I                             3                            24
  STAGE II                            8                            68
  STAGE III                          20                            62
  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  20  17  30
  DEL PEAK  4(2Q21.2) WILD-TYPE    44 117  83 143
D32V4, multiclass
       clus
vv      DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  T0+T1                           6                            44
  T2                             20                           117
  T3                             17                            83
  T4                             30                           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  14  21   2
  DEL PEAK  4(2Q21.2) WILD-TYPE 148  54 147   6
D32V5, multiclass
    clus
vv   DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  N0                          31                           148
  N1                          14                            54
  N2                          21                           147
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED    32   0
  DEL PEAK  4(2Q21.2) WILD-TYPE 158   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     32    0
  DEL PEAK  4(2Q21.2) WILD-TYPE  158    1
   clus
vv  DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  0                          32                           158
  1                           0                             1
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED    31  47
  DEL PEAK  4(2Q21.2) WILD-TYPE 109 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     31   47
  DEL PEAK  4(2Q21.2) WILD-TYPE  109  335
        clus
vv       DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  FEMALE                          31                           109
  MALE                            47                           335
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q21.2) MUTATED    26  46
  DEL PEAK  4(2Q21.2) WILD-TYPE 136 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED     26   46
  DEL PEAK  4(2Q21.2) WILD-TYPE  136  255
     clus
vv    DEL PEAK  4(2Q21.2) MUTATED DEL PEAK  4(2Q21.2) WILD-TYPE
  NO                           26                           136
  YES                          46                           255
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q21.2) MUTATED                                    76
  DEL PEAK  4(2Q21.2) WILD-TYPE                                 435
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  4(2Q21.2) MUTATED                                                   2
  DEL PEAK  4(2Q21.2) WILD-TYPE                                                 8
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  4(2Q21.2) MUTATED                                                           0
  DEL PEAK  4(2Q21.2) WILD-TYPE                                                         1
D32V9, multiclass
                                                           clus
vv                                                          DEL PEAK  4(2Q21.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                76
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK  4(2Q21.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 435
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
D32V11, continuous
D32V12, 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                          10    64
  DEL PEAK  4(2Q21.2) WILD-TYPE                        38   382
D32V13, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     64
                                  clus
vv                                 DEL PEAK  4(2Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      382
[1] 4 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  4(2Q21.2) MUTATED     6  68
  DEL PEAK  4(2Q21.2) WILD-TYPE  20 391
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q21.2) MUTATED      6   68
  DEL PEAK  4(2Q21.2) WILD-TYPE   20  391
                        clus
vv                       DEL PEAK  4(2Q21.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK  4(2Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           391
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    66  55
  DEL PEAK  5(2Q22.1) WILD-TYPE 235 164
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                          121                           399 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           55                           164 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-BA-4077 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-6023 TCGA-CN-6997 TCGA-CR-6472 
       37.28         3.55        25.71        52.08        32.48        34.52 
TCGA-DQ-5629 TCGA-DQ-7593 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5558 TCGA-BA-6873 
       30.94        40.24        13.64        42.35        65.59         4.01 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DF TCGA-BB-7861 TCGA-BB-7862 TCGA-C9-A47Z 
       41.85        20.45         7.82        22.42        36.72         6.28 
TCGA-CN-4723 TCGA-CN-4736 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5369 
       55.86        12.99        46.32        12.39         8.32        12.49 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6994 
       56.94        50.07        30.67        19.07         6.74        38.89 
TCGA-CN-6995 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A641 TCGA-CQ-5327 
        3.68        23.57        17.29        29.72        12.07        54.58 
TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4CD TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6484 
       64.87        41.88        33.60        11.77        18.54        11.64 
TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7402 
       47.34         3.09        47.01        49.58         5.95        29.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6945 
       76.24        19.20        94.88        86.83         7.07        12.03 
TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7177 TCGA-CV-7235 
       42.38        53.95         4.14       111.16        21.80        77.16 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7423 
        4.96        11.87         2.10        35.54        22.85       100.57 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7437 TCGA-CV-A45Q TCGA-CV-A45R 
       14.89       156.49         3.52        16.64       169.38       180.16 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JU 
       35.47         1.05        45.96         7.07        29.79         3.62 
TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 
       21.24        10.42        25.41        11.44        24.95        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-5624 TCGA-F7-A50J TCGA-F7-A61V 
       12.36         7.63        13.94        58.45        31.13        24.95 
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        37.71 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       37.41        13.68        15.48        19.27        17.98        15.78 
TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       13.15        21.47        12.89         5.62        12.20        17.82 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A71E 
        8.32        12.72        13.71         3.12         2.83        49.45 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JT 
       74.47        17.95        24.30        55.43        20.75        32.65 
TCGA-KU-A66T 
       18.15 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
        9.30        20.48        68.48        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 
        9.07         9.24        11.08        35.05        19.82        24.39 
TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 
       48.20        32.88        70.13        16.73        43.04        11.61 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 
        6.02         0.36        34.36        14.04        46.32        21.11 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       12.66        22.85        48.03         2.96         3.35        15.19 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        9.07        26.50        23.74        57.93        17.10        23.84 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6D8 
       15.52        21.17        14.83        12.62        29.42        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DI 
       11.54         7.10         5.69        14.47         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       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.80         4.41        18.38        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
       27.19        12.92         8.81        12.69        48.76        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       57.11        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 
       13.05        42.02         8.58        71.31        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6013 
       11.84        11.57         8.52        52.08        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 
       47.44        28.04        34.13        10.45        32.22        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       11.74        35.01        25.41        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        12.39        16.57         4.41         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 
       20.88        19.53        52.37        21.50         2.93        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.38        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       38.76        53.52        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       29.36        29.49        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-6473 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       36.99        16.90        11.90        10.22        11.34         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
       12.46        22.78        15.75         9.27        47.18        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.45        24.95        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-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       32.78        27.06        12.89        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 
       44.25        30.58        24.79         5.13        35.41        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 
      139.43        17.16       129.21       108.95        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-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-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-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        19.79 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 
       15.09        30.08         6.08        65.82        10.98         7.13 
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       172.67        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-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       12.92        71.21        10.75       130.88         4.73        89.65 
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-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
       47.97        49.71        18.41        57.47        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67         0.46        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
       34.09        56.48        54.94        16.27        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
        7.17       153.86         6.38        22.19        27.98        21.01 
TCGA-CV-A45T TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
      159.65         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-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 
        6.48        28.01        23.47        19.92        22.52        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       18.84        51.12        13.25         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       16.14        18.67        25.32        28.77        22.59        24.95 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       12.10        12.79        23.34        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       46.45        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S 
       37.18        32.71        21.63        20.25         3.02        18.94 
TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
        0.46        11.80        12.43        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       33.76        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        38.53        14.50        11.84         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
        5.29        13.84        19.04        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       30.05         1.84        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       16.08        29.92        71.74        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        21.21        23.15         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 
        9.34        12.72        27.39        21.07        19.73        14.76 
TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 
       15.32        16.96         6.87        15.91         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       13.55        13.25        20.35        64.80        54.67        49.51 
TCGA-UF-A7J9 TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UP-A6WW 
       44.65        29.46        18.05        13.94        22.36        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       20.55        14.56        13.35 

  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 
                        20.45                         21.17 
[1] "1.1 - 180.2 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  5(2Q22.1) MUTATED         2       13        20        65         6
  DEL PEAK  5(2Q22.1) WILD-TYPE      25       63        62       187         6
                               vv
clus                            STAGE IVC
  DEL PEAK  5(2Q22.1) MUTATED           1
  DEL PEAK  5(2Q22.1) WILD-TYPE         0
D33V3, multiclass
           clus
vv          DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                             2                            25
  STAGE II                           13                            63
  STAGE III                          20                            62
  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  27  24  54
  DEL PEAK  5(2Q22.1) WILD-TYPE    45 110  76 119
D33V4, multiclass
       clus
vv      DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T0+T1                           5                            45
  T2                             27                           110
  T3                             24                            76
  T4                             54                           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  17  42   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 138  51 126   5
D33V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          41                           138
  N1                          17                            51
  N2                          42                           126
  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"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    54   1
  DEL PEAK  5(2Q22.1) WILD-TYPE 136   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     54    1
  DEL PEAK  5(2Q22.1) WILD-TYPE  136    0
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                          54                           136
  1                           1                             0
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    42  79
  DEL PEAK  5(2Q22.1) WILD-TYPE  98 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     42   79
  DEL PEAK  5(2Q22.1) WILD-TYPE   98  303
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          42                            98
  MALE                            79                           303
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    32  78
  DEL PEAK  5(2Q22.1) WILD-TYPE 130 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     32   78
  DEL PEAK  5(2Q22.1) WILD-TYPE  130  223
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           32                           130
  YES                          78                           223
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                                   118
  DEL PEAK  5(2Q22.1) WILD-TYPE                                 393
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  5(2Q22.1) MUTATED                                                   3
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                 7
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  5(2Q22.1) MUTATED                                                           0
  DEL PEAK  5(2Q22.1) WILD-TYPE                                                         1
D33V9, multiclass
                                                           clus
vv                                                          DEL PEAK  5(2Q22.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               118
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK  5(2Q22.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 393
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, continuous
D33V12, 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                          14   100
  DEL PEAK  5(2Q22.1) WILD-TYPE                        34   346
D33V13, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 14
  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                                                      346
[1] 4 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  5(2Q22.1) MUTATED     7 103
  DEL PEAK  5(2Q22.1) WILD-TYPE  19 356
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      7  103
  DEL PEAK  5(2Q22.1) WILD-TYPE   19  356
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         103
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           356
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  6(2Q36.2) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q36.2) MUTATED    88  69
  DEL PEAK  6(2Q36.2) WILD-TYPE 213 150
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                          157                           363 
  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                           69                           150 
$`DEL PEAK  6(2Q36.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 
        9.30        37.28        68.48         3.55        28.11        51.29 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CR-6472 
        9.07        11.08        32.48        24.39        48.20        34.52 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-BA-4076 
       30.94        46.32        40.24        21.11        48.03        13.64 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A6D8 
       42.35        17.10        65.59        15.52         4.01        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-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       55.86        12.99        27.58        73.61        13.05        46.32 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
       71.31         8.32         8.52        56.94        30.67        48.00 
TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       19.07        38.89         3.68        23.57        17.29        29.72 
TCGA-CN-A63W TCGA-CN-A6V6 TCGA-CQ-5327 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6225 
       12.39        20.88        54.58        10.42        41.19        13.25 
TCGA-CQ-7064 TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6493 TCGA-CR-7364 
       64.87        31.23        16.90        11.64         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
       47.34        35.84         3.45         3.09        29.23         0.99 
TCGA-CR-7380 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 
       19.92         5.95        29.95        48.39        17.16       108.95 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6003 
       19.20       107.51        17.92        86.83         7.07        54.74 
TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
       21.07        90.12         9.70        11.24       140.78        12.03 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7103 
        2.50         4.14       111.16        18.81        12.66        52.31 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
       17.13         4.96        11.87        47.97        49.71        57.47 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7422 
       35.54        17.85         9.67        25.08        25.94        34.09 
TCGA-CV-7424 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JE 
       14.89        22.19       180.16        45.96         7.07        35.34 
TCGA-CV-A6JN TCGA-CV-A6JY TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EP 
       29.79        21.24        11.44        12.36         7.63        13.94 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A620 TCGA-F7-A623 
       37.58        40.04        20.25        31.13        17.85        20.25 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G 
       28.47        14.66        13.84         3.65        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MZ-A6I9 
       37.41        13.68        19.04        15.48        19.27        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6IJ 
       17.98        15.78        12.99        13.15         7.30        12.72 
TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T3-A92N 
       12.89        17.82         8.32        16.96        15.91         3.12 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UP-A6WW TCGA-WA-A7GZ 
        2.83        49.45        29.46        18.05        17.03        20.55 
TCGA-KU-A66T 
       18.15 

$`DEL PEAK  6(2Q36.2) WILD-TYPE`
TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 
       20.48        30.18        25.71         9.24        52.08        35.05 
TCGA-CN-A6V1 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 
       19.82        32.88        70.13        16.73        43.04        11.61 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-HD-8634 TCGA-HD-8635 
        6.02         0.36        34.36        14.04        12.66        22.85 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
        2.96         3.35        15.19         9.07        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       57.93        23.84        21.17        14.83        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF 
       29.42        20.45        11.54         7.10         5.69         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        11.05        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
        4.80        18.38        44.98        66.28        24.66        38.40 
TCGA-BB-8596 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4725 
       71.05        27.19        12.92         8.81        48.76        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5358 
       57.11        20.55        14.33        45.83        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       12.39        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
       52.08        50.07        23.90        47.44        28.04        34.13 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
        6.74        10.45        32.22        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       25.41        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41        12.07         2.70        23.44        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50         2.93        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        4.24        32.38        46.95        56.58         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        53.52        41.88        43.10        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        14.14        12.46 
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-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        36.99        18.54        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        22.78        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        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
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       172.67 
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        89.65 
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        21.01       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        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
        3.62        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       18.84        51.12        13.25        25.41         9.60        23.05 
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-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       28.77        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       39.12        41.59        37.18        32.71        21.63         3.02 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       18.94        24.95         0.46        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
       27.48        27.48        22.03         0.36         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61J 
       34.75        15.95        38.53        14.50         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
        5.29        13.84        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-P3-A5Q5 
        1.84        12.62         6.25        15.42         7.13        29.92 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
       71.74        51.25        10.85        36.82        47.01        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z 
       75.55        18.97         2.04        29.00        16.01        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB 
       21.21        23.15        21.47         9.34        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TO 
       19.73         5.62        14.76        12.20        15.32        12.72 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ 
        6.87         7.10        32.45        13.71        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA 
       20.35        64.80        54.67        49.51        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       17.95        24.30        55.43        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        14.56        13.35 

  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE 
                         0.99                          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 
                        19.20                         21.93 
[1] "1.0 - 180.2 (19.2)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1.1"
D34V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  6(2Q36.2) MUTATED         3       17        33        73         6
  DEL PEAK  6(2Q36.2) WILD-TYPE      24       59        49       179         6
                               vv
clus                            STAGE IVC
  DEL PEAK  6(2Q36.2) MUTATED           0
  DEL PEAK  6(2Q36.2) WILD-TYPE         1
D34V3, multiclass
           clus
vv          DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  STAGE I                             3                            24
  STAGE II                           17                            59
  STAGE III                          33                            49
  STAGE IVA                          73                           179
  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  33  41  55
  DEL PEAK  6(2Q36.2) WILD-TYPE    43 104  59 118
D34V4, multiclass
       clus
vv      DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  T0+T1                           7                            43
  T2                             33                           104
  T3                             41                            59
  T4                             55                           118
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  6(2Q36.2) MUTATED    52  23  46   4
  DEL PEAK  6(2Q36.2) WILD-TYPE 127  45 122   4
D34V5, multiclass
    clus
vv   DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  N0                          52                           127
  N1                          23                            45
  N2                          46                           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"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    55   0
  DEL PEAK  6(2Q36.2) WILD-TYPE 135   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     55    0
  DEL PEAK  6(2Q36.2) WILD-TYPE  135    1
   clus
vv  DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  0                          55                           135
  1                           0                             1
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    44 113
  DEL PEAK  6(2Q36.2) WILD-TYPE  96 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     44  113
  DEL PEAK  6(2Q36.2) WILD-TYPE   96  269
        clus
vv       DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  FEMALE                          44                            96
  MALE                           113                           269
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    43  94
  DEL PEAK  6(2Q36.2) WILD-TYPE 119 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     43   94
  DEL PEAK  6(2Q36.2) WILD-TYPE  119  207
     clus
vv    DEL PEAK  6(2Q36.2) MUTATED DEL PEAK  6(2Q36.2) WILD-TYPE
  NO                           43                           119
  YES                          94                           207
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(2Q36.2) MUTATED                                   154
  DEL PEAK  6(2Q36.2) WILD-TYPE                                 357
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  6(2Q36.2) MUTATED                                                   3
  DEL PEAK  6(2Q36.2) WILD-TYPE                                                 7
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  6(2Q36.2) MUTATED                                                           0
  DEL PEAK  6(2Q36.2) WILD-TYPE                                                         1
D34V9, multiclass
                                                           clus
vv                                                          DEL PEAK  6(2Q36.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               154
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK  6(2Q36.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 357
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
D34V11, continuous
D34V12, 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                          22   125
  DEL PEAK  6(2Q36.2) WILD-TYPE                        26   321
D34V13, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q36.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    125
                                  clus
vv                                 DEL PEAK  6(2Q36.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q36.2) MUTATED    14 134
  DEL PEAK  6(2Q36.2) WILD-TYPE  12 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q36.2) MUTATED     14  134
  DEL PEAK  6(2Q36.2) WILD-TYPE   12  325
                        clus
vv                       DEL PEAK  6(2Q36.2) MUTATED
  HISPANIC OR LATINO                              14
  NOT HISPANIC OR LATINO                         134
                        clus
vv                       DEL PEAK  6(2Q36.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           325
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  7(3P26.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.2) MUTATED   188 158
  DEL PEAK  7(3P26.2) WILD-TYPE 113  61
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          346                           174 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                          158                            61 
$`DEL PEAK  7(3P26.2) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 
        9.30        68.48         3.55        30.18        25.71         9.07 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7067 
       11.08        35.05        32.48        24.39        32.88        16.73 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       11.61         6.02         0.36        34.36        30.94        14.04 
TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-4074 
       46.32        21.11        12.66        22.85         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
       13.64         9.07        26.50        17.10        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
       21.17        14.83        12.62        29.42        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-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 
       20.52        27.19         8.81         6.28        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 
        4.67        56.68        12.89        26.86        32.81        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
       12.99        20.55        14.33        45.83        27.58        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       42.02        46.32         8.58        12.39        71.31         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        52.08 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
       50.07        30.67        48.00        23.90        47.44        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       34.13         6.74        32.22        38.89         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        25.41        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CQ-5325 
        7.40        31.69        12.39         4.41        12.07        21.50 
TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
        2.93        62.37        10.42        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       53.52        41.88        77.56        23.24        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6473 TCGA-CR-6474 
       29.49        31.23        84.23        11.77        36.99        18.54 
TCGA-CR-6477 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       16.90        11.34        11.64         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       15.75         9.27        47.18        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 
       35.84         3.09        24.95        29.23         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 
       19.92        17.13        47.01        12.89        49.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.13        35.41        29.95       139.43        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-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       80.12        17.92        13.35        86.83        48.59        60.49 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 
        7.07        43.23        54.74         9.60        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 
        9.70         5.46        20.52        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       172.67 
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        89.65        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        49.71 
TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 
       18.41        17.85       210.97         9.67         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 
       25.08        25.94         0.07       100.57        14.89        54.94 
TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45R 
        3.52        84.49        19.76         7.17       153.86       180.16 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
       35.47        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT 
       67.86        56.61         7.07        35.34        29.79        28.01 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6516 
        3.62        23.47        22.52        18.84        51.12        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
        9.60        23.05        16.14        11.44        24.95        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       12.36         7.63        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 
       23.34        58.45        33.86        18.02        20.45        37.58 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       39.12        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7832 
       20.25        15.06        33.76        28.47        21.93        27.48 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       13.84         3.65        15.95        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       15.48        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 
       71.74        47.01        18.97         2.04        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
       13.15        21.07        21.21        21.47        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       21.07        19.73        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N 
       17.82        15.32         8.32        15.91        13.71         3.12 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       44.65        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7H4 TCGA-KU-A66T 
       20.75        22.36        14.56        18.15 

$`DEL PEAK  7(3P26.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 
       37.28        20.48        28.11        51.29         9.24        52.08 
TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-DQ-7593 
       19.82        48.20        70.13        43.04        34.52        40.24 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
       48.03         2.96        23.74        42.35        57.93        23.84 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
        4.01        41.85        20.45         5.69         7.82         2.27 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
       13.38         6.15       105.90         4.80        18.38        22.42 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-C9-A480 
       33.70        50.20        44.98        10.55        12.92        12.69 
TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6017 
       48.76        52.14        73.61        12.49        56.94        28.04 
TCGA-CN-6988 TCGA-CN-A499 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY 
       10.45        23.57        22.32        16.57         2.70        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       20.88        19.53        52.37        54.58        70.45        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CG TCGA-CQ-A4CH 
       11.21         4.24        43.10        44.48        14.14        12.46 
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-6480 TCGA-CR-6481 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 
       11.90        10.22         3.45         0.99        31.96        26.17 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       32.78        27.06        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
       30.58         5.95        48.39        76.50        91.53        23.05 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 
       21.07        62.43         4.73        21.90       140.78        19.79 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 
       53.95        10.98       130.88        77.16        95.34        57.47 
TCGA-CV-7407 TCGA-CV-7411 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7430 
       35.54        89.33        34.09        56.48       156.49        16.27 
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        21.01       169.38 
TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM 
      159.65         1.05         0.76        15.25         5.98         6.38 
TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 
        6.48        21.24        19.92        10.42        10.55        13.25 
TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-DQ-5625 
        2.53        18.67        17.72        28.77        22.59        37.25 
TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       46.45        40.04        41.59        12.43        13.38        15.16 
TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       20.94        25.74        27.48        14.66        22.03         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A6H7 
        4.27         6.90        34.75        38.53        14.50        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       10.75        30.05        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       16.08        29.92        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-RS-A6TO 
       75.55        12.99        23.15         7.30         9.34        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL 
       16.96         6.87         7.10        32.45        13.55        20.35 
TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S 
       74.47        18.05        32.65        17.03        20.55        13.35 

  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 
                       20.535                        22.255 
[1] "0.1 - 211.0 (20.5)" "0.4 - 169.4 (22.3)"
[1] "hr=" "1.4"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  7(3P26.2) MUTATED        18       47        57       178        10
  DEL PEAK  7(3P26.2) WILD-TYPE       9       29        25        74         2
                               vv
clus                            STAGE IVC
  DEL PEAK  7(3P26.2) MUTATED           1
  DEL PEAK  7(3P26.2) WILD-TYPE         0
D35V3, multiclass
           clus
vv          DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  STAGE I                            18                             9
  STAGE II                           47                            29
  STAGE III                          57                            25
  STAGE IVA                         178                            74
  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  84  76 126
  DEL PEAK  7(3P26.2) WILD-TYPE    20  53  24  47
D35V4, multiclass
       clus
vv      DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  T0+T1                          30                            20
  T2                             84                            53
  T3                             76                            24
  T4                            126                            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   118  47 125   6
  DEL PEAK  7(3P26.2) WILD-TYPE  61  21  43   2
D35V5, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  N0                         118                            61
  N1                          47                            21
  N2                         125                            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"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED   127   1
  DEL PEAK  7(3P26.2) WILD-TYPE  63   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED    127    1
  DEL PEAK  7(3P26.2) WILD-TYPE   63    0
   clus
vv  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  0                         127                            63
  1                           1                             0
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    79 269
  DEL PEAK  7(3P26.2) WILD-TYPE  61 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     79  269
  DEL PEAK  7(3P26.2) WILD-TYPE   61  113
        clus
vv       DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  FEMALE                          79                            61
  MALE                           269                           113
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED   109 196
  DEL PEAK  7(3P26.2) WILD-TYPE  53 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED    109  196
  DEL PEAK  7(3P26.2) WILD-TYPE   53  105
     clus
vv    DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  NO                          109                            53
  YES                         196                           105
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P26.2) MUTATED                                   343
  DEL PEAK  7(3P26.2) WILD-TYPE                                 168
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  7(3P26.2) MUTATED                                                   4
  DEL PEAK  7(3P26.2) WILD-TYPE                                                 6
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  7(3P26.2) MUTATED                                                           1
  DEL PEAK  7(3P26.2) WILD-TYPE                                                         0
D35V9, multiclass
                                                           clus
vv                                                          DEL PEAK  7(3P26.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               343
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          DEL PEAK  7(3P26.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 168
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, continuous
D35V11, continuous
D35V12, 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                          44   285
  DEL PEAK  7(3P26.2) WILD-TYPE                         4   161
D35V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 44
  WHITE                                                    285
                                  clus
vv                                 DEL PEAK  7(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                      161
[1] 4 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  7(3P26.2) MUTATED    18 303
  DEL PEAK  7(3P26.2) WILD-TYPE   8 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     18  303
  DEL PEAK  7(3P26.2) WILD-TYPE    8  156
                        clus
vv                       DEL PEAK  7(3P26.2) MUTATED
  HISPANIC OR LATINO                              18
  NOT HISPANIC OR LATINO                         303
                        clus
vv                       DEL PEAK  7(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           156
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  8(3P24.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P24.1) MUTATED   198 168
  DEL PEAK  8(3P24.1) WILD-TYPE 103  51
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          366                           154 
  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE 
                          168                            51 
$`DEL PEAK  8(3P24.1) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        68.48         3.55        30.18        25.71 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 
        9.07         9.24        11.08        35.05        32.48        24.39 
TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       32.88        16.73        11.61         6.02         0.36        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       30.94        14.04        46.32        21.11        12.66        22.85 
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 
        3.35        15.19        13.64         9.07        26.50        17.10 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 
       65.59        15.52        21.17        14.83        12.62        41.85 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       29.42        27.95        11.54         7.10         5.69        14.47 
TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
       11.05        20.48        16.41         9.14         4.41        18.38 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       36.72        50.20        66.28        24.66        38.40        71.05 
TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 
       20.52        27.19         8.81         6.28        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 
        4.67        56.68        12.89        26.86        32.81        57.11 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
       12.99        20.55        14.33        45.83        27.58        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       42.02        46.32         8.58        12.39        71.31         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        52.08 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 
       50.07        30.67        48.00        23.90        47.44        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       34.13         6.74        10.45        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        11.74        35.01        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 
       21.21         7.40        31.69        12.39         4.41        12.07 
TCGA-CN-A6UY TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       23.44         2.93        62.37        10.42        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        53.52        41.88        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.36        33.60        29.49        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       54.67        26.27        36.99        18.54        16.90        11.90 
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        22.78        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-7377 TCGA-CR-7379 
        3.45         3.09        24.95        29.23         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       19.92        17.13        47.01        27.06        12.89        49.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
       24.79         5.13        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-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       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-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       71.21        10.75         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       26.20        18.97        17.13         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        49.71        18.41        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-7428 TCGA-CV-7429 TCGA-CV-7430 
       34.09       100.57        14.89        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U 
       84.49        19.76         7.17       153.86       180.16        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
       45.96         6.51        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        28.01         3.62        23.47 
TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       22.52        18.84        51.12        25.41         9.60        23.05 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EM 
       16.14        11.44        24.95        25.32        12.36         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 
       33.86        18.02        20.45        37.58        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       37.18        32.71        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-8502 
       18.94        24.95         0.46        17.85        11.80        15.06 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       33.76        28.47        21.93        27.48        27.48        14.66 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       13.84         3.65        15.95        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A5BI 
       15.48        19.27        14.37         7.96         1.84         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 
       17.98        15.78        71.74        47.01        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
       29.00        16.01        13.15        21.07        21.21        21.47 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.72        27.39        21.07        19.73        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ 
       14.76        12.20        17.82        15.32         8.32        15.91 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.71         3.12        13.25        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
       49.51        49.45        44.65        17.95        24.30        55.43 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-KU-A66T 
       29.46        13.94        20.75        22.36        20.55        18.15 

$`DEL PEAK  8(3P24.1) WILD-TYPE`
TCGA-BA-5557 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CQ-5323 
       20.48        28.11        51.29        52.08        19.82        48.20 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-DQ-7593 TCGA-UF-A71D TCGA-UF-A7JV 
       70.13        43.04        34.52        40.24        48.03         2.96 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-A4IH 
       23.74        42.35        57.93        23.84         4.01        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       105.90         4.80 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-C9-A480 
       22.42        33.70        44.98        10.55        12.92        12.69 
TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-5369 TCGA-CN-5374 TCGA-CN-6017 
       48.76        52.14        73.61        12.49        56.94        28.04 
TCGA-CN-A499 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 
       23.57        22.32        16.57         2.70        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 
       52.37        21.50        54.58        70.45        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 TCGA-CR-6467 
        4.24        43.10        14.14        12.46        37.87        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6481 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 
       50.01        39.52        10.22         0.99        31.96        26.17 
TCGA-CR-7385 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       32.78        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 
        5.95        48.39        76.50        91.53        23.05        21.07 
TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 
       62.43         4.73       140.78        19.79        53.95        10.98 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7411 TCGA-CV-7425 
      130.88        77.16        95.34        57.47        89.33        56.48 
TCGA-CV-7427 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P 
      156.49        16.64         6.38        22.19        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A468 
      169.38       159.65         1.05        88.87         0.76        15.25 
TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 
        5.98         6.38         6.48        21.24        19.92        10.42 
TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EK 
       10.55        13.25         2.53        18.67        17.72        28.77 
TCGA-D6-A6EN TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-F7-A623 TCGA-F7-A624 
       22.59        37.25        46.45        40.04        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 
       13.38        15.16        20.94        25.74        22.03         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-KU-A6H8 
        4.27         6.90        34.75        38.53        14.50        10.75 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       30.05        12.62         6.25        15.42        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 
       23.15         7.30         9.34        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A7JA TCGA-UF-A7JJ 
        7.10        32.45        13.55        20.35        74.47        18.05 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        14.56        13.35 

  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 
                        20.65                         22.11 
[1] "0.1 - 211.0 (20.6)" "0.4 - 169.4 (22.1)"
[1] "hr=" "1.5"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  8(3P24.1) MUTATED        17       49        59       187        10
  DEL PEAK  8(3P24.1) WILD-TYPE      10       27        23        65         2
                               vv
clus                            STAGE IVC
  DEL PEAK  8(3P24.1) MUTATED           1
  DEL PEAK  8(3P24.1) WILD-TYPE         0
D36V3, multiclass
           clus
vv          DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  STAGE I                            17                            10
  STAGE II                           49                            27
  STAGE III                          59                            23
  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  8(3P24.1) MUTATED      28  90  79 132
  DEL PEAK  8(3P24.1) WILD-TYPE    22  47  21  41
D36V4, multiclass
       clus
vv      DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  T0+T1                          28                            22
  T2                             90                            47
  T3                             79                            21
  T4                            132                            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   120  50 131   6
  DEL PEAK  8(3P24.1) WILD-TYPE  59  18  37   2
D36V5, multiclass
    clus
vv   DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  N0                         120                            59
  N1                          50                            18
  N2                         131                            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"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED   131   1
  DEL PEAK  8(3P24.1) WILD-TYPE  59   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED    131    1
  DEL PEAK  8(3P24.1) WILD-TYPE   59    0
   clus
vv  DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  0                         131                            59
  1                           1                             0
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED    85 283
  DEL PEAK  8(3P24.1) WILD-TYPE  55  99
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     85  283
  DEL PEAK  8(3P24.1) WILD-TYPE   55   99
        clus
vv       DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  FEMALE                          85                            55
  MALE                           283                            99
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED   113 207
  DEL PEAK  8(3P24.1) WILD-TYPE  49  94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED    113  207
  DEL PEAK  8(3P24.1) WILD-TYPE   49   94
     clus
vv    DEL PEAK  8(3P24.1) MUTATED DEL PEAK  8(3P24.1) WILD-TYPE
  NO                          113                            49
  YES                         207                            94
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P24.1) MUTATED                                   363
  DEL PEAK  8(3P24.1) WILD-TYPE                                 148
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  8(3P24.1) MUTATED                                                   4
  DEL PEAK  8(3P24.1) WILD-TYPE                                                 6
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  8(3P24.1) MUTATED                                                           1
  DEL PEAK  8(3P24.1) WILD-TYPE                                                         0
D36V9, multiclass
                                                           clus
vv                                                          DEL PEAK  8(3P24.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               363
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          DEL PEAK  8(3P24.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 148
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
D36V11, continuous
D36V12, 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                          45   304
  DEL PEAK  8(3P24.1) WILD-TYPE                         3   142
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  8(3P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 45
  WHITE                                                    304
                                  clus
vv                                 DEL PEAK  8(3P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                      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"
D36V14, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P24.1) MUTATED    18 322
  DEL PEAK  8(3P24.1) WILD-TYPE   8 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P24.1) MUTATED     18  322
  DEL PEAK  8(3P24.1) WILD-TYPE    8  137
                        clus
vv                       DEL PEAK  8(3P24.1) MUTATED
  HISPANIC OR LATINO                              18
  NOT HISPANIC OR LATINO                         322
                        clus
vv                       DEL PEAK  8(3P24.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           137
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  9(3P14.2) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P14.2) MUTATED   200 170
  DEL PEAK  9(3P14.2) WILD-TYPE 101  49
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          370                           150 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                          170                            49 
$`DEL PEAK  9(3P14.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II 
        9.30        37.28        20.48        68.48         3.55        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
       25.71        51.29         9.07         9.24        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 
       32.48        24.39        48.20        32.88        16.73        11.61 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
        6.02         0.36        34.36        30.94        14.04        46.32 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       21.11        12.66        22.85         3.35        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
        9.07        26.50        57.93        17.10        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
       21.17        14.83        12.62        41.85        29.42        27.95 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL 
       11.54         7.10         5.69        14.47        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 
       16.41         9.14         4.41        36.72        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
       27.19         8.81         6.28        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
       56.68        12.89        26.86        32.81        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        45.83        27.58        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         8.32        16.21        11.54 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
       11.84        11.57         8.52        52.08        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
       48.00        23.90        47.44        19.07        34.13         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       10.45        32.22        38.89         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        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A6UY 
        7.40        31.69        12.39         4.41        12.07        23.44 
TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       19.53         2.93        62.37        10.42        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        53.52        41.88        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       29.36        29.49        31.23        84.23        11.77        54.67 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       26.27        58.42        36.99        18.54        16.90        11.90 
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        22.78        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-7377 
        3.45         3.09        24.95        29.23         0.99         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
       34.06        19.92        17.13        47.01        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       49.58        24.79         5.13         5.95        35.41        29.95 
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-5444 TCGA-CV-5966 TCGA-CV-5970 
       17.95       107.51        94.88        80.12        17.92        13.35 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       86.83        48.59        60.49         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-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 
       21.90        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-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50         4.14        64.83       111.16        18.81        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-7236 TCGA-CV-7238 TCGA-CV-7242 
       21.80        71.21        10.75         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        18.97        17.13         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 
       47.97         2.10        49.71        18.41        35.54        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-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 
        0.07        34.09       100.57        14.89        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
       16.27        84.49        19.76         7.17       153.86        22.19 
TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 
      180.16        35.47        45.96         6.51        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
       67.86         7.07        35.34        28.01         3.62        23.47 
TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       22.52        18.84        51.12        25.41         9.60        23.05 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM 
       16.14        24.95        25.32        17.72        12.36         7.63 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 
       33.86        18.02        20.45        37.58        39.12        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
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        33.76 
TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-A633 TCGA-HD-A6HZ 
       28.47        21.93        27.48        27.48        13.84         3.65 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        37.71        11.84        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       14.37         7.96         1.84         7.13        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       71.74        10.85        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        21.21        21.47        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       27.39        21.07        12.89         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N 
       17.82        15.32         8.32        15.91        13.71         3.12 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       44.65        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-KU-A66T 
       20.75        22.36        20.55        18.15 

$`DEL PEAK  9(3P14.2) WILD-TYPE`
TCGA-BA-A4IG TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 
       28.11        52.08        19.82        70.13        43.04        34.52 
TCGA-DQ-7593 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 
       40.24        48.03         2.96        23.74        42.35        23.84 
TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
        4.01        20.45         7.82         2.27        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-A6UM 
      105.90         4.80        18.38        22.42        33.70        12.92 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5369 
       12.69        48.76        52.14        57.11        73.61        12.49 
TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6V6 
       56.94        28.04        22.32        16.57         2.70        20.88 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 
       52.37        21.50        54.58        70.45        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-7071 TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 
        4.24        43.10        33.60        14.14        12.46        37.87 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6481 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 
       50.01        39.52        10.22        31.96        26.17        32.78 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7404 
       30.02        46.85        32.65        44.25        30.58        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-6942 TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7090 TCGA-CV-7183 
      140.78        19.79        53.95        10.98       172.67       130.88 
TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7411 TCGA-CV-7425 TCGA-CV-7427 
       77.16        95.34        57.47        89.33        56.48       156.49 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
       16.64         6.38        27.98        21.01       169.38       159.65 
TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1.05        88.87         0.76        56.61        15.25         5.98 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 
        6.38        29.79         6.48        21.24        19.92        10.42 
TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK 
       10.55        13.25         2.53        11.44        18.67        28.77 
TCGA-D6-A6EN TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-A61V 
       22.59        37.25        46.45        40.04        41.59        24.95 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8224 
       12.43        13.38        15.16        20.94        25.74        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
       22.03         0.36         4.27         6.90        34.75        38.53 
TCGA-IQ-7632 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       14.50        10.75        30.05        12.62         6.25        15.42 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
       16.08        29.92        51.25        36.82        19.00        75.55 
TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6VC TCGA-RS-A6TO 
       12.99        23.15         7.30         9.34        19.73        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL 
       16.96         6.87         7.10        32.45        13.55        20.35 
TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       74.47        18.05        32.65        17.03        14.56        13.35 

  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                        172.67 
  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE 
                       20.535                        22.505 
[1] "0.1 - 211.0 (20.5)" "0.4 - 172.7 (22.5)"
[1] "hr=" "1.6"
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK  9(3P14.2) MUTATED        18       49        59       189        10
  DEL PEAK  9(3P14.2) WILD-TYPE       9       27        23        63         2
                               vv
clus                            STAGE IVC
  DEL PEAK  9(3P14.2) MUTATED           1
  DEL PEAK  9(3P14.2) WILD-TYPE         0
D37V3, multiclass
           clus
vv          DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  STAGE I                            18                             9
  STAGE II                           49                            27
  STAGE III                          59                            23
  STAGE IVA                         189                            63
  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  94  77 131
  DEL PEAK  9(3P14.2) WILD-TYPE    19  43  23  42
D37V4, multiclass
       clus
vv      DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  T0+T1                          31                            19
  T2                             94                            43
  T3                             77                            23
  T4                            131                            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   120  51 134   6
  DEL PEAK  9(3P14.2) WILD-TYPE  59  17  34   2
D37V5, multiclass
    clus
vv   DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  N0                         120                            59
  N1                          51                            17
  N2                         134                            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"
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED   131   1
  DEL PEAK  9(3P14.2) WILD-TYPE  59   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED    131    1
  DEL PEAK  9(3P14.2) WILD-TYPE   59    0
   clus
vv  DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  0                         131                            59
  1                           1                             0
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    87 285
  DEL PEAK  9(3P14.2) WILD-TYPE  53  97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     87  285
  DEL PEAK  9(3P14.2) WILD-TYPE   53   97
        clus
vv       DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  FEMALE                          87                            53
  MALE                           285                            97
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED   111 212
  DEL PEAK  9(3P14.2) WILD-TYPE  51  89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED    111  212
  DEL PEAK  9(3P14.2) WILD-TYPE   51   89
     clus
vv    DEL PEAK  9(3P14.2) MUTATED DEL PEAK  9(3P14.2) WILD-TYPE
  NO                          111                            51
  YES                         212                            89
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P14.2) MUTATED                                   367
  DEL PEAK  9(3P14.2) WILD-TYPE                                 144
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK  9(3P14.2) MUTATED                                                   4
  DEL PEAK  9(3P14.2) WILD-TYPE                                                 6
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK  9(3P14.2) MUTATED                                                           1
  DEL PEAK  9(3P14.2) WILD-TYPE                                                         0
D37V9, multiclass
                                                           clus
vv                                                          DEL PEAK  9(3P14.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               367
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          DEL PEAK  9(3P14.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 144
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
D37V11, continuous
D37V12, 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                          44   308
  DEL PEAK  9(3P14.2) WILD-TYPE                         4   138
D37V13, multiclass
                                  clus
vv                                 DEL PEAK  9(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 44
  WHITE                                                    308
                                  clus
vv                                 DEL PEAK  9(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                      138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P14.2) MUTATED    19 325
  DEL PEAK  9(3P14.2) WILD-TYPE   7 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P14.2) MUTATED     19  325
  DEL PEAK  9(3P14.2) WILD-TYPE    7  134
                        clus
vv                       DEL PEAK  9(3P14.2) MUTATED
  HISPANIC OR LATINO                              19
  NOT HISPANIC OR LATINO                         325
                        clus
vv                       DEL PEAK  9(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           134
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 10(3P12.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(3P12.1) MUTATED   182 159
  DEL PEAK 10(3P12.1) WILD-TYPE 119  60
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          341                           179 
  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                          159                            60 
$`DEL PEAK 10(3P12.1) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II 
        9.30        37.28        20.48        68.48         3.55        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       25.71        51.29         9.07        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 
       32.48        24.39        48.20        32.88        16.73        11.61 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
        6.02         0.36        34.36        30.94        14.04        46.32 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       21.11        22.85         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       26.50        57.93        17.10        65.59        15.52        21.17 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DD 
       14.83        12.62        41.85        29.42        27.95         5.69 
TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7864 
       14.47        11.05        20.48        16.41         9.14        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
       27.19         8.81         6.28        55.86        38.04         4.67 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        26.86        32.81        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       14.33        45.83        27.58        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         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        52.08        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 
       47.44        19.07        34.13         6.74        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 
       29.72        21.21         7.40        31.69        12.39         4.41 
TCGA-CN-A641 TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 
       12.07        19.53         2.93        62.37        10.42        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       32.38        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
       38.76        64.87        53.52        41.88        77.56        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        29.36        33.60        29.49        31.23        84.23 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 
       11.77        58.42        18.54        16.90        11.90        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        22.78        15.75         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-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 
        3.09        24.95        29.23         0.99         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 
       19.92        17.13        27.06        12.89        49.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.13        35.41        29.95       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 
      108.95        76.24        19.20        17.95       107.51        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       17.92        13.35        86.83        48.59        60.49        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-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
       30.08        65.82         7.13         8.42        28.34         2.50 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        4.14        64.83       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-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       71.21        10.75         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       26.20        18.97        17.13         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        49.71        18.41        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-7428 TCGA-CV-7429 TCGA-CV-7430 
       34.09       100.57        14.89        54.94         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45X 
       84.49         7.17       153.86        22.19        35.47         6.51 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN 
       48.20        60.43        67.86         7.07        35.34        29.79 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-A4AQ 
       28.01         3.62        23.47        22.52        18.84        51.12 
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        24.95        13.94        12.10        23.34 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 
       58.45        33.86        37.58        39.12        37.18        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W 
       21.63        20.25         3.02        31.13        18.94         0.46 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       17.85        20.25        15.06        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G 
       14.66        13.84         3.65        15.95        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41         0.07        33.57        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       15.48        14.37         7.96         1.84        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       71.74        10.85        47.01        18.97         2.04        29.00 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A6V9 
       16.01        13.15        21.07        21.21        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       21.07        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ 
       15.32         8.32        15.91        13.71         3.12        13.25 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       64.80        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-KU-A66S TCGA-KU-A66T 
       20.75        22.36        20.55        13.35        18.15 

$`DEL PEAK 10(3P12.1) WILD-TYPE`
TCGA-BA-A4IG TCGA-CN-6022 TCGA-CN-A6V1 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 
       28.11         9.24        19.82        70.13        43.04        34.52 
TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-5151 TCGA-BA-5152 
       40.24        12.66        48.03         2.96        23.74        42.35 
TCGA-BA-5556 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DF 
       23.84         4.01        20.45        11.54         7.10         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        2.27        13.38         6.15       105.90         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-A6UM 
       18.38        22.42        36.72        33.70        44.98        12.92 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-4742 
       12.69        48.76        56.68        52.14        73.61        13.05 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6017 TCGA-CN-6988 TCGA-CN-A49A 
       12.49         8.52        56.94        28.04        10.45        17.29 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 
       22.32        16.57         2.70        23.44        20.88        52.37 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       21.50        54.58        70.45        45.99        11.21         4.24 
TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       43.10        14.14        12.46        54.67        37.87        26.27 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-7376 TCGA-CR-7382 
       50.01        39.52        36.99        10.22        31.96        26.17 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       32.78        47.01        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
       30.58         5.95        48.39        94.88        76.50        91.53 
TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 
       23.05         7.07        21.07        62.43         4.73        21.90 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7090 
      140.78        19.79         6.08        53.95        10.98       172.67 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7411 TCGA-CV-7425 
      130.88        77.16        95.34        57.47        89.33        56.48 
TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P 
      156.49        19.76        16.64         6.38        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Y 
      169.38       180.16       159.65         1.05        45.96        88.87 
TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO 
        0.76        56.61        15.25         5.98         6.38         6.48 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6823 
       21.24        19.92        10.42        10.55        13.25        23.05 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6ES 
        2.53        16.14        18.67        28.77        22.59        12.79 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7596 
       37.25        18.02        46.45        20.45        40.04        41.59 
TCGA-F7-A61V TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       24.95        11.80        12.43        13.38        15.16        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 
       33.76        28.47        25.74        22.03         0.36         4.27 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61K TCGA-KU-A6H7 
        6.90        34.75        38.53        14.50         5.29        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
       10.75        30.05        12.62         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
       16.08        29.92        51.25        36.82        19.00        75.55 
TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6VC 
       12.99        23.15         7.30        21.47         9.34        19.73 
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-A7HL TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 
       20.35        18.05        32.65        17.03        14.56 

  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE 
                         0.07                          0.36 
  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 
                        21.07                         21.47 
[1] "0.1 - 211.0 (21.1)" "0.4 - 180.2 (21.5)"
[1] "hr=" "1.5"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 10(3P12.1) MUTATED        14       47        57       177         7
  DEL PEAK 10(3P12.1) WILD-TYPE      13       29        25        75         5
                               vv
clus                            STAGE IVC
  DEL PEAK 10(3P12.1) MUTATED           1
  DEL PEAK 10(3P12.1) WILD-TYPE         0
D38V3, multiclass
           clus
vv          DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  STAGE I                            14                            13
  STAGE II                           47                            29
  STAGE III                          57                            25
  STAGE IVA                         177                            75
  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  90  72 120
  DEL PEAK 10(3P12.1) WILD-TYPE    22  47  28  53
D38V4, multiclass
       clus
vv      DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  T0+T1                          28                            22
  T2                             90                            47
  T3                             72                            28
  T4                            120                            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   112  50 122   5
  DEL PEAK 10(3P12.1) WILD-TYPE  67  18  46   3
D38V5, multiclass
    clus
vv   DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  N0                         112                            67
  N1                          50                            18
  N2                         122                            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"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED   121   1
  DEL PEAK 10(3P12.1) WILD-TYPE  69   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED    121    1
  DEL PEAK 10(3P12.1) WILD-TYPE   69    0
   clus
vv  DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  0                         121                            69
  1                           1                             0
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED    80 263
  DEL PEAK 10(3P12.1) WILD-TYPE  60 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     80  263
  DEL PEAK 10(3P12.1) WILD-TYPE   60  119
        clus
vv       DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  FEMALE                          80                            60
  MALE                           263                           119
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(3P12.1) MUTATED   103 195
  DEL PEAK 10(3P12.1) WILD-TYPE  59 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED    103  195
  DEL PEAK 10(3P12.1) WILD-TYPE   59  106
     clus
vv    DEL PEAK 10(3P12.1) MUTATED DEL PEAK 10(3P12.1) WILD-TYPE
  NO                          103                            59
  YES                         195                           106
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3P12.1) MUTATED                                   337
  DEL PEAK 10(3P12.1) WILD-TYPE                                 174
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 10(3P12.1) MUTATED                                                   5
  DEL PEAK 10(3P12.1) WILD-TYPE                                                 5
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 10(3P12.1) MUTATED                                                           1
  DEL PEAK 10(3P12.1) WILD-TYPE                                                         0
D38V9, multiclass
                                                           clus
vv                                                          DEL PEAK 10(3P12.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               337
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          DEL PEAK 10(3P12.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 174
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
D38V11, continuous
D38V12, 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                          42   281
  DEL PEAK 10(3P12.1) WILD-TYPE                         6   165
D38V13, multiclass
                                  clus
vv                                 DEL PEAK 10(3P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 42
  WHITE                                                    281
                                  clus
vv                                 DEL PEAK 10(3P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    6
  WHITE                                                      165
[1] 4 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 10(3P12.1) MUTATED    17 298
  DEL PEAK 10(3P12.1) WILD-TYPE   9 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3P12.1) MUTATED     17  298
  DEL PEAK 10(3P12.1) WILD-TYPE    9  161
                        clus
vv                       DEL PEAK 10(3P12.1) MUTATED
  HISPANIC OR LATINO                              17
  NOT HISPANIC OR LATINO                         298
                        clus
vv                       DEL PEAK 10(3P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           161
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 11(4P16.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4P16.3) MUTATED   110  95
  DEL PEAK 11(4P16.3) WILD-TYPE 191 124
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                          205                           315 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                           95                           124 
$`DEL PEAK 11(4P16.3) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6021 
        9.30        37.28        20.48         3.55        28.11         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 
       52.08        11.08        35.05        32.48        24.39        48.20 
TCGA-CQ-7067 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       16.73        34.52         0.36        30.94        14.04        46.32 
TCGA-H7-A6C5 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5555 
       21.11        15.19        13.64        26.50        23.74        17.10 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
       65.59        15.52        14.83        29.42        27.95         7.10 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7861 
       20.48        16.41       105.90         9.14         4.41        22.42 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 
       66.28        71.05        20.52        27.19         6.28        12.69 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4735 
       55.86        38.04         4.67        12.89        26.86        57.11 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       45.83        13.05        42.02         8.58        71.31         8.32 
TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       16.21        11.57        56.94        30.67        48.00        19.07 
TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       34.13        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
       35.01        23.57        17.29        29.72         7.40        31.69 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 
       12.39        12.07         2.93        32.38        46.95        13.25 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI 
       14.99        64.87        77.56        23.24        33.60        31.23 
TCGA-CR-5248 TCGA-CR-6474 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 
       54.67        18.54         7.69        22.78        39.16        47.34 
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-7379 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 
       34.06        19.92        17.13        27.06        49.58         5.13 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       48.39        17.16       129.21       108.95        76.24        19.20 
TCGA-CV-5440 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6939 
      107.51        90.12         2.14         9.70         5.46        21.90 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
       26.43        11.24       140.78        42.38        15.09        30.08 
TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        7.13         2.50         4.14       111.16        12.66         5.26 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 
       77.16         4.73        89.65        36.00        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7413 
       17.13        47.97        49.71        57.47        35.54         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7429 
        0.46        22.85        25.94        34.09       100.57         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 
       16.27        84.49        19.76       153.86         6.38        22.19 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A465 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       45.96         6.51         7.07        25.41         9.60        23.05 
TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q 
       17.72         7.63        24.95        13.94        12.10        23.34 
TCGA-DQ-7595 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-8502 
       39.12        32.71        20.25        24.95         0.46        15.06 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E 
       28.47        27.48        22.03        13.84         3.65        37.71 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       11.84        33.57         6.25        15.42        16.08        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
       15.78        71.74        36.82        47.01         2.04        13.15 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J 
       21.07        19.73        12.89         5.62        12.20        15.32 
TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A71B 
        8.32        15.91        13.71         3.12         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
       49.45        44.65        24.30        55.43        29.46        22.36 
TCGA-WA-A7GZ 
       20.55 

$`DEL PEAK 11(4P16.3) WILD-TYPE`
TCGA-BA-5559 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-A6V1 
       68.48        30.18        25.71        51.29         9.24        19.82 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 
       32.88        70.13        43.04        11.61         6.02        34.36 
TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       40.24        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-6872 
        9.07        42.35        57.93        23.84        21.17        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE 
        4.01        41.85        20.45        11.54         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4225 
        7.82         2.27        11.05        13.38         6.15         4.80 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
       18.38        36.72        33.70        50.20        44.98        24.66 
TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4728 
       38.40        10.55        12.92         8.81        48.76        56.68 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
       32.81        52.14        12.99        20.55        14.33        27.58 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 
       73.61        46.32        12.39        11.54        11.84        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        50.07        23.90        47.44        28.04 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y 
        6.74        10.45        25.41        21.21        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
       21.50        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
       11.21         4.24        41.19        56.58         4.24        38.76 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       53.52        41.88        43.10        44.48        29.36        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 
       14.14        12.46        84.23        11.77        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        16.90        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
       10.22        11.34        11.64        12.46        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7385 
       47.18        40.93        31.96         9.17        26.17        32.78 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       47.01        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
       30.58        24.79         5.95        35.41        29.95       139.43 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
       17.95        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-5978 
       13.35        23.05        86.83        48.59        60.49         7.07 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6937 
       43.23        54.74        21.07        62.43         9.60        20.52 
TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 
        4.73        19.79        12.03         6.08        53.95        65.82 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 
       10.98         8.42        28.34        64.83       172.67        18.81 
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-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7252 
       71.21        10.75       130.88        31.36        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       11.87         2.10        18.41        17.85       210.97        89.33 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.08         0.07        14.89        56.48       156.49        54.94 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
        7.17        16.64        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
      159.65        35.47         1.05        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61        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        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
       51.12        13.25         2.53        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6ES 
       24.95        25.32        12.36        28.77        22.59        12.79 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I 
       37.58        40.04        41.59        37.18        21.63         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       31.13        18.94        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       13.38        15.16        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       27.48        14.66         0.36         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K 
       15.95        38.53        14.50        37.41         0.07         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI 
       14.37         7.96        30.05         1.84        12.62         7.13 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       29.92        51.25        10.85        19.00        75.55        18.97 
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        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 
        7.30        21.47         9.34        12.72        27.39        14.76 
TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       17.82        12.72        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JA 
       13.55        13.25        20.35        64.80        54.67        74.47 
TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW 
       17.95        18.05        13.94        20.75        32.65        17.03 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE 
                        22.03                         21.01 
[1] "0.4 - 153.9 (22.0)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.2"
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 11(4P16.3) MUTATED        13       25        30       107         6
  DEL PEAK 11(4P16.3) WILD-TYPE      14       51        52       145         6
                               vv
clus                            STAGE IVC
  DEL PEAK 11(4P16.3) MUTATED           1
  DEL PEAK 11(4P16.3) WILD-TYPE         0
D39V3, multiclass
           clus
vv          DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  STAGE I                            13                            14
  STAGE II                           25                            51
  STAGE III                          30                            52
  STAGE IVA                         107                           145
  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 11(4P16.3) MUTATED      21 46 44 75
  DEL PEAK 11(4P16.3) WILD-TYPE    29 91 56 98
D39V4, multiclass
       clus
vv      DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  T0+T1                          21                            29
  T2                             46                            91
  T3                             44                            56
  T4                             75                            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 11(4P16.3) MUTATED    69  28  73   4
  DEL PEAK 11(4P16.3) WILD-TYPE 110  40  95   4
D39V5, multiclass
    clus
vv   DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  N0                          69                           110
  N1                          28                            40
  N2                          73                            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"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED    66   1
  DEL PEAK 11(4P16.3) WILD-TYPE 124   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED     66    1
  DEL PEAK 11(4P16.3) WILD-TYPE  124    0
   clus
vv  DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  0                          66                           124
  1                           1                             0
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED    44 161
  DEL PEAK 11(4P16.3) WILD-TYPE  96 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED     44  161
  DEL PEAK 11(4P16.3) WILD-TYPE   96  221
        clus
vv       DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  FEMALE                          44                            96
  MALE                           161                           221
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED    59 123
  DEL PEAK 11(4P16.3) WILD-TYPE 103 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED     59  123
  DEL PEAK 11(4P16.3) WILD-TYPE  103  178
     clus
vv    DEL PEAK 11(4P16.3) MUTATED DEL PEAK 11(4P16.3) WILD-TYPE
  NO                           59                           103
  YES                         123                           178
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P16.3) MUTATED                                   199
  DEL PEAK 11(4P16.3) WILD-TYPE                                 312
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 11(4P16.3) MUTATED                                                   6
  DEL PEAK 11(4P16.3) WILD-TYPE                                                 4
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 11(4P16.3) MUTATED                                                           0
  DEL PEAK 11(4P16.3) WILD-TYPE                                                         1
D39V9, multiclass
                                                           clus
vv                                                          DEL PEAK 11(4P16.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               199
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 11(4P16.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 312
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, continuous
D39V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4P16.3) MUTATED                                  0     3
  DEL PEAK 11(4P16.3) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P16.3) MUTATED                          23   173
  DEL PEAK 11(4P16.3) WILD-TYPE                        25   273
D39V13, multiclass
                                  clus
vv                                 DEL PEAK 11(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 23
  WHITE                                                    173
                                  clus
vv                                 DEL PEAK 11(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P16.3) MUTATED     9 182
  DEL PEAK 11(4P16.3) WILD-TYPE  17 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P16.3) MUTATED      9  182
  DEL PEAK 11(4P16.3) WILD-TYPE   17  277
                        clus
vv                       DEL PEAK 11(4P16.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         182
                        clus
vv                       DEL PEAK 11(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           277
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 12(4P15.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4P15.2) MUTATED   114  94
  DEL PEAK 12(4P15.2) WILD-TYPE 187 125
  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE 
                          208                           312 
  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE 
                           94                           125 
$`DEL PEAK 12(4P15.2) MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6021 
        9.30        37.28        20.48         3.55        28.11         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-5323 
       52.08        11.08        35.05        32.48        24.39        48.20 
TCGA-CQ-7067 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       16.73        34.52         0.36        30.94        14.04        46.32 
TCGA-H7-A6C5 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
       21.11        15.19        13.64         9.07        26.50        23.74 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
       17.10        65.59        15.52        14.83        29.42        27.95 
TCGA-BA-A6DB TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
        7.10        20.48        16.41       105.90         9.14         4.41 
TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z 
       22.42        24.66        71.05        20.52        27.19         6.28 
TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
       12.69        55.86        38.04         4.67        56.68        26.86 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       57.11        45.83        13.05        42.02         8.58        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        8.32        16.21        56.94        50.07        30.67        48.00 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       19.07        34.13        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
       11.74        35.01        23.57        17.29        29.72         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6220 
       31.69        12.39        12.07         2.93        10.42        32.38 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4C9 
       46.95        13.25        14.99        64.87        77.56        23.24 
TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6474 TCGA-CR-6487 
       33.60        31.23        11.77        54.67        18.54         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 
       12.46        22.78        39.16        47.34        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 
        3.09        24.95        29.23         0.99        17.13        27.06 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       49.58         5.13        48.39        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6933 
       76.24        19.20       107.51        80.12         7.07        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
        2.14         9.70        20.52        21.90        26.43        11.24 
TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6956 TCGA-CV-6961 
      140.78        42.38        15.09        30.08         7.13         2.50 
TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7236 
        4.14       111.16        12.66         5.26        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7254 
       89.65        36.00        26.20        18.97        17.13        47.97 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 
       49.71        57.47        35.54         9.67        22.85        25.94 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
       34.09       100.57        16.27        84.49        19.76       153.86 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A465 TCGA-D6-6516 
        6.38        22.19        45.96         6.51         7.07        25.41 
TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
       23.05        17.72        12.36         7.63        24.95        13.94 
TCGA-D6-A74Q TCGA-DQ-7595 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A61W 
       23.34        39.12        32.71        20.25        24.95         0.46 
TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 
       15.06        28.47        27.48        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        37.71        11.84        37.41        33.57         6.25 
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        71.74        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        21.07        19.73        12.89 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T2-A6X0 
       14.76        12.20        15.32         8.32        15.91         7.10 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JD 
        3.12        13.25         2.83        49.51        44.65        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS TCGA-WA-A7GZ 
       55.43        29.46        22.36        20.55 

$`DEL PEAK 12(4P15.2) WILD-TYPE`
TCGA-BA-5559 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-A6V1 
       68.48        30.18        25.71        51.29         9.24        19.82 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 
       32.88        70.13        43.04        11.61         6.02        34.36 
TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       40.24        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       42.35        57.93        23.84        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       41.85        20.45        11.54         5.69        14.47         7.82 
TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4228 
        2.27        11.05        13.38         6.15         4.80        18.38 
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-A5HY TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4731 
       10.55        12.92         8.81        48.76        12.89        32.81 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
       52.14        12.99        20.55        14.33        27.58        73.61 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       46.32        12.39        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 
        8.52        52.08        23.90        47.44        28.04         6.74 
TCGA-CN-6988 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       10.45        25.41        21.21        22.32        16.57         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        62.37        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 
       41.19        56.58         4.24        38.76        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       43.10        44.48        29.36        29.49        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-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       36.99        16.90        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        46.85        32.65        44.25        30.58        24.79 
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 
      172.67        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        21.01       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        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        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-A6EN TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
       25.32        28.77        22.59        12.10        12.79        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       37.25        33.86        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       40.04        41.59        37.18        21.63         3.02        31.13 
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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       15.16        20.94        33.76        25.74        21.93        27.48 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        0.36         4.27         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       14.50         0.07         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF 
        1.84        12.62         7.13        29.92        51.25        10.85 
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-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
       21.07        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP 
       12.72        27.39         5.62        17.82        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 
        6.87        32.45        13.71        13.55        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JK 
       54.67        49.45        74.47        17.95        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.75        32.65        17.03        14.56        13.35        18.15 

  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE 
                       22.110                        20.975 
[1] "0.4 - 153.9 (22.1)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 12(4P15.2) MUTATED        13       28        30       105         6
  DEL PEAK 12(4P15.2) WILD-TYPE      14       48        52       147         6
                               vv
clus                            STAGE IVC
  DEL PEAK 12(4P15.2) MUTATED           0
  DEL PEAK 12(4P15.2) WILD-TYPE         1
D40V3, multiclass
           clus
vv          DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE
  STAGE I                            13                            14
  STAGE II                           28                            48
  STAGE III                          30                            52
  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 12(4P15.2) MUTATED      21  48  46  71
  DEL PEAK 12(4P15.2) WILD-TYPE    29  89  54 102
D40V4, multiclass
       clus
vv      DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE
  T0+T1                          21                            29
  T2                             48                            89
  T3                             46                            54
  T4                             71                           102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 12(4P15.2) MUTATED    70  26  73   5
  DEL PEAK 12(4P15.2) WILD-TYPE 109  42  95   3
D40V5, multiclass
    clus
vv   DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE
  N0                          70                           109
  N1                          26                            42
  N2                          73                            95
  N3                           5                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(4P15.2) MUTATED    66   0
  DEL PEAK 12(4P15.2) WILD-TYPE 124   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4P15.2) MUTATED     66    0
  DEL PEAK 12(4P15.2) WILD-TYPE  124    1
   clus
vv  DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE
  0                          66                           124
  1                           0                             1
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4P15.2) MUTATED    44 164
  DEL PEAK 12(4P15.2) WILD-TYPE  96 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4P15.2) MUTATED     44  164
  DEL PEAK 12(4P15.2) WILD-TYPE   96  218
        clus
vv       DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE
  FEMALE                          44                            96
  MALE                           164                           218
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4P15.2) MUTATED    58 124
  DEL PEAK 12(4P15.2) WILD-TYPE 104 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4P15.2) MUTATED     58  124
  DEL PEAK 12(4P15.2) WILD-TYPE  104  177
     clus
vv    DEL PEAK 12(4P15.2) MUTATED DEL PEAK 12(4P15.2) WILD-TYPE
  NO                           58                           104
  YES                         124                           177
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4P15.2) MUTATED                                   203
  DEL PEAK 12(4P15.2) WILD-TYPE                                 308
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 12(4P15.2) MUTATED                                                   5
  DEL PEAK 12(4P15.2) WILD-TYPE                                                 5
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 12(4P15.2) MUTATED                                                           0
  DEL PEAK 12(4P15.2) WILD-TYPE                                                         1
D40V9, multiclass
                                                           clus
vv                                                          DEL PEAK 12(4P15.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               203
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 12(4P15.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 308
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, continuous
D40V11, continuous
D40V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(4P15.2) MUTATED                                  0     3
  DEL PEAK 12(4P15.2) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4P15.2) MUTATED                          25   174
  DEL PEAK 12(4P15.2) WILD-TYPE                        23   272
D40V13, multiclass
                                  clus
vv                                 DEL PEAK 12(4P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    174
                                  clus
vv                                 DEL PEAK 12(4P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      272
[1] 4 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 12(4P15.2) MUTATED    10 185
  DEL PEAK 12(4P15.2) WILD-TYPE  16 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4P15.2) MUTATED     10  185
  DEL PEAK 12(4P15.2) WILD-TYPE   16  274
                        clus
vv                       DEL PEAK 12(4P15.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         185
                        clus
vv                       DEL PEAK 12(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           274
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 13(4Q21.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q21.3) MUTATED    88  68
  DEL PEAK 13(4Q21.3) WILD-TYPE 213 151
  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE 
                          156                           364 
  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE 
                           68                           151 
$`DEL PEAK 13(4Q21.3) MUTATED`
TCGA-BA-4075 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6997 TCGA-CQ-5323 
        9.30        28.11         9.07        11.08        32.48        48.20 
TCGA-CQ-7067 TCGA-CR-6472 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 
       16.73        34.52        30.94        14.04        46.32        21.11 
TCGA-HD-8634 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 
       12.66        48.03         3.35         9.07        17.10        14.83 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DI TCGA-BA-A6DL 
        4.01        29.42        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        57.11        20.55 
TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       45.83        71.31        50.07        30.67        48.00        19.07 
TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 
       34.13        32.22        38.89         3.68        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A6V7 
       25.41        23.57        29.72         7.40        12.39        19.53 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 
        4.24        32.38        56.58        14.99        64.87        77.56 
TCGA-CQ-A4C9 TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6484 TCGA-CR-6487 
       23.24        12.46        31.23        54.67        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        46.85         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       140.78 
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        49.71 
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-7592 TCGA-F7-A50G TCGA-F7-A50J 
        7.63        13.94        23.34        37.58        20.25        31.13 
TCGA-F7-A61S TCGA-HD-7831 TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
       18.94        21.93         3.65        37.41        33.57        13.68 
TCGA-IQ-A6SG TCGA-MT-A67G TCGA-MT-A7BN TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 
       19.04         6.25        15.42        71.74        47.01         2.04 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6VB TCGA-QK-A8ZA 
       21.21        23.15         7.30         9.34        21.07        12.20 
TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A719 
        8.32        15.91         7.10        13.71         3.12        54.67 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.95        24.30        55.43        20.75        17.03        20.55 

$`DEL PEAK 13(4Q21.3) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48         3.55        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 
       51.29         9.24        52.08        35.05        19.82        24.39 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 
       32.88        70.13        43.04        11.61         6.02         0.36 
TCGA-CX-7219 TCGA-DQ-7593 TCGA-HD-8635 TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 
       34.36        40.24        22.85         2.96        15.19        13.64 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA 
       15.52        21.17        12.62        41.85        20.45        11.54 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
        5.69        14.47         7.82         2.27        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         4.80        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HZ 
       33.70        50.20        44.98        66.28        38.40        27.19 
TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
       12.92         8.81        48.76        55.86         4.67        56.68 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 
       26.86        32.81        52.14        12.99        14.33        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       73.61        13.05        42.02        46.32         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-6013 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        56.94        23.90        47.44        28.04 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U 
        6.74        10.45        17.42        17.29        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6223 
       62.37        45.99        10.42        11.21        41.19        46.95 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       13.25         4.24        38.76        53.52        41.88        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 
       44.48        29.36        33.60        29.49        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-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        11.90        10.22        11.34 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       22.78        15.75        47.18        47.34        40.93        35.84 
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-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 
       47.01        27.06        12.89        49.58        30.02        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         5.95        35.41        29.95 
TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
      139.43        19.20        94.88        76.50        91.53        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-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
       43.23        21.07        62.43        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6943 TCGA-CV-6945 
        5.46         4.73        21.90        26.43        19.79        12.03 
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       172.67        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-7245 TCGA-CV-7248 
        4.73        89.65        36.00        31.36        26.20        17.13 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 
       95.34         4.96        11.87        47.97         2.10        18.41 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 
       57.47        17.85       210.97        89.33         0.46        22.85 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        0.07       100.57       156.49        54.94        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        21.01 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      159.65        35.47         1.05         6.51        88.87        48.20 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61        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        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       51.12        13.25        25.41         9.60         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EN 
       11.44        18.67        24.95        25.32        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       24.95        12.10        12.79        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        46.45        20.45        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W 
       37.18        32.71        21.63         3.02        24.95         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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 
       15.06        20.94        33.76        28.47        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         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        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H7 
       11.84         0.07         5.29        13.84        15.48        19.27 
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-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE 
        7.13        16.08        17.98        29.92        15.78        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 
       10.85        36.82        19.00        75.55        18.97        29.00 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
       12.99        16.01        13.15        21.07        21.47        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       27.39        19.73        12.89         5.62        14.76        17.82 
TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HI 
       15.32        12.72        16.96         6.87        32.45        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        20.35        64.80         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS 
       44.65        74.47        29.46        18.05        13.94        22.36 
TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        14.56        13.35        18.15 

  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE 
                       20.550                        21.355 
[1] "1.0 - 180.2 (20.6)" "0.1 - 211.0 (21.4)"
[1] "hr=" "1"  
D41V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 13(4Q21.3) MUTATED         9       21        33        68         2
  DEL PEAK 13(4Q21.3) WILD-TYPE      18       55        49       184        10
                               vv
clus                            STAGE IVC
  DEL PEAK 13(4Q21.3) MUTATED           0
  DEL PEAK 13(4Q21.3) WILD-TYPE         1
D41V3, multiclass
           clus
vv          DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE
  STAGE I                             9                            18
  STAGE II                           21                            55
  STAGE III                          33                            49
  STAGE IVA                          68                           184
  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(4Q21.3) MUTATED      16  42  39  40
  DEL PEAK 13(4Q21.3) WILD-TYPE    34  95  61 133
D41V4, multiclass
       clus
vv      DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE
  T0+T1                          16                            34
  T2                             42                            95
  T3                             39                            61
  T4                             40                           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 13(4Q21.3) MUTATED    50  22  50   2
  DEL PEAK 13(4Q21.3) WILD-TYPE 129  46 118   6
D41V5, multiclass
    clus
vv   DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE
  N0                          50                           129
  N1                          22                            46
  N2                          50                           118
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q21.3) MUTATED    50   0
  DEL PEAK 13(4Q21.3) WILD-TYPE 140   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q21.3) MUTATED     50    0
  DEL PEAK 13(4Q21.3) WILD-TYPE  140    1
   clus
vv  DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE
  0                          50                           140
  1                           0                             1
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q21.3) MUTATED    42 114
  DEL PEAK 13(4Q21.3) WILD-TYPE  98 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q21.3) MUTATED     42  114
  DEL PEAK 13(4Q21.3) WILD-TYPE   98  268
        clus
vv       DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE
  FEMALE                          42                            98
  MALE                           114                           268
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q21.3) MUTATED    45  96
  DEL PEAK 13(4Q21.3) WILD-TYPE 117 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q21.3) MUTATED     45   96
  DEL PEAK 13(4Q21.3) WILD-TYPE  117  205
     clus
vv    DEL PEAK 13(4Q21.3) MUTATED DEL PEAK 13(4Q21.3) WILD-TYPE
  NO                           45                           117
  YES                          96                           205
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q21.3) MUTATED                                   155
  DEL PEAK 13(4Q21.3) WILD-TYPE                                 356
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 13(4Q21.3) MUTATED                                                   1
  DEL PEAK 13(4Q21.3) WILD-TYPE                                                 9
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 13(4Q21.3) MUTATED                                                           0
  DEL PEAK 13(4Q21.3) WILD-TYPE                                                         1
D41V9, multiclass
                                                           clus
vv                                                          DEL PEAK 13(4Q21.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               155
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 13(4Q21.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 356
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, continuous
D41V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(4Q21.3) MUTATED                                  1     5
  DEL PEAK 13(4Q21.3) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q21.3) MUTATED                          17   128
  DEL PEAK 13(4Q21.3) WILD-TYPE                        31   318
D41V13, multiclass
                                  clus
vv                                 DEL PEAK 13(4Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    128
                                  clus
vv                                 DEL PEAK 13(4Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   31
  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"
D41V14, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q21.3) MUTATED    12 133
  DEL PEAK 13(4Q21.3) WILD-TYPE  14 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q21.3) MUTATED     12  133
  DEL PEAK 13(4Q21.3) WILD-TYPE   14  326
                        clus
vv                       DEL PEAK 13(4Q21.3) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         133
                        clus
vv                       DEL PEAK 13(4Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           326
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 14(4Q22.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(4Q22.1) MUTATED    92  77
  DEL PEAK 14(4Q22.1) WILD-TYPE 209 142
  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE 
                          169                           351 
  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE 
                           77                           142 
$`DEL PEAK 14(4Q22.1) MUTATED`
TCGA-BA-4075 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6997 TCGA-CQ-5323 
        9.30        28.11         9.07        11.08        32.48        48.20 
TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-DQ-5629 TCGA-DQ-7588 
       32.88        16.73        11.61        34.52        30.94        14.04 
TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 
       46.32        21.11        12.66         9.07        17.10        14.83 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DI TCGA-BA-A6DL 
        4.01        29.42        27.95         7.10        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 
       16.41         4.41        66.28        24.66        71.05        20.52 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 
       10.55         6.28        12.69        38.04        12.89        57.11 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 
       20.55        45.83        71.31        11.57        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 
       48.00        19.07        34.13         6.74        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
        3.68        11.74        35.01        25.41        23.57        29.72 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-6220 TCGA-CQ-6224 TCGA-CQ-6228 
        7.40        12.39        19.53        32.38        56.58        14.99 
TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 
       64.87        77.56        23.24        12.46        31.23        54.67 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
       11.64         7.69        12.46         9.27        39.16        47.34 
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-7392 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       46.85         5.13        48.39        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-6003 
       76.24        17.95       107.51        80.12        48.59        54.74 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
        9.60         9.70        20.52        11.24       140.78        12.03 
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-7245 TCGA-CV-7247 
        5.26        52.31        12.92        10.75        26.20        18.97 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7418 
       49.71        57.47        35.54         9.67        25.08        25.94 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7437 
       34.09        14.89         3.52        16.27       153.86        16.64 
TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A460 
       22.19       169.38        35.47         1.05        45.96        60.43 
TCGA-CV-A465 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
        7.07        18.84        25.41        23.05        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S 
        7.63        13.94        23.34        37.58        31.13        18.94 
TCGA-HD-7831 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
       21.93         3.65        37.71        11.84        37.41        33.57 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       19.04        15.48         6.25        15.42        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6VB 
       71.74        47.01         2.04        23.15         7.30        21.07 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N 
       14.76        12.20        15.91         7.10        13.71         3.12 
TCGA-UF-A719 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UP-A6WW 
       54.67        17.95        24.30        55.43        20.75        17.03 
TCGA-WA-A7GZ 
       20.55 

$`DEL PEAK 14(4Q22.1) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48         3.55        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 
       51.29         9.24        52.08        35.05        19.82        24.39 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7593 
       70.13        43.04         6.02         0.36        34.36        40.24 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 
       22.85        48.03         2.96         3.35        15.19        13.64 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
       26.50        23.74        42.35        57.93        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA 
       15.52        21.17        12.62        41.85        20.45        11.54 
TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
        5.69        14.47         7.82         2.27        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         4.80        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM 
       33.70        50.20        44.98        38.40        27.19        12.92 
TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
        8.81        48.76        55.86         4.67        56.68        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
       32.81        52.14        12.99        14.33        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
       13.05        42.02        46.32         8.58        12.39         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        52.08 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6988 TCGA-CN-6996 
       56.94        23.90        47.44        28.04        10.45        17.42 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       17.29        21.21        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 
       12.07         2.70        23.44        20.88        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 
       11.21         4.24        41.19        46.95        13.25         4.24 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       38.76        53.52        41.88        43.10        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
       33.60        29.49        14.14        84.23        11.77        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6492 
       16.90        11.90        10.22        11.34        22.78        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 
       49.58        30.02        32.65        44.25        30.58        24.79 
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       172.67        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        89.65        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        21.01       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        28.01 
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-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
       10.55        51.12        13.25         9.60         2.53        16.14 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EN 
       11.44        18.67        24.95        25.32        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       24.95        12.10        12.79        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        46.45        20.45        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V 
       37.18        32.71        21.63        20.25         3.02        24.95 
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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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        38.53        14.50 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 
        0.07         5.29        13.68        13.84        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI 
       14.37         7.96        30.05         1.84        12.62         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       16.08        29.92        51.25        10.85        36.82        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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.07        21.21        21.47         9.34        12.72        27.39 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
       19.73        12.89         5.62        17.82        15.32         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ 
       12.72        16.96         6.87        32.45        13.55        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       20.35        64.80         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       74.47        29.46        18.05        13.94        22.36        32.65 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE 
                        20.52                         21.47 
[1] "1.0 - 169.4 (20.5)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1.2"
D42V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 14(4Q22.1) MUTATED        10       22        34        77         2
  DEL PEAK 14(4Q22.1) WILD-TYPE      17       54        48       175        10
                               vv
clus                            STAGE IVC
  DEL PEAK 14(4Q22.1) MUTATED           0
  DEL PEAK 14(4Q22.1) WILD-TYPE         1
D42V3, multiclass
           clus
vv          DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE
  STAGE I                            10                            17
  STAGE II                           22                            54
  STAGE III                          34                            48
  STAGE IVA                          77                           175
  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 14(4Q22.1) MUTATED      16  44  40  50
  DEL PEAK 14(4Q22.1) WILD-TYPE    34  93  60 123
D42V4, multiclass
       clus
vv      DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE
  T0+T1                          16                            34
  T2                             44                            93
  T3                             40                            60
  T4                             50                           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 14(4Q22.1) MUTATED    55  24  55   2
  DEL PEAK 14(4Q22.1) WILD-TYPE 124  44 113   6
D42V5, multiclass
    clus
vv   DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE
  N0                          55                           124
  N1                          24                            44
  N2                          55                           113
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q22.1) MUTATED    52   0
  DEL PEAK 14(4Q22.1) WILD-TYPE 138   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q22.1) MUTATED     52    0
  DEL PEAK 14(4Q22.1) WILD-TYPE  138    1
   clus
vv  DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE
  0                          52                           138
  1                           0                             1
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q22.1) MUTATED    42 127
  DEL PEAK 14(4Q22.1) WILD-TYPE  98 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q22.1) MUTATED     42  127
  DEL PEAK 14(4Q22.1) WILD-TYPE   98  255
        clus
vv       DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE
  FEMALE                          42                            98
  MALE                           127                           255
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q22.1) MUTATED    47 101
  DEL PEAK 14(4Q22.1) WILD-TYPE 115 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q22.1) MUTATED     47  101
  DEL PEAK 14(4Q22.1) WILD-TYPE  115  200
     clus
vv    DEL PEAK 14(4Q22.1) MUTATED DEL PEAK 14(4Q22.1) WILD-TYPE
  NO                           47                           115
  YES                         101                           200
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q22.1) MUTATED                                   168
  DEL PEAK 14(4Q22.1) WILD-TYPE                                 343
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 14(4Q22.1) MUTATED                                                   1
  DEL PEAK 14(4Q22.1) WILD-TYPE                                                 9
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 14(4Q22.1) MUTATED                                                           0
  DEL PEAK 14(4Q22.1) WILD-TYPE                                                         1
D42V9, multiclass
                                                           clus
vv                                                          DEL PEAK 14(4Q22.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               168
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 14(4Q22.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 343
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, continuous
D42V11, continuous
D42V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(4Q22.1) MUTATED                                  1     5
  DEL PEAK 14(4Q22.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(4Q22.1) MUTATED                          19   138
  DEL PEAK 14(4Q22.1) WILD-TYPE                        29   308
D42V13, multiclass
                                  clus
vv                                 DEL PEAK 14(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    138
                                  clus
vv                                 DEL PEAK 14(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      308
[1] 4 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 14(4Q22.1) MUTATED    12 146
  DEL PEAK 14(4Q22.1) WILD-TYPE  14 313
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q22.1) MUTATED     12  146
  DEL PEAK 14(4Q22.1) WILD-TYPE   14  313
                        clus
vv                       DEL PEAK 14(4Q22.1) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         146
                        clus
vv                       DEL PEAK 14(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           313
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 15(4Q35.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(4Q35.2) MUTATED   120  92
  DEL PEAK 15(4Q35.2) WILD-TYPE 181 127
  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE 
                          212                           308 
  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE 
                           92                           127 
$`DEL PEAK 15(4Q35.2) MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-A4IG TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 
        9.30        20.48        28.11         9.24        35.05        32.48 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       16.73        11.61        34.52        34.36        30.94        14.04 
TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-BA-4078 
       46.32        21.11        12.66        22.85        48.03         9.07 
TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
       17.10        65.59        14.83        12.62         4.01        29.42 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-7871 
       27.95         7.10        11.05        16.41        66.28        24.66 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z 
       38.40        71.05        20.52        10.55        27.19         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4736 
       12.69        48.76        55.86        38.04        12.89        12.99 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 
       20.55        45.83        13.05        42.02        12.39        71.31 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       11.57         8.52        50.07        30.67        48.00        19.07 
TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 
       34.13        38.89         3.68        17.42        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
       25.41        23.57        29.72         7.40        31.69        12.39 
TCGA-CN-A6V7 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6225 
       19.53         2.93        70.45        62.37        32.38        13.25 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 
       14.99        64.87        77.56        23.24        31.23        54.67 
TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 
       18.54        11.64         7.69        12.46        47.18        39.16 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7380 
        3.45         3.09        24.95        29.23         0.99        19.92 
TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
       12.89        46.85         5.13         5.95        35.41        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-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5976 
       76.50        91.53        80.12        17.92        86.83        48.59 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 
        7.07        54.74         9.60        90.12         2.14         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6954 
        5.46        20.52        11.24       140.78        42.38        65.82 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        7.13         8.42         4.14       111.16        12.66         5.26 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 
       52.31        12.92        10.75        36.00        31.36        18.97 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7413 TCGA-CV-7414 
       17.13        47.97        49.71        35.54         9.67         0.46 
TCGA-CV-7416 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 
       25.08        34.09        56.48         3.52        16.27        19.76 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45U TCGA-CV-A45W 
      153.86        16.64         6.38       169.38        35.47        45.96 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CX-7086 TCGA-D6-6823 
       60.43         7.07         3.62        23.47        18.84        23.05 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
       17.72        12.36        28.77         7.63        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 
       12.10        12.79        23.34        18.02        37.58        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-HD-7229 
       21.63        20.25         3.02        31.13        18.94        33.76 
TCGA-HD-7831 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61H 
       21.93        13.84         4.27         3.65        37.71        37.41 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 
       33.57         5.29        13.68        19.27         6.25        16.08 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF 
       15.78        71.74        47.01        13.15        21.07        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
        7.30        21.47        21.07        12.89         5.62        12.20 
TCGA-QK-A8ZB TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A718 
       17.82        15.91        13.71         3.12        13.25        64.80 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-WA-A7GZ 
       20.75        20.55 

$`DEL PEAK 15(4Q35.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
       37.28        68.48         3.55        30.18        25.71        51.29 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
        9.07        52.08        11.08        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7593 
       32.88        70.13        43.04         6.02         0.36        40.24 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 
        2.96         3.35        15.19        13.64        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-7269 
       42.35        57.93        23.84        15.52        21.17        41.85 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       20.45        11.54         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       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
       44.98        12.92         8.81         4.67        56.68        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
       32.81        52.14        57.11        14.33        27.58        73.61 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       46.32         8.58         8.32        16.21        11.54        11.84 
TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       12.49        52.08        56.94        23.90        47.44        28.04 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63V 
        6.74        10.45        32.22        17.29        21.21        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       52.37        21.50        54.58        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
        4.24        41.19        46.95        56.58         4.24        38.76 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       53.52        41.88        43.10        44.48        29.36        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
       29.49        14.14        12.46        84.23        11.77        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       11.90        10.22        11.34        22.78        15.75         9.27 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       47.34        40.93        35.84        31.96         9.17        34.06 
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        49.58 
TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7402 
       30.02        32.65        44.25        30.58        24.79        29.95 
TCGA-CV-5430 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 
      139.43        19.20        94.88        13.35        23.05        60.49 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
       43.23        21.07        62.43         4.73        21.90        26.43 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        15.09        30.08         6.08        53.95 
TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 
       10.98        28.34         2.50        64.83       172.67        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-7245 TCGA-CV-7250 TCGA-CV-7252 
       77.16         4.73        89.65        26.20        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-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7424 
       89.33        22.85        25.94         0.07       100.57        14.89 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
      156.49        54.94        84.49         7.17        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
       21.01       180.16       159.65         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-A6JY 
       35.34         6.38        29.79         6.48        28.01        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.42        10.55        51.12        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-A6EN TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       24.95        25.32        22.59        58.45        37.25        33.86 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       46.45        20.45        40.04        39.12        41.59        37.18 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 
       13.38        15.16        15.06        20.94        28.47        25.74 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A6I0 
       27.48        27.48        14.66        22.03         0.36         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I 
       34.75        15.95        38.53        14.50        11.84         0.07 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.84        19.04        15.48        10.75        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 
       30.05         1.84        12.62        15.42         7.13        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-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 
       18.97         2.04        29.00        12.99        16.01        21.21 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-AA3J 
        9.34        12.72        27.39        19.73        14.76        15.32 
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-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.55        20.35        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 
       44.65        18.05        22.36        32.65        17.03        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE 
                         0.46                          0.07 
  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE 
                       20.535                        21.650 
[1] "0.5 - 169.4 (20.5)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 15(4Q35.2) MUTATED        11       25        44       101         6
  DEL PEAK 15(4Q35.2) WILD-TYPE      16       51        38       151         6
                               vv
clus                            STAGE IVC
  DEL PEAK 15(4Q35.2) MUTATED           1
  DEL PEAK 15(4Q35.2) WILD-TYPE         0
D43V3, multiclass
           clus
vv          DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE
  STAGE I                            11                            16
  STAGE II                           25                            51
  STAGE III                          44                            38
  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 15(4Q35.2) MUTATED      19 48 52 74
  DEL PEAK 15(4Q35.2) WILD-TYPE    31 89 48 99
D43V4, multiclass
       clus
vv      DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE
  T0+T1                          19                            31
  T2                             48                            89
  T3                             52                            48
  T4                             74                            99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 15(4Q35.2) MUTATED    71  34  68   3
  DEL PEAK 15(4Q35.2) WILD-TYPE 108  34 100   5
D43V5, multiclass
    clus
vv   DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE
  N0                          71                           108
  N1                          34                            34
  N2                          68                           100
  N3                           3                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q35.2) MUTATED    74   1
  DEL PEAK 15(4Q35.2) WILD-TYPE 116   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q35.2) MUTATED     74    1
  DEL PEAK 15(4Q35.2) WILD-TYPE  116    0
   clus
vv  DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE
  0                          74                           116
  1                           1                             0
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q35.2) MUTATED    66 147
  DEL PEAK 15(4Q35.2) WILD-TYPE  74 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q35.2) MUTATED     66  147
  DEL PEAK 15(4Q35.2) WILD-TYPE   74  235
        clus
vv       DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE
  FEMALE                          66                            74
  MALE                           147                           235
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q35.2) MUTATED    60 129
  DEL PEAK 15(4Q35.2) WILD-TYPE 102 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q35.2) MUTATED     60  129
  DEL PEAK 15(4Q35.2) WILD-TYPE  102  172
     clus
vv    DEL PEAK 15(4Q35.2) MUTATED DEL PEAK 15(4Q35.2) WILD-TYPE
  NO                           60                           102
  YES                         129                           172
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(4Q35.2) MUTATED                                   211
  DEL PEAK 15(4Q35.2) WILD-TYPE                                 300
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 15(4Q35.2) MUTATED                                                   2
  DEL PEAK 15(4Q35.2) WILD-TYPE                                                 8
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 15(4Q35.2) MUTATED                                                           0
  DEL PEAK 15(4Q35.2) WILD-TYPE                                                         1
D43V9, multiclass
                                                           clus
vv                                                          DEL PEAK 15(4Q35.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               211
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 15(4Q35.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 300
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
D43V11, continuous
D43V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(4Q35.2) MUTATED                                  1     4
  DEL PEAK 15(4Q35.2) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(4Q35.2) MUTATED                          24   177
  DEL PEAK 15(4Q35.2) WILD-TYPE                        24   269
D43V13, multiclass
                                  clus
vv                                 DEL PEAK 15(4Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                    177
                                  clus
vv                                 DEL PEAK 15(4Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   24
  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"
D43V14, binary
                               cls
clus                              0   1
  DEL PEAK 15(4Q35.2) MUTATED    10 188
  DEL PEAK 15(4Q35.2) WILD-TYPE  16 271
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(4Q35.2) MUTATED     10  188
  DEL PEAK 15(4Q35.2) WILD-TYPE   16  271
                        clus
vv                       DEL PEAK 15(4Q35.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         188
                        clus
vv                       DEL PEAK 15(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           271
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 16(5Q12.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(5Q12.1) MUTATED   122  93
  DEL PEAK 16(5Q12.1) WILD-TYPE 179 126
  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE 
                          215                           305 
  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE 
                           93                           126 
$`DEL PEAK 16(5Q12.1) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6024 TCGA-CN-6992 
        9.30         3.55        28.11        51.29        11.08        35.05 
TCGA-CN-6997 TCGA-CQ-7067 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 
       32.48        16.73         6.02         0.36        30.94        14.04 
TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5555 
       46.32        21.11        48.03        15.19         9.07        17.10 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH 
       15.52        14.83        12.62         4.01        41.85        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-4729 
       71.05        20.52        10.55         6.28        38.04        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 
       26.86        32.81        20.55        45.83        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
       46.32        71.31        11.84        50.07        30.67        48.00 
TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
       34.13        10.45        23.57        31.69        12.39        12.07 
TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
        2.93        62.37        10.42        56.58        13.25         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 
       38.76        64.87        53.52        41.88        77.56        23.24 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 
       29.49        31.23        11.77        18.54        16.90        12.46 
TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
       22.78         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        49.58 
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       172.67       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 
       49.71        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-7086 
       60.43         7.07        35.34        29.79        22.52        18.84 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5630 TCGA-DQ-5631 
       23.05        16.14        12.10        23.34        33.86        18.02 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61V 
       37.58        40.04        39.12        37.18        20.25        24.95 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
       28.47        27.48         6.90        11.84        37.41        33.57 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A7D7 
       13.84        19.04        15.48         1.84        15.42        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 
       15.78        71.74        10.85        47.01        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
       29.00        13.15        21.21         7.30        21.47        12.72 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
       21.07        19.73        14.76        12.20        17.82        15.32 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       15.91        13.71        54.67         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       44.65        74.47        17.95        24.30        55.43        29.46 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-KU-A66T 
       13.94        20.75        22.36        20.55        18.15 

$`DEL PEAK 16(5Q12.1) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 
       37.28        20.48        68.48        30.18        25.71         9.07 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
        9.24        52.08        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-7593 
       70.13        43.04        11.61        34.52        34.36        40.24 
TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 
       12.66        22.85         2.96         3.35        13.64        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 
       23.74        42.35        57.93        23.84        65.59        21.17 
TCGA-BA-A4IF TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4223 
       29.42         5.69         7.82         2.27        13.38       105.90 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.80        18.38        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       66.28        38.40        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 
       48.76        55.86         4.67        56.68        52.14        57.11 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 
       12.99        14.33        27.58        73.61         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-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       52.08        56.94        23.90        47.44        28.04        19.07 
TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
        6.74        32.22        38.89         3.68        17.42        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        17.29        29.72        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       22.32        16.57         4.41         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       19.53        52.37        21.50        54.58        70.45        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6228 
       11.21         4.24        41.19        32.38        46.95        14.99 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH 
       43.10        44.48        29.36        33.60        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-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-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        7.69        15.75        47.34        29.23         0.99        31.96 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5436 TCGA-CV-5439 
       24.79        35.41        29.95        48.39        19.20        17.95 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 
       76.50        91.53        17.92        23.05        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 
        9.60         2.14         9.70         5.46        20.52         4.73 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6951 
       21.90        11.24       140.78        19.79        12.03        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7099 
        6.08        53.95        10.98         2.50        64.83         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
        9.01         1.84        71.21       130.88         4.73        89.65 
TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7409 TCGA-CV-7410 
       18.97        95.34         4.96        11.87        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7422 TCGA-CV-7425 TCGA-CV-7427 
       89.33         9.67        22.85        34.09        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 
       54.94        84.49        19.76         7.17        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X 
       27.98        21.01       169.38       159.65         1.05         6.51 
TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       88.87        67.86         0.76        56.61        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        28.01         3.62        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       19.92        10.42        10.55        51.12        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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       17.72        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 
       13.94        12.79        58.45        37.25        46.45        20.45 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       41.59        32.71        21.63         3.02        31.13        18.94 
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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65        34.75        15.95        38.53        14.50        37.71 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
        0.07         5.29        13.68        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
        7.96        30.05        12.62         6.25         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 
       29.92        51.25        36.82        19.00        75.55        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 
       16.01        21.07        23.15         9.34        27.39        12.89 
TCGA-QK-A8Z8 TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        5.62         8.32        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A7JJ TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       18.05        32.65        17.03        14.56        13.35 

  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE 
                        21.80                         20.94 
[1] "0.1 - 180.2 (21.8)" "0.1 - 211.0 (20.9)"
[1] "hr=" "1"  
D44V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 16(5Q12.1) MUTATED         9       33        32       111         4
  DEL PEAK 16(5Q12.1) WILD-TYPE      18       43        50       141         8
                               vv
clus                            STAGE IVC
  DEL PEAK 16(5Q12.1) MUTATED           0
  DEL PEAK 16(5Q12.1) WILD-TYPE         1
D44V3, multiclass
           clus
vv          DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE
  STAGE I                             9                            18
  STAGE II                           33                            43
  STAGE III                          32                            50
  STAGE IVA                         111                           141
  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(5Q12.1) MUTATED      14 58 38 84
  DEL PEAK 16(5Q12.1) WILD-TYPE    36 79 62 89
D44V4, multiclass
       clus
vv      DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE
  T0+T1                          14                            36
  T2                             58                            79
  T3                             38                            62
  T4                             84                            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 16(5Q12.1) MUTATED    66  32  76   3
  DEL PEAK 16(5Q12.1) WILD-TYPE 113  36  92   5
D44V5, multiclass
    clus
vv   DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE
  N0                          66                           113
  N1                          32                            36
  N2                          76                            92
  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 16(5Q12.1) MUTATED    75   0
  DEL PEAK 16(5Q12.1) WILD-TYPE 115   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q12.1) MUTATED     75    0
  DEL PEAK 16(5Q12.1) WILD-TYPE  115    1
   clus
vv  DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE
  0                          75                           115
  1                           0                             1
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q12.1) MUTATED    47 168
  DEL PEAK 16(5Q12.1) WILD-TYPE  93 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q12.1) MUTATED     47  168
  DEL PEAK 16(5Q12.1) WILD-TYPE   93  214
        clus
vv       DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE
  FEMALE                          47                            93
  MALE                           168                           214
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q12.1) MUTATED    63 127
  DEL PEAK 16(5Q12.1) WILD-TYPE  99 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q12.1) MUTATED     63  127
  DEL PEAK 16(5Q12.1) WILD-TYPE   99  174
     clus
vv    DEL PEAK 16(5Q12.1) MUTATED DEL PEAK 16(5Q12.1) WILD-TYPE
  NO                           63                            99
  YES                         127                           174
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q12.1) MUTATED                                   210
  DEL PEAK 16(5Q12.1) WILD-TYPE                                 301
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 16(5Q12.1) MUTATED                                                   4
  DEL PEAK 16(5Q12.1) WILD-TYPE                                                 6
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 16(5Q12.1) MUTATED                                                           1
  DEL PEAK 16(5Q12.1) WILD-TYPE                                                         0
D44V9, multiclass
                                                           clus
vv                                                          DEL PEAK 16(5Q12.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               210
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          DEL PEAK 16(5Q12.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 301
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, continuous
D44V11, continuous
D44V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(5Q12.1) MUTATED                                  1     3
  DEL PEAK 16(5Q12.1) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(5Q12.1) MUTATED                          31   173
  DEL PEAK 16(5Q12.1) WILD-TYPE                        17   273
D44V13, multiclass
                                  clus
vv                                 DEL PEAK 16(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 31
  WHITE                                                    173
                                  clus
vv                                 DEL PEAK 16(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q12.1) MUTATED    14 178
  DEL PEAK 16(5Q12.1) WILD-TYPE  12 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q12.1) MUTATED     14  178
  DEL PEAK 16(5Q12.1) WILD-TYPE   12  281
                        clus
vv                       DEL PEAK 16(5Q12.1) MUTATED
  HISPANIC OR LATINO                              14
  NOT HISPANIC OR LATINO                         178
                        clus
vv                       DEL PEAK 16(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           281
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 17(5Q15) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(5Q15) MUTATED   128  97
  DEL PEAK 17(5Q15) WILD-TYPE 173 122
  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE 
                        225                         295 
  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE 
                         97                         122 
$`DEL PEAK 17(5Q15) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6024 
        9.30         3.55        28.11        51.29         9.07        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-7067 TCGA-CX-7082 TCGA-DQ-5629 
       35.05        32.48        24.39        16.73         0.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4078 
       14.04        46.32        21.11        48.03        15.19         9.07 
TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       17.10        15.52        14.83        12.62         4.01        41.85 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        27.95        11.54         7.10        14.47         7.82 
TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7863 
       11.05        16.41         6.15         9.14         4.41        33.70 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-C9-A47Z 
       66.28        24.66        71.05        20.52        10.55         6.28 
TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
       38.04        12.89        26.86        32.81        12.99        20.55 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 
       45.83        13.05        42.02        46.32        71.31        11.84 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6019 TCGA-CN-6988 
       50.07        30.67        48.00        23.90        34.13        10.45 
TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 
       23.57        31.69        12.39        12.07         2.93        10.42 
TCGA-CQ-5333 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       11.21        13.25         4.24        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI 
       41.88        77.56        23.24        29.49        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        22.78         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        49.58         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       172.67       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 
       49.71        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-7086 TCGA-D6-6823 TCGA-D6-6825 
       35.34        29.79        22.52        18.84        23.05        16.14 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        12.36        13.94        12.10        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
       33.86        18.02        37.58        40.04        39.12        37.18 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-HD-7753 TCGA-HD-7917 
        3.02        24.95         0.46        11.80        28.47        27.48 
TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
        6.90        11.84        37.41        13.84        19.04        15.48 
TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
        1.84        15.42        17.98        15.78        71.74        10.85 
TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 
       47.01        18.97         2.04        29.00        12.99        13.15 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
       21.21         7.30        21.47        12.72        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ 
       12.89        14.76        12.20        17.82        15.32        15.91 
TCGA-T3-A92M TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
       13.71        54.67         2.83        49.51        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        29.46        13.94 
TCGA-UF-A7JO TCGA-WA-A7GZ TCGA-KU-A66T 
       20.75        20.55        18.15 

$`DEL PEAK 17(5Q15) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 
       37.28        20.48        68.48        30.18        25.71         9.24 
TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
       52.08        19.82        48.20        32.88        70.13        43.04 
TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7593 TCGA-HD-8634 
       11.61        34.52         6.02        34.36        40.24        12.66 
TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 
       22.85         2.96         3.35        13.64        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-A4IF 
       42.35        57.93        23.84        65.59        21.17        29.42 
TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 
        5.69         2.27        13.38        20.48       105.90         4.80 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 
       18.38        22.42        36.72        50.20        44.98        38.40 
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        48.76        55.86 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4740 
        4.67        56.68        52.14        57.11        14.33        27.58 
TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
       73.61         8.58        12.39         8.32        16.21        11.54 
TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 
       11.57        12.49         8.52        52.08        56.94        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 
       28.04        19.07         6.74        32.22        38.89         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        11.74        35.01        25.41        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       21.21         7.40        22.32        16.57         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
       23.44        20.88        19.53        52.37        21.50        54.58 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       70.45        62.37        45.99         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       46.95        56.58        14.99        43.10        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       33.60        14.14        84.23        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
       58.42        50.01        39.52        36.99        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7373 TCGA-CR-7374 
       11.34        11.64         7.69        15.75        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        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5434 TCGA-CV-5436 
       30.58        24.79        35.41        29.95       108.95        19.20 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-6433 
       76.50        91.53        17.92        13.35        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       140.78        19.79        12.03 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7099 
        6.08        53.95        10.98         2.50        64.83         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
        9.01         1.84        71.21       130.88         4.73        89.65 
TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7406 TCGA-CV-7409 
       18.97        95.34         4.96        11.87        57.47        17.85 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7422 TCGA-CV-7423 
      210.97        89.33         9.67        22.85        34.09       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-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
       16.64        22.19        27.98        21.01       169.38       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
       35.47         1.05        88.87        67.86         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       15.25         5.98         6.38         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ 
       21.24        23.47        19.92        10.42        10.55        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
       13.25        25.41         9.60         2.53        11.44        18.67 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        17.72        28.77         7.63        22.59        24.95 
TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7596 TCGA-F7-8298 
       12.79        37.25        46.45        20.45        41.59        32.71 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-F7-A623 
       21.63        20.25        31.13        18.94        17.85        20.25 
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        20.94        33.76 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        14.66        22.03         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        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        37.71         0.07        33.57         5.29        13.68 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
       19.27        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 
        6.25         7.13        16.08        29.92        51.25        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6II 
       19.00        75.55        16.01        21.07        23.15         9.34 
TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       27.39         5.62         8.32        12.72        16.96         6.87 
TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
        7.10        32.45         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 
       64.80        18.05        22.36        32.65        17.03        14.56 
TCGA-KU-A66S 
       13.35 

  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE 
                     180.16                      210.97 
  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE 
                      20.75                       21.21 
[1] "0.1 - 180.2 (20.8)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D45V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 17(5Q15) MUTATED         9       34        35       116         4
  DEL PEAK 17(5Q15) WILD-TYPE      18       42        47       136         8
                             vv
clus                          STAGE IVC
  DEL PEAK 17(5Q15) MUTATED           0
  DEL PEAK 17(5Q15) WILD-TYPE         1
D45V3, multiclass
           clus
vv          DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE
  STAGE I                           9                          18
  STAGE II                         34                          42
  STAGE III                        35                          47
  STAGE IVA                       116                         136
  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(5Q15) MUTATED      14 60 41 88
  DEL PEAK 17(5Q15) WILD-TYPE    36 77 59 85
D45V4, multiclass
       clus
vv      DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE
  T0+T1                        14                          36
  T2                           60                          77
  T3                           41                          59
  T4                           88                          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 17(5Q15) MUTATED    73  32  76   3
  DEL PEAK 17(5Q15) WILD-TYPE 106  36  92   5
D45V5, multiclass
    clus
vv   DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE
  N0                        73                         106
  N1                        32                          36
  N2                        76                          92
  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 17(5Q15) MUTATED    83   0
  DEL PEAK 17(5Q15) WILD-TYPE 107   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(5Q15) MUTATED     83    0
  DEL PEAK 17(5Q15) WILD-TYPE  107    1
   clus
vv  DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE
  0                        83                         107
  1                         0                           1
[1] 2 2
[1] FALSE
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(5Q15) MUTATED    51 175
  DEL PEAK 17(5Q15) WILD-TYPE  89 207
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(5Q15) MUTATED     51  175
  DEL PEAK 17(5Q15) WILD-TYPE   89  207
        clus
vv       DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE
  FEMALE                        51                          89
  MALE                         175                         207
[1] 2 2
[1] FALSE
D45V8, binary
                             cls
clus                            0   1
  DEL PEAK 17(5Q15) MUTATED    68 132
  DEL PEAK 17(5Q15) WILD-TYPE  94 169
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(5Q15) MUTATED     68  132
  DEL PEAK 17(5Q15) WILD-TYPE   94  169
     clus
vv    DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE
  NO                         68                          94
  YES                       132                         169
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(5Q15) MUTATED                                   220
  DEL PEAK 17(5Q15) WILD-TYPE                                 291
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 17(5Q15) MUTATED                                                   5
  DEL PEAK 17(5Q15) WILD-TYPE                                                 5
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 17(5Q15) MUTATED                                                           1
  DEL PEAK 17(5Q15) WILD-TYPE                                                         0
D45V9, multiclass
                                                           clus
vv                                                          DEL PEAK 17(5Q15) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                             220
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                         1
                                                           clus
vv                                                          DEL PEAK 17(5Q15) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               291
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
D45V11, continuous
D45V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(5Q15) MUTATED                                  1     5
  DEL PEAK 17(5Q15) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(5Q15) MUTATED                          31   182
  DEL PEAK 17(5Q15) WILD-TYPE                        17   264
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 17(5Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               31
  WHITE                                                  182
                                  clus
vv                                 DEL PEAK 17(5Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                             cls
clus                            0   1
  DEL PEAK 17(5Q15) MUTATED    14 189
  DEL PEAK 17(5Q15) WILD-TYPE  12 270
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(5Q15) MUTATED     14  189
  DEL PEAK 17(5Q15) WILD-TYPE   12  270
                        clus
vv                       DEL PEAK 17(5Q15) MUTATED DEL PEAK 17(5Q15) WILD-TYPE
  HISPANIC OR LATINO                            14                          12
  NOT HISPANIC OR LATINO                       189                         270
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 18(5Q35.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(5Q35.3) MUTATED   115  83
  DEL PEAK 18(5Q35.3) WILD-TYPE 186 136
  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE 
                          198                           322 
  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE 
                           83                           136 
$`DEL PEAK 18(5Q35.3) MUTATED`
TCGA-BA-4075 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 
        9.30        28.11        51.29         9.07        11.08        35.05 
TCGA-CN-6997 TCGA-CQ-7067 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       32.48        16.73         0.36        30.94        14.04        46.32 
TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 
       48.03        15.19         9.07        17.10        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        41.85        20.45        27.95        11.54         7.10 
TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7862 
       14.47        11.05        16.41         6.15         9.14        36.72 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 
       50.20        66.28        71.05        20.52         6.28        38.04 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 
       12.89        26.86        32.81        20.55        45.83        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-6010 
       42.02        46.32        71.31        16.21        11.84        50.07 
TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 
       48.00        34.13        10.45        38.89        17.42        23.57 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6225 
       31.69        12.39        12.07         2.93        10.42        13.25 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 
        4.24        38.76        64.87        53.52        41.88        77.56 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 
       23.24        29.49        12.46        31.23        11.77        18.54 
TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
       16.90        12.46         9.27        47.18        39.16        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 
       35.84         3.45         3.09        24.95         0.99        34.06 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
       49.58         5.13         5.95        48.39        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5976 
      108.95        76.24       107.51        94.88        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-6940 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6956 
       26.43        11.24        15.09        30.08        65.82         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
        8.42        28.34       172.67       111.16        18.81         5.26 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
       52.31        21.80        10.75        36.00        31.36        26.20 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7414 TCGA-CV-7416 
       17.13        47.97        49.71        18.41         0.46        25.08 
TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7438 
        0.07        34.09        14.89         3.52       153.86         6.38 
TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A465 TCGA-CV-A6JE 
      180.16        45.96         6.51        48.20         7.07        35.34 
TCGA-CV-A6JU TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A6EO 
        3.62        18.84        23.05        11.44        24.95        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 
       13.94        12.10        23.34        33.86        18.02        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61V TCGA-F7-A622 
       40.04        39.12        37.18        20.25        24.95        11.80 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-IQ-A61G TCGA-IQ-A61H 
       28.47        25.74        27.48        14.66        11.84        37.41 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67D TCGA-MZ-A6I9 TCGA-MZ-A7D7 
       13.84        19.04        15.48         1.84        16.08        17.98 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T5 
       15.78        71.74        10.85        47.01        18.97        29.00 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
       21.21         7.30        21.47        12.72        21.07        19.73 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A719 
       12.89        14.76        15.32        15.91        13.25        54.67 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       49.51        49.45        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-WA-A7GZ TCGA-KU-A66T 
       55.43        29.46        18.05        20.75        20.55        18.15 

$`DEL PEAK 18(5Q35.3) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48         3.55        30.18        25.71 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
        9.24        52.08        19.82        24.39        48.20        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 
       70.13        43.04        11.61        34.52         6.02        34.36 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J 
       40.24        21.11        12.66        22.85         2.96         3.35 
TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
       13.64        26.50        23.74        42.35        57.93        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DD TCGA-BA-A6DF 
       65.59        15.52        21.17        29.42         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       105.90         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
       18.38        22.42        33.70        44.98        24.66        38.40 
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        48.76 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       55.86         4.67        56.68        52.14        57.11        12.99 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
       14.33        27.58        73.61         8.58        12.39         8.32 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
       11.54        11.57        12.49         8.52        52.08        56.94 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 
       30.67        23.90        47.44        28.04        19.07         6.74 
TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       32.22         3.68        11.74        35.01        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       29.72        21.21         7.40        22.32        16.57         4.41 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        62.37        45.99        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7071 
       41.19        32.38        46.95        56.58        14.99        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 
       44.48        29.36        33.60        14.14        84.23        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-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        22.78 
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        46.85        32.65        44.25        30.58        24.79 
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       140.78        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        89.65        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        21.01       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 
       28.01        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       10.55        51.12        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        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7590 
        7.63        22.59        12.79        58.45        37.25        46.45 
TCGA-DQ-7591 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
       20.45        41.59        32.71        21.63         3.02        31.13 
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-A76A TCGA-HD-7229 TCGA-HD-7831 TCGA-HD-7832 
       15.16        15.06        20.94        33.76        21.93        27.48 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         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-A61I 
       34.75        15.95        38.53        14.50        37.71         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57         5.29        13.68        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        7.96        30.05        12.62         6.25        15.42         7.13 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
       29.92        51.25        36.82        19.00        75.55         2.04 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6II 
       12.99        16.01        13.15        21.07        23.15         9.34 
TCGA-QK-A6V9 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO 
       27.39         5.62        12.20        17.82         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       16.96         6.87         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A7JK TCGA-UF-A7JS 
       13.55        20.35        64.80         2.83        13.94        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        17.03        14.56        13.35 

  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE 
                        21.34                         21.07 
[1] "0.1 - 180.2 (21.3)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D46V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 18(5Q35.3) MUTATED         8       28        36        99         4
  DEL PEAK 18(5Q35.3) WILD-TYPE      19       48        46       153         8
                               vv
clus                            STAGE IVC
  DEL PEAK 18(5Q35.3) MUTATED           0
  DEL PEAK 18(5Q35.3) WILD-TYPE         1
D46V3, multiclass
           clus
vv          DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE
  STAGE I                             8                            19
  STAGE II                           28                            48
  STAGE III                          36                            46
  STAGE IVA                          99                           153
  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 18(5Q35.3) MUTATED      11  54  42  72
  DEL PEAK 18(5Q35.3) WILD-TYPE    39  83  58 101
D46V4, multiclass
       clus
vv      DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE
  T0+T1                          11                            39
  T2                             54                            83
  T3                             42                            58
  T4                             72                           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 18(5Q35.3) MUTATED    66  30  67   2
  DEL PEAK 18(5Q35.3) WILD-TYPE 113  38 101   6
D46V5, multiclass
    clus
vv   DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE
  N0                          66                           113
  N1                          30                            38
  N2                          67                           101
  N3                           2                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(5Q35.3) MUTATED    75   0
  DEL PEAK 18(5Q35.3) WILD-TYPE 115   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(5Q35.3) MUTATED     75    0
  DEL PEAK 18(5Q35.3) WILD-TYPE  115    1
   clus
vv  DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE
  0                          75                           115
  1                           0                             1
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(5Q35.3) MUTATED    47 152
  DEL PEAK 18(5Q35.3) WILD-TYPE  93 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(5Q35.3) MUTATED     47  152
  DEL PEAK 18(5Q35.3) WILD-TYPE   93  230
        clus
vv       DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE
  FEMALE                          47                            93
  MALE                           152                           230
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(5Q35.3) MUTATED    59 119
  DEL PEAK 18(5Q35.3) WILD-TYPE 103 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(5Q35.3) MUTATED     59  119
  DEL PEAK 18(5Q35.3) WILD-TYPE  103  182
     clus
vv    DEL PEAK 18(5Q35.3) MUTATED DEL PEAK 18(5Q35.3) WILD-TYPE
  NO                           59                           103
  YES                         119                           182
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(5Q35.3) MUTATED                                   193
  DEL PEAK 18(5Q35.3) WILD-TYPE                                 318
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 18(5Q35.3) MUTATED                                                   5
  DEL PEAK 18(5Q35.3) WILD-TYPE                                                 5
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 18(5Q35.3) MUTATED                                                           1
  DEL PEAK 18(5Q35.3) WILD-TYPE                                                         0
D46V9, multiclass
                                                           clus
vv                                                          DEL PEAK 18(5Q35.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               193
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          DEL PEAK 18(5Q35.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 318
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, continuous
D46V11, continuous
D46V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(5Q35.3) MUTATED                                  1     4
  DEL PEAK 18(5Q35.3) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(5Q35.3) MUTATED                          25   162
  DEL PEAK 18(5Q35.3) WILD-TYPE                        23   284
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 18(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    162
                                  clus
vv                                 DEL PEAK 18(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      284
[1] 4 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 18(5Q35.3) MUTATED    12 168
  DEL PEAK 18(5Q35.3) WILD-TYPE  14 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(5Q35.3) MUTATED     12  168
  DEL PEAK 18(5Q35.3) WILD-TYPE   14  291
                        clus
vv                       DEL PEAK 18(5Q35.3) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                         168
                        clus
vv                       DEL PEAK 18(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           291
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 19(6P25.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(6P25.3) MUTATED    49  47
  DEL PEAK 19(6P25.3) WILD-TYPE 252 172
  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE 
                           96                           424 
  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE 
                           47                           172 
$`DEL PEAK 19(6P25.3) MUTATED`
TCGA-BA-5559 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6997 TCGA-CQ-6221 TCGA-CR-6478 
       68.48         9.24        11.08        32.48        32.88         6.02 
TCGA-DQ-7589 TCGA-4P-AA8J TCGA-BA-5152 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7862 
       46.32         3.35        42.35         4.80         4.41        36.72 
TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4740 
       10.55        55.86        38.04        56.68        57.11        27.58 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6989 
       12.39        16.21         8.52        50.07        47.44        32.22 
TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A640 TCGA-CN-A641 
       38.89        25.41        17.29         7.40         4.41        12.07 
TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI 
       19.53        10.42        46.95        23.24        33.60        31.23 
TCGA-CR-6473 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7371 TCGA-CR-7373 
       36.99        12.46         9.27        39.16         3.09        29.23 
TCGA-CR-7388 TCGA-CR-7399 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
       27.06         5.95       129.21       108.95        76.24        19.20 
TCGA-CV-5440 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6934 TCGA-CV-6940 
      107.51        91.53        80.12         7.07         2.14        26.43 
TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7247 
       12.03        28.34         4.14        18.81         5.26        18.97 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7416 TCGA-CV-7418 
       17.13        11.87        47.97        18.41        25.08        25.94 
TCGA-CV-7430 TCGA-CV-A465 TCGA-CV-A6JT TCGA-CV-A6JY TCGA-D6-6823 TCGA-D6-6826 
       16.27         7.07        28.01        21.24        23.05        11.44 
TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7591 TCGA-F7-A50I TCGA-F7-A623 
       12.10        23.34        58.45        20.45         3.02        20.25 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-A61I TCGA-MT-A67G 
       28.47        27.48        14.66         3.65         0.07         6.25 
TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T8 
       15.42        17.98        15.78        71.74        19.00        13.15 
TCGA-QK-A8ZA TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7JJ TCGA-UP-A6WW 
       12.20         3.12         2.83        49.45        18.05        17.03 

$`DEL PEAK 19(6P25.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-A6V1 
       25.71        51.29         9.07        52.08        35.05        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 
       24.39        48.20        70.13        16.73        43.04        11.61 
TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 
       34.52         0.36        34.36        30.94        14.04        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 
       21.11        12.66        22.85        48.03         2.96        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 
       13.64         9.07        26.50        23.74        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       23.84        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        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-4224 
       13.38        20.48        16.41         6.15       105.90         9.14 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        22.42        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM 
       24.66        38.40        71.05        20.52        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 
        8.81         6.28        12.69        48.76         4.67        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.81        52.14        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       45.83        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       71.31         8.32        11.54        11.84        11.57        12.49 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6017 
       52.08        56.94        30.67        48.00        23.90        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6995 TCGA-CN-6996 
       19.07        34.13         6.74        10.45         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        23.57        29.72        21.21        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       22.32        12.39        16.57         2.70        23.44        20.88 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6224 
       45.99        11.21         4.24        41.19        32.38        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CE 
       41.88        43.10        77.56        44.48        29.36        29.49 
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-6470 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6477 
       26.27        58.42        50.01        39.52        18.54        16.90 
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        22.78 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       15.75        47.18        47.34        40.93        35.84         3.45 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       24.95         0.99        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 
       26.17        17.13        32.78        47.01        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.13        35.41        29.95        48.39       139.43        17.16 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       17.95        94.88        76.50        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-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60        90.12         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
        4.73        21.90        11.24       140.78        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-6959 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        7.13         8.42         2.50        64.83       172.67       111.16 
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-7250 TCGA-CV-7252 
       89.65        36.00        31.36        26.20        95.34         4.96 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        49.71        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 
       89.33         9.67         0.46        22.85         0.07        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-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        21.01       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-A468 TCGA-CV-A6JD 
       60.43        67.86         0.76        56.61        15.25         5.98 
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-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
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-A6EM 
       24.95        25.32        17.72        12.36        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 
       22.59        24.95        13.94        12.79        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       18.02        46.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
       37.18        32.71        21.63        20.25        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
       27.48        22.03         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        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.41        33.57         5.29        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       15.48        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
        1.84        12.62         7.13        16.08        29.92        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       10.85        36.82        47.01        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        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
       19.73        12.89         5.62        14.76        17.82        15.32 
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-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
       54.67        49.51        44.65        74.47        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        29.46        13.94        20.75        22.36        32.65 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       20.55        14.56        13.35        18.15 

  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE 
                       129.21                        210.97 
  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE 
                        19.10                         21.34 
[1] "0.1 - 129.2 (19.1)" "0.1 - 211.0 (21.3)"
[1] "hr=" "1.3"
D47V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 19(6P25.3) MUTATED         2       10        13        58         2
  DEL PEAK 19(6P25.3) WILD-TYPE      25       66        69       194        10
                               vv
clus                            STAGE IVC
  DEL PEAK 19(6P25.3) MUTATED           0
  DEL PEAK 19(6P25.3) WILD-TYPE         1
D47V3, multiclass
           clus
vv          DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE
  STAGE I                             2                            25
  STAGE II                           10                            66
  STAGE III                          13                            69
  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 19(6P25.3) MUTATED       5  20  22  39
  DEL PEAK 19(6P25.3) WILD-TYPE    45 117  78 134
D47V4, multiclass
       clus
vv      DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE
  T0+T1                           5                            45
  T2                             20                           117
  T3                             22                            78
  T4                             39                           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 19(6P25.3) MUTATED    29  11  37   1
  DEL PEAK 19(6P25.3) WILD-TYPE 150  57 131   7
D47V5, multiclass
    clus
vv   DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE
  N0                          29                           150
  N1                          11                            57
  N2                          37                           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"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 19(6P25.3) MUTATED    27   0
  DEL PEAK 19(6P25.3) WILD-TYPE 163   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6P25.3) MUTATED     27    0
  DEL PEAK 19(6P25.3) WILD-TYPE  163    1
   clus
vv  DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE
  0                          27                           163
  1                           0                             1
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(6P25.3) MUTATED    19  77
  DEL PEAK 19(6P25.3) WILD-TYPE 121 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6P25.3) MUTATED     19   77
  DEL PEAK 19(6P25.3) WILD-TYPE  121  305
        clus
vv       DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE
  FEMALE                          19                           121
  MALE                            77                           305
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(6P25.3) MUTATED    28  54
  DEL PEAK 19(6P25.3) WILD-TYPE 134 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6P25.3) MUTATED     28   54
  DEL PEAK 19(6P25.3) WILD-TYPE  134  247
     clus
vv    DEL PEAK 19(6P25.3) MUTATED DEL PEAK 19(6P25.3) WILD-TYPE
  NO                           28                           134
  YES                          54                           247
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(6P25.3) MUTATED                                    94
  DEL PEAK 19(6P25.3) WILD-TYPE                                 417
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 19(6P25.3) MUTATED                                                   2
  DEL PEAK 19(6P25.3) WILD-TYPE                                                 8
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 19(6P25.3) MUTATED                                                           0
  DEL PEAK 19(6P25.3) WILD-TYPE                                                         1
D47V9, multiclass
                                                           clus
vv                                                          DEL PEAK 19(6P25.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                94
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 19(6P25.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 417
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
D47V11, continuous
D47V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(6P25.3) MUTATED                                  0     0
  DEL PEAK 19(6P25.3) WILD-TYPE                                2    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(6P25.3) MUTATED                          15    76
  DEL PEAK 19(6P25.3) WILD-TYPE                        33   370
D47V13, multiclass
                                  clus
vv                                 DEL PEAK 19(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     76
                                  clus
vv                                 DEL PEAK 19(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                               cls
clus                              0   1
  DEL PEAK 19(6P25.3) MUTATED     5  81
  DEL PEAK 19(6P25.3) WILD-TYPE  21 378
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(6P25.3) MUTATED      5   81
  DEL PEAK 19(6P25.3) WILD-TYPE   21  378
                        clus
vv                       DEL PEAK 19(6P25.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       DEL PEAK 19(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           378
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 20(7Q31.1) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(7Q31.1) MUTATED    41  35
  DEL PEAK 20(7Q31.1) WILD-TYPE 260 184
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           76                           444 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                           35                           184 
$`DEL PEAK 20(7Q31.1) MUTATED`
TCGA-BA-5559 TCGA-CN-A6V3 TCGA-CX-7082 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 
       68.48        24.39         0.36        15.19        13.64        26.50 
TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-A4IH TCGA-BA-A6DE TCGA-BB-7861 
       42.35        15.52        12.62        20.45        14.47        22.42 
TCGA-BB-7872 TCGA-BB-A5HY TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4730 TCGA-CN-4731 
       38.40        10.55         6.28        12.69        26.86        32.81 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6018 
       57.11        20.55        12.39        56.94        30.67        19.07 
TCGA-CN-6988 TCGA-CN-6998 TCGA-CN-A49B TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CR-5247 
       10.45        11.74        29.72        41.19        32.38        11.77 
TCGA-CR-6474 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7398 
       18.54        39.16        47.34        40.93         0.99         5.13 
TCGA-CR-7399 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6954 
        5.95        80.12        86.83        54.74        90.12        65.82 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7415 TCGA-CV-7429 
       28.34         2.50       111.16        10.75        22.85         3.52 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A6JE 
       19.76       153.86         6.38        22.19        35.47        35.34 
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-HD-7831 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A6SH TCGA-KU-A6H7 
       21.93        14.50        11.84        37.41        15.48        19.27 
TCGA-MZ-A5BI TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A8Z9 
        7.13        51.25        47.01         2.04        21.07        14.76 
TCGA-QK-A8ZB TCGA-T3-A92M TCGA-UF-A7JK TCGA-KU-A66T 
       17.82        13.71        13.94        18.15 

$`DEL PEAK 20(7Q31.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       35.05        32.48        19.82        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 
       16.73        43.04        11.61        34.52         6.02        34.36 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       30.94        14.04        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5151 
       22.85        48.03         2.96         3.35         9.07        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
       57.93        17.10        23.84        65.59        21.17        14.83 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        41.85        29.42        27.95        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
        5.69         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       105.90         9.14         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        36.72        33.70        50.20        44.98        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       24.66        71.05        20.52        27.19        12.92         8.81 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       48.76        55.86        38.04         4.67        56.68        12.89 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       52.14        12.99        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       13.05        42.02        46.32         8.58        71.31         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-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
       52.08        50.07        48.00        23.90        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       34.13         6.74        32.22        38.89         3.68        17.42 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
       35.01        25.41        23.57        17.29        21.21         7.40 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       31.69        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        2.93        54.58        70.45        62.37        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
       11.21         4.24        46.95        56.58        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
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-6477 
       26.27        58.42        50.01        39.52        36.99        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-7369 TCGA-CR-7370 
       22.78        15.75         9.27        47.18        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-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        26.17        17.13        32.78        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
       30.58        24.79        35.41        29.95        48.39       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-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
      107.51        94.88        76.50        91.53        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       23.05        48.59        60.49         7.07        43.23        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-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        4.73        21.90        26.43        11.24       140.78        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-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       10.98         7.13         8.42         4.14        64.83       172.67 
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-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 
       52.31        12.92        21.80        71.21       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        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 
       49.71        18.41        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         9.67         0.46        25.08        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       34.09       100.57        14.89        56.48       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P 
       16.27        84.49         7.17        16.64        27.98        21.01 
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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
        7.07        15.25         5.98         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
       28.01         3.62        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
        9.60         2.53        16.14        18.67        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP 
       17.72        12.36        28.77        22.59        24.95        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        46.45        20.45        37.58        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       41.59        37.18        32.71         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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        38.53 
TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.71         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.04        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       12.62         6.25        15.42        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
       15.78        71.74        10.85        36.82        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 
       18.97        29.00        12.99        16.01        13.15        21.21 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       23.15         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J 
       21.07        19.73        12.89         5.62        12.20        15.32 
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-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JO 
       17.95        24.30        55.43        29.46        18.05        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 

  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE 
                        20.35                         21.21 
[1] "0.4 - 153.9 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.2"
D48V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 20(7Q31.1) MUTATED         3        9        14        42         0
  DEL PEAK 20(7Q31.1) WILD-TYPE      24       67        68       210        12
                               vv
clus                            STAGE IVC
  DEL PEAK 20(7Q31.1) MUTATED           0
  DEL PEAK 20(7Q31.1) WILD-TYPE         1
D48V3, multiclass
           clus
vv          DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  STAGE I                             3                            24
  STAGE II                            9                            67
  STAGE III                          14                            68
  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 20(7Q31.1) MUTATED       5  23  15  26
  DEL PEAK 20(7Q31.1) WILD-TYPE    45 114  85 147
D48V4, multiclass
       clus
vv      DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  T0+T1                           5                            45
  T2                             23                           114
  T3                             15                            85
  T4                             26                           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 20(7Q31.1) MUTATED    18  17  29   0
  DEL PEAK 20(7Q31.1) WILD-TYPE 161  51 139   8
D48V5, multiclass
    clus
vv   DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  N0                          18                           161
  N1                          17                            51
  N2                          29                           139
  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 20(7Q31.1) MUTATED    27   0
  DEL PEAK 20(7Q31.1) WILD-TYPE 163   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     27    0
  DEL PEAK 20(7Q31.1) WILD-TYPE  163    1
   clus
vv  DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  0                          27                           163
  1                           0                             1
[1] 2 2
[1] FALSE
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED    20  57
  DEL PEAK 20(7Q31.1) WILD-TYPE 120 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     20   57
  DEL PEAK 20(7Q31.1) WILD-TYPE  120  325
        clus
vv       DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  FEMALE                          20                           120
  MALE                            57                           325
[1] 2 2
[1] FALSE
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED    23  49
  DEL PEAK 20(7Q31.1) WILD-TYPE 139 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED     23   49
  DEL PEAK 20(7Q31.1) WILD-TYPE  139  252
     clus
vv    DEL PEAK 20(7Q31.1) MUTATED DEL PEAK 20(7Q31.1) WILD-TYPE
  NO                           23                           139
  YES                          49                           252
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q31.1) MUTATED                                    75
  DEL PEAK 20(7Q31.1) WILD-TYPE                                 436
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 20(7Q31.1) MUTATED                                                   2
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                 8
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 20(7Q31.1) MUTATED                                                           0
  DEL PEAK 20(7Q31.1) WILD-TYPE                                                         1
D48V9, multiclass
                                                           clus
vv                                                          DEL PEAK 20(7Q31.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                75
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 20(7Q31.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 436
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, continuous
D48V11, continuous
D48V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(7Q31.1) MUTATED                                  0     3
  DEL PEAK 20(7Q31.1) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(7Q31.1) MUTATED                           9    63
  DEL PEAK 20(7Q31.1) WILD-TYPE                        39   383
D48V13, multiclass
                                  clus
vv                                 DEL PEAK 20(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK 20(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   39
  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"
D48V14, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q31.1) MUTATED     3  70
  DEL PEAK 20(7Q31.1) WILD-TYPE  23 389
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q31.1) MUTATED      3   70
  DEL PEAK 20(7Q31.1) WILD-TYPE   23  389
                        clus
vv                       DEL PEAK 20(7Q31.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       DEL PEAK 20(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                23
  NOT HISPANIC OR LATINO                           389
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 21(7Q36.1) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(7Q36.1) MUTATED    70  61
  DEL PEAK 21(7Q36.1) WILD-TYPE 231 158
  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE 
                          131                           389 
  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE 
                           61                           158 
$`DEL PEAK 21(7Q36.1) MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-7067 
       68.48         3.55        28.11        32.48        32.88        16.73 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-BA-4074 
       11.61         6.02         0.36        34.36        14.04        15.19 
TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-6868 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DE 
       13.64        42.35        15.52        41.85        20.45        14.47 
TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7863 TCGA-BB-7872 TCGA-BB-A6UM TCGA-CN-4729 
       11.05        16.41        33.70        38.40        12.92        12.89 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       26.86        32.81        57.11        12.99        20.55        14.33 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 
       42.02         8.58        12.39         8.32        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6995 
       48.00        23.90        47.44        19.07        10.45         3.68 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
       11.74        23.57        29.72        31.69        12.39        16.57 
TCGA-CQ-5326 TCGA-CQ-5331 TCGA-CQ-6220 TCGA-CQ-6228 TCGA-CQ-A4CB TCGA-CR-5247 
        2.93        45.99        32.38        14.99        29.36        11.77 
TCGA-CR-6474 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7374 
       18.54        22.78        39.16        40.93        35.84         0.99 
TCGA-CR-7385 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6441 
       32.78         5.13        17.16        80.12        54.74         9.60 
TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6960 
       90.12         9.70        11.24        42.38        65.82        28.34 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7409 
        2.50       111.16        10.75        18.97        47.97        17.85 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7433 
        9.67         0.46        22.85        14.89         3.52        19.76 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45U TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JU 
      153.86         6.38        35.47        35.34         6.38         3.62 
TCGA-CV-A6K1 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ 
       22.52        23.05        11.44         7.63        24.95        12.10 
TCGA-DQ-7594 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 
       40.04        21.63        20.25         0.46        11.80        20.25 
TCGA-H7-8502 TCGA-HD-7831 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7632 TCGA-IQ-A61H 
       15.06        21.93         3.65        34.75        14.50        37.41 
TCGA-IQ-A61J TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67A TCGA-MZ-A5BI 
       33.57        15.48        19.27        14.37        30.05         7.13 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       51.25        47.01         2.04        13.15        14.76        17.82 
TCGA-QK-AA3J TCGA-T3-A92M TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A7JA 
       15.32        13.71        13.25        20.35        64.80        74.47 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-KU-A66T 
       20.75        22.36        32.65        20.55        18.15 

$`DEL PEAK 21(7Q36.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 
        9.30        37.28        20.48        30.18        25.71        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A6V1 
        9.07         9.24        52.08        11.08        35.05        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-DQ-5629 
       24.39        48.20        70.13        43.04        34.52        30.94 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       46.32        40.24        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
        2.96         3.35         9.07        26.50        23.74        57.93 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       17.10        23.84        65.59        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
        4.01        29.42        27.95        11.54         7.10         5.69 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        13.38        20.48         6.15       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        9.14         4.80         4.41        18.38        22.42        36.72 
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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
       10.55        27.19         8.81         6.28        12.69        48.76 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4739 
       55.86        38.04         4.67        56.68        52.14        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5364 
       27.58        73.61        13.05        46.32        71.31        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        52.08 
TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 
       50.07        28.04        34.13         6.74        32.22        38.89 
TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
       17.42        35.01        25.41        17.29        21.21         7.40 
TCGA-CN-A63V TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       22.32         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       19.53        52.37        21.50        54.58        70.45        62.37 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
       10.42        11.21         4.24        41.19        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
       13.25         4.24        38.76        64.87        53.52        41.88 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.10        77.56        44.48        23.24        33.60        29.49 
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-6477 
       26.27        58.42        50.01        39.52        36.99        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-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 
       15.75         9.27        47.18        47.34         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-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       26.17        17.13        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.95        35.41        29.95        48.39       139.43       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-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-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
       48.59        60.49         7.07        43.23        21.07        62.43 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        2.14         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        12.03        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 
       53.95        10.98         7.13         8.42         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
      172.67        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-7183 
        1.84        52.31        12.92        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        89.65        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        49.71 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7416 
       18.41        57.47        35.54       210.97        89.33        25.08 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 
       25.94         0.07        34.09       100.57        56.48       156.49 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 
       54.94        16.27        84.49         7.17        16.64        22.19 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        21.01       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-A6JN 
        0.76        56.61         7.07        15.25         5.98        29.79 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 
        6.48        28.01        21.24        23.47        19.92        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.55        18.84        51.12        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-A6EN TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q 
       12.36        28.77        22.59        13.94        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I 
       37.58        39.12        41.59        37.18        32.71         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A624 TCGA-H7-7774 
       31.13        18.94        24.95        17.85        12.43        13.38 
TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 
       15.16        20.94        33.76        28.47        25.74        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         0.36        13.84         4.27 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I 
        6.90        15.95        38.53        37.71        11.84         0.07 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H8 TCGA-MT-A51X 
        5.29        13.68        13.84        19.04        10.75         7.96 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 
        1.84        12.62         6.25        15.42        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       29.92        15.78        71.74        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z 
       75.55        18.97        29.00        12.99        16.01        21.07 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
       21.21        23.15         7.30        21.47         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       27.39        21.07        19.73        12.89         5.62        12.20 
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-T3-A92N TCGA-TN-A7HI TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
       32.45         3.12        13.55        54.67         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       49.45        44.65        17.95        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       18.05        13.94        17.03        14.56        13.35 

  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE 
                         0.36                          0.07 
  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE 
                       153.86                        210.97 
  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE 
                        19.27                         21.90 
[1] "0.4 - 153.9 (19.3)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1.3"
D49V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 21(7Q36.1) MUTATED         7       13        21        65         5
  DEL PEAK 21(7Q36.1) WILD-TYPE      20       63        61       187         7
                               vv
clus                            STAGE IVC
  DEL PEAK 21(7Q36.1) MUTATED           0
  DEL PEAK 21(7Q36.1) WILD-TYPE         1
D49V3, multiclass
           clus
vv          DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE
  STAGE I                             7                            20
  STAGE II                           13                            63
  STAGE III                          21                            61
  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 21(7Q36.1) MUTATED      14  34  21  49
  DEL PEAK 21(7Q36.1) WILD-TYPE    36 103  79 124
D49V4, multiclass
       clus
vv      DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE
  T0+T1                          14                            36
  T2                             34                           103
  T3                             21                            79
  T4                             49                           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 21(7Q36.1) MUTATED    39  21  44   4
  DEL PEAK 21(7Q36.1) WILD-TYPE 140  47 124   4
D49V5, multiclass
    clus
vv   DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE
  N0                          39                           140
  N1                          21                            47
  N2                          44                           124
  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 21(7Q36.1) MUTATED    46   0
  DEL PEAK 21(7Q36.1) WILD-TYPE 144   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.1) MUTATED     46    0
  DEL PEAK 21(7Q36.1) WILD-TYPE  144    1
   clus
vv  DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE
  0                          46                           144
  1                           0                             1
[1] 2 2
[1] FALSE
D49V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.1) MUTATED    31 101
  DEL PEAK 21(7Q36.1) WILD-TYPE 109 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.1) MUTATED     31  101
  DEL PEAK 21(7Q36.1) WILD-TYPE  109  281
        clus
vv       DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE
  FEMALE                          31                           109
  MALE                           101                           281
[1] 2 2
[1] FALSE
D49V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.1) MUTATED    47  72
  DEL PEAK 21(7Q36.1) WILD-TYPE 115 229
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.1) MUTATED     47   72
  DEL PEAK 21(7Q36.1) WILD-TYPE  115  229
     clus
vv    DEL PEAK 21(7Q36.1) MUTATED DEL PEAK 21(7Q36.1) WILD-TYPE
  NO                           47                           115
  YES                          72                           229
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(7Q36.1) MUTATED                                   129
  DEL PEAK 21(7Q36.1) WILD-TYPE                                 382
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 21(7Q36.1) MUTATED                                                   3
  DEL PEAK 21(7Q36.1) WILD-TYPE                                                 7
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 21(7Q36.1) MUTATED                                                           0
  DEL PEAK 21(7Q36.1) WILD-TYPE                                                         1
D49V9, multiclass
                                                           clus
vv                                                          DEL PEAK 21(7Q36.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               129
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 21(7Q36.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 382
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
D49V11, continuous
D49V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(7Q36.1) MUTATED                                  0     3
  DEL PEAK 21(7Q36.1) WILD-TYPE                                2     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(7Q36.1) MUTATED                          17   110
  DEL PEAK 21(7Q36.1) WILD-TYPE                        31   336
D49V13, multiclass
                                  clus
vv                                 DEL PEAK 21(7Q36.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    110
                                  clus
vv                                 DEL PEAK 21(7Q36.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.1) MUTATED     5 117
  DEL PEAK 21(7Q36.1) WILD-TYPE  21 342
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.1) MUTATED      5  117
  DEL PEAK 21(7Q36.1) WILD-TYPE   21  342
                        clus
vv                       DEL PEAK 21(7Q36.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         117
                        clus
vv                       DEL PEAK 21(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           342
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 22(8P23.2) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(8P23.2) MUTATED   159 145
  DEL PEAK 22(8P23.2) WILD-TYPE 142  74
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          304                           216 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          145                            74 
$`DEL PEAK 22(8P23.2) MUTATED`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6024 
       37.28        20.48        30.18        25.71        51.29        11.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 
       35.05        32.48        70.13        16.73        43.04        11.61 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7589 TCGA-HD-8635 TCGA-UF-A71D 
        6.02         0.36        34.36        46.32        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 
        2.96         3.35        15.19        26.50        23.74        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       65.59        15.52        14.83        12.62         4.01        41.85 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI 
       27.95         7.10         5.69        14.47         7.82        11.05 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 
       13.38        16.41         9.14         4.41        36.72        33.70 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO 
       66.28        24.66        38.40        10.55        27.19         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 
        6.28        12.69        55.86        38.04         4.67        12.89 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 
       57.11        12.99        14.33        27.58        13.05        46.32 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        8.52        52.08        56.94        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 
       47.44        19.07         6.74        32.22         3.68        17.42 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63W TCGA-CN-A640 
       35.01        25.41        17.29        29.72        12.39         4.41 
TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 
       12.07        21.50         2.93        70.45        62.37        10.42 
TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
        4.24        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
       38.76        64.87        53.52        41.88        43.10        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       44.48        29.36        33.60        31.23        84.23        11.77 
TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7367 
       39.52        18.54        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        49.58        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-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 
       76.24        19.20       107.51        94.88        80.12        17.92 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       86.83        48.59        60.49        62.43         9.60        90.12 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6942 
        9.70         5.46        20.52         4.73        26.43       140.78 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 
       19.79        42.38         6.08        65.82         7.13         8.42 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
       28.34         4.14        64.83       172.67        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7235 
        7.99         9.01         1.84        12.92        71.21        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        4.73        89.65        31.36        26.20        18.97        17.13 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 
       47.97         2.10        49.71        35.54        17.85         9.67 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        0.46        22.85        25.08         0.07        34.09       100.57 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
       14.89       156.49        54.94        16.27        19.76         7.17 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45U 
       16.64         6.38        22.19       169.38       180.16        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 
        1.05        45.96         6.51        48.20        60.43        56.61 
TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        7.07         5.98        35.34         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 
       21.24        23.47        19.92         9.60        23.05        16.14 
TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       11.44        24.95        17.72         7.63        22.59        24.95 
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        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       18.02        37.58        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
        3.02        31.13        18.94         0.46        17.85        11.80 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 
       20.25        15.16        15.06        33.76        28.47        21.93 
TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E 
       14.66        13.84         6.90        34.75        15.95        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A6I9 
       19.04        15.48         7.96         1.84        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 
       17.98        15.78        71.74        47.01        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        21.21 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        7.30        21.47        12.72        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A71A TCGA-UF-A71B 
       15.91        13.71         3.12        13.25         2.83        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       49.45        44.65        74.47        18.05        13.94        20.75 
TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       32.65        20.55        14.56        18.15 

$`DEL PEAK 22(8P23.2) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6022 
        9.30        68.48         3.55        28.11         9.07         9.24 
TCGA-CN-6023 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CR-6472 
       52.08        19.82        24.39        48.20        32.88        34.52 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-BA-4076 
       30.94        14.04        40.24        21.11        12.66        13.64 
TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A4IF 
        9.07        42.35        57.93        17.10        21.17        29.42 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 
       20.45        11.54         2.27        20.48         6.15       105.90 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-8596 
        4.80        18.38        22.42        50.20        44.98        71.05 
TCGA-BB-8601 TCGA-BB-A6UM TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
       20.52        12.92        48.76        56.68        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 
       52.14        20.55        45.83        73.61        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5369 TCGA-CN-6010 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6988 
       12.39        12.49        50.07        28.04        34.13        10.45 
TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       38.89        11.74        23.57        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
       22.32        16.57         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6220 
       52.37        54.58        45.99        11.21        41.19        32.38 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
       23.24        29.49        14.14        12.46        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 
       26.27        58.42        50.01        36.99        16.90        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        22.78        15.75         9.27 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7379 TCGA-CR-7382 
       39.16        40.93         3.45         3.09        34.06        26.17 
TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       32.78        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5439 TCGA-CV-5442 
       24.79         5.13        29.95        48.39        17.95        76.50 
TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
       91.53        13.35        23.05         7.07        43.23        54.74 
TCGA-CV-6433 TCGA-CV-6934 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 
       21.07         2.14        21.90        11.24        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7101 
       30.08        53.95        10.98         2.50       111.16         5.26 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7250 
       52.31        21.80        10.75       130.88        36.00        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 
        4.96        11.87        18.41        57.47       210.97        89.33 
TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45O 
       25.94        56.48         3.52        84.49       153.86        27.98 
TCGA-CV-A45P TCGA-CV-A45T TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A468 
       21.01       159.65        88.87        67.86         0.76        15.25 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
        6.38        29.79        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8569 
       51.12        13.25        25.41         2.53        18.67        25.32 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A74Q TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
       12.36        28.77        23.34        46.45        20.45        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A61V TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A76A 
       39.12        41.59        24.95        12.43        13.38        20.94 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 
       25.74        27.48        27.48        22.03         0.36         4.27 
TCGA-HD-A6HZ TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 
        3.65        38.53        14.50        13.84        19.27        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         6.25         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        23.15 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
        9.34        27.39        12.89        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        20.35        64.80        54.67        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UP-A6WW TCGA-KU-A66S 
       24.30        55.43        29.46        22.36        17.03        13.35 

  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                         0.07                          0.36 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                       180.16                        210.97 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                       19.855                        22.650 
[1] "0.1 - 180.2 (19.9)" "0.4 - 211.0 (22.6)"
[1] "hr=" "1.5"
D50V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 22(8P23.2) MUTATED        16       43        53       158         9
  DEL PEAK 22(8P23.2) WILD-TYPE      11       33        29        94         3
                               vv
clus                            STAGE IVC
  DEL PEAK 22(8P23.2) MUTATED           1
  DEL PEAK 22(8P23.2) WILD-TYPE         0
D50V3, multiclass
           clus
vv          DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  STAGE I                            16                            11
  STAGE II                           43                            33
  STAGE III                          53                            29
  STAGE IVA                         158                            94
  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 22(8P23.2) MUTATED      28  77  62 116
  DEL PEAK 22(8P23.2) WILD-TYPE    22  60  38  57
D50V4, multiclass
       clus
vv      DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  T0+T1                          28                            22
  T2                             77                            60
  T3                             62                            38
  T4                            116                            57
[1] 4 2
[1] TRUE
[1] "dimension of 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(8P23.2) MUTATED   104  48 103   5
  DEL PEAK 22(8P23.2) WILD-TYPE  75  20  65   3
D50V5, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  N0                         104                            75
  N1                          48                            20
  N2                         103                            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 22(8P23.2) MUTATED   121   1
  DEL PEAK 22(8P23.2) WILD-TYPE  69   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED    121    1
  DEL PEAK 22(8P23.2) WILD-TYPE   69    0
   clus
vv  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  0                         121                            69
  1                           1                             0
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED    88 217
  DEL PEAK 22(8P23.2) WILD-TYPE  52 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     88  217
  DEL PEAK 22(8P23.2) WILD-TYPE   52  165
        clus
vv       DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  FEMALE                          88                            52
  MALE                           217                           165
[1] 2 2
[1] FALSE
D50V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED   102 171
  DEL PEAK 22(8P23.2) WILD-TYPE  60 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED    102  171
  DEL PEAK 22(8P23.2) WILD-TYPE   60  130
     clus
vv    DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  NO                          102                            60
  YES                         171                           130
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(8P23.2) MUTATED                                   302
  DEL PEAK 22(8P23.2) WILD-TYPE                                 209
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 22(8P23.2) MUTATED                                                   3
  DEL PEAK 22(8P23.2) WILD-TYPE                                                 7
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 22(8P23.2) MUTATED                                                           0
  DEL PEAK 22(8P23.2) WILD-TYPE                                                         1
D50V9, multiclass
                                                           clus
vv                                                          DEL PEAK 22(8P23.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               302
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 22(8P23.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 209
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, continuous
D50V11, continuous
D50V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(8P23.2) MUTATED                                  1     9
  DEL PEAK 22(8P23.2) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(8P23.2) MUTATED                          29   257
  DEL PEAK 22(8P23.2) WILD-TYPE                        19   189
D50V13, multiclass
                                  clus
vv                                 DEL PEAK 22(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 29
  WHITE                                                    257
                                  clus
vv                                 DEL PEAK 22(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 22(8P23.2) MUTATED    19 264
  DEL PEAK 22(8P23.2) WILD-TYPE   7 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     19  264
  DEL PEAK 22(8P23.2) WILD-TYPE    7  195
                        clus
vv                       DEL PEAK 22(8P23.2) MUTATED
  HISPANIC OR LATINO                              19
  NOT HISPANIC OR LATINO                         264
                        clus
vv                       DEL PEAK 22(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           195
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 23(9P23) MUTATION ANALYSIS
D51V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 23(9P23) MUTATED   141  97
  DEL PEAK 23(9P23) WILD-TYPE 160 122
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        238                         282 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                         97                         122 
$`DEL PEAK 23(9P23) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 
        9.30         3.55        30.18        25.71        51.29         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-7063 
        9.24        11.08        35.05        32.48        32.88        70.13 
TCGA-CQ-7067 TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       16.73        34.52         0.36        34.36        30.94        14.04 
TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4076 
       46.32        21.11        22.85        48.03        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
        9.07        26.50        17.10        15.52        21.17        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DE 
       12.62        41.85        29.42        27.95         5.69        14.47 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7870 
       20.48        16.41         9.14        36.72        33.70        66.28 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4723 
       24.66        38.40        71.05        20.52        10.55        55.86 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 
        4.67        12.89        26.86        32.81        57.11        20.55 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 
       27.58        13.05        46.32        71.31        11.54        11.57 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A497 TCGA-CN-A49A 
       48.00         6.74        10.45        32.22        35.01        17.29 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5327 
       31.69        22.32        12.39        12.07         2.93        54.58 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 
       10.42        56.58        13.25         4.24        14.99        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CQ-A4CI TCGA-CR-5247 
       53.52        41.88        77.56        29.36        31.23        11.77 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 
       18.54        16.90        11.64        12.46        22.78        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       39.16        47.34        40.93        24.95        29.23         0.99 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
       17.13        27.06        12.89        49.58        24.79         5.13 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
       35.41       139.43       129.21        76.24        19.20        17.95 
TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6933 
       80.12        86.83        48.59        43.23         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 
        2.14         9.70        20.52       140.78        12.03        42.38 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 
       28.34       172.67       111.16        12.66         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7235 
       52.31        12.92        21.80        71.21        10.75        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
        4.73        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7413 
        4.96        11.87         2.10        49.71        18.41         9.67 
TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7430 
       22.85        25.94         0.07        34.09       100.57        16.27 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45Q 
       84.49        19.76       153.86        16.64        22.19       169.38 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 
       88.87        60.43        67.86         0.76        56.61         7.07 
TCGA-CV-A6JM TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-CX-7086 
        6.38        28.01         3.62        21.24        10.42        18.84 
TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 
       51.12        25.41         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        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50I 
       12.79        23.34        18.02        39.12        37.18         3.02 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
        0.46        20.25        15.16        33.76        28.47        25.74 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A6SG 
       13.84         3.65        15.95        11.84        33.57        19.04 
TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       15.48         7.96         1.84         7.13        17.98        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
       71.74        47.01        18.97         2.04        13.15        21.07 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       21.47        12.72        21.07        19.73        12.89         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-UF-A718 
       17.82        15.32        15.91        32.45        13.71        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JS 
       24.30        55.43        29.46        18.05        13.94        22.36 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       17.03        20.55        14.56        18.15 

$`DEL PEAK 23(9P23) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-CN-6023 TCGA-CN-A6V1 
       37.28        20.48        68.48        28.11        52.08        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-DQ-7593 
       24.39        48.20        43.04        11.61         6.02        40.24 
TCGA-HD-8634 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       12.66         2.96         3.35        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB 
       23.84        65.59         4.01        20.45        11.54         7.10 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
        7.82         2.27        11.05        13.38         6.15       105.90 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 
        4.80         4.41        18.38        22.42        50.20        44.98 
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        48.76 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       38.04        56.68        52.14        12.99        14.33        45.83 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 
       73.61        42.02         8.58        12.39         8.32        16.21 
TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
       11.84        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       30.67        23.90        47.44        28.04        19.07        34.13 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
       38.89         3.68        17.42        11.74        25.41        23.57 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
       29.72        21.21         7.40        16.57         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 
       23.44        20.88        19.53        52.37        21.50        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       62.37        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD 
       46.95        38.76        43.10        44.48        23.24        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       29.49        14.14        12.46        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6480 
       26.27        58.42        50.01        39.52        36.99        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7369 
       10.22        11.34         7.69        15.75         9.27        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
        3.45         3.09        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       26.17        32.78        47.01        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
       44.25        30.58         5.95        29.95        48.39        17.16 
TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
      108.95       107.51        94.88        76.50        91.53        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
       13.35        23.05        60.49         7.07        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 
       62.43         5.46         4.73        21.90        26.43        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-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
       10.98         7.13         8.42         2.50         4.14        64.83 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7248 TCGA-CV-7250 
       18.81         7.99         9.01       130.88        17.13        95.34 
TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
       47.97        57.47        35.54        17.85       210.97        89.33 
TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
        0.46        25.08        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R 
        3.52         7.17         6.38        27.98        21.01       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Z 
      159.65        35.47         1.05        45.96         6.51        48.20 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ 
       15.25         5.98        35.34        29.79         6.48        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 
       19.92        22.52        10.55        13.25         2.53        16.14 
TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-DQ-5624 TCGA-DQ-5625 
       18.67        28.77         7.63        22.59        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7596 
       33.86        46.45        20.45        37.58        40.04        41.59 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       32.71        21.63        20.25        31.13        18.94        24.95 
TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A76A 
       17.85        11.80        12.43        13.38        15.06        20.94 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       21.93        27.48        27.48        14.66        22.03         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        4.27         6.90        34.75        38.53        14.50        37.71 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 
       37.41         0.07         5.29        13.68        13.84        19.27 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       10.75        14.37        30.05        12.62         6.25        15.42 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       16.08        29.92        51.25        10.85        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IF 
       75.55        29.00        12.99        16.01        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K 
        7.30         9.34        27.39        14.76        12.20         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T3-A92N TCGA-TN-A7HI 
       12.72        16.96         6.87         7.10         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7JC TCGA-UF-A7JO TCGA-UF-A7JT TCGA-KU-A66S 
       13.25        20.35        17.95        20.75        32.65        13.35 

  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                     172.67                      210.97 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                      21.09                       21.14 
[1] "0.1 - 172.7 (21.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D51V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 23(9P23) MUTATED        11       34        35       124         6
  DEL PEAK 23(9P23) WILD-TYPE      16       42        47       128         6
                             vv
clus                          STAGE IVC
  DEL PEAK 23(9P23) MUTATED           1
  DEL PEAK 23(9P23) WILD-TYPE         0
D51V3, multiclass
           clus
vv          DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  STAGE I                          11                          16
  STAGE II                         34                          42
  STAGE III                        35                          47
  STAGE IVA                       124                         128
  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 23(9P23) MUTATED      19 59 48 89
  DEL PEAK 23(9P23) WILD-TYPE    31 78 52 84
D51V4, multiclass
       clus
vv      DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  T0+T1                        19                          31
  T2                           59                          78
  T3                           48                          52
  T4                           89                          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 23(9P23) MUTATED   89 31 77  3
  DEL PEAK 23(9P23) WILD-TYPE 90 37 91  5
D51V5, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  N0                        89                          90
  N1                        31                          37
  N2                        77                          91
  N3                         3                           5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    88   1
  DEL PEAK 23(9P23) WILD-TYPE 102   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     88    1
  DEL PEAK 23(9P23) WILD-TYPE  102    0
   clus
vv  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  0                        88                         102
  1                         1                           0
[1] 2 2
[1] FALSE
D51V7, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    54 185
  DEL PEAK 23(9P23) WILD-TYPE  86 197
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     54  185
  DEL PEAK 23(9P23) WILD-TYPE   86  197
        clus
vv       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  FEMALE                        54                          86
  MALE                         185                         197
[1] 2 2
[1] FALSE
D51V8, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    71 136
  DEL PEAK 23(9P23) WILD-TYPE  91 165
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     71  136
  DEL PEAK 23(9P23) WILD-TYPE   91  165
     clus
vv    DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  NO                         71                          91
  YES                       136                         165
[1] 2 2
[1] FALSE
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P23) MUTATED                                   235
  DEL PEAK 23(9P23) WILD-TYPE                                 276
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 23(9P23) MUTATED                                                   4
  DEL PEAK 23(9P23) WILD-TYPE                                                 6
                             vv
clus                          HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 23(9P23) MUTATED                                                           0
  DEL PEAK 23(9P23) WILD-TYPE                                                         1
D51V9, multiclass
                                                           clus
vv                                                          DEL PEAK 23(9P23) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                             235
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                 4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                         0
                                                           clus
vv                                                          DEL PEAK 23(9P23) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               276
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, continuous
D51V11, continuous
D51V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(9P23) MUTATED                                  1     5
  DEL PEAK 23(9P23) WILD-TYPE                                1     6
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P23) MUTATED                          29   194
  DEL PEAK 23(9P23) WILD-TYPE                        19   252
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 23(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    5
  BLACK OR AFRICAN AMERICAN                               29
  WHITE                                                  194
                                  clus
vv                                 DEL PEAK 23(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    252
[1] 4 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 23(9P23) MUTATED    14 201
  DEL PEAK 23(9P23) WILD-TYPE  12 258
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     14  201
  DEL PEAK 23(9P23) WILD-TYPE   12  258
                        clus
vv                       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  HISPANIC OR LATINO                            14                          12
  NOT HISPANIC OR LATINO                       201                         258
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 24(9P21.3) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 24(9P21.3) MUTATED   162 139
  DEL PEAK 24(9P21.3) WILD-TYPE 139  80
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          301                           219 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          139                            80 
$`DEL PEAK 24(9P21.3) MUTATED`
TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 
        3.55        30.18        25.71        51.29         9.07         9.24 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7067 
       11.08        35.05        32.48        24.39        32.88        16.73 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        34.52         6.02         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
       14.04        46.32        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5555 
        2.96        15.19        13.64         9.07        26.50        17.10 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
       15.52        21.17        14.83        12.62        41.85        29.42 
TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 
       27.95         5.69        14.47        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-A5HY TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
       20.52        10.55        12.69        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 
       56.68        12.89        26.86        32.81        57.11        20.55 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 
       45.83        27.58        13.05        42.02        46.32        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 
        8.32        16.21        11.54        11.57        12.49        52.08 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 
       30.67        48.00        47.44        19.07         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W 
       32.22        11.74        35.01        17.29        31.69        12.39 
TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5332 
       12.07        52.37        21.50         2.93        54.58        10.42 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 
       41.19        46.95        56.58        13.25         4.24        14.99 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 
       64.87        53.52        41.88        43.10        77.56        23.24 
TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 
       29.36        11.77        18.54        16.90        12.46        22.78 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       47.18        39.16        40.93        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7397 
       31.96        26.17        17.13        27.06        49.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.13         5.95        35.41       139.43        17.16       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 
      108.95        76.24        19.20        17.95        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 
       13.35        86.83        48.59        43.23        62.43         9.60 
TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 
       90.12         2.14         9.70         5.46        20.52        26.43 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6960 
       11.24        12.03        42.38        10.98         7.13        28.34 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 
       64.83       111.16        12.66         7.99         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 
       52.31        12.92        21.80        10.75        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7252 
       89.65        36.00        31.36        26.20        18.97         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7411 
       11.87         2.10        49.71        18.41        35.54        89.33 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
        9.67        22.85        25.94         0.07        34.09       100.57 
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-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A45U 
        7.17       153.86         6.38        22.19       169.38        35.47 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 
        6.51        88.87        60.43        67.86         0.76        56.61 
TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        7.07         6.38        28.01         3.62        21.24        23.47 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6517 
       22.52        10.42        10.55        18.84        51.12         9.60 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       23.05        11.44        24.95        25.32        17.72        12.36 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
       24.95        13.94        12.10        12.79        23.34        37.25 
TCGA-DQ-5631 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
       18.02        39.12        37.18        32.71        20.25         3.02 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 
       24.95         0.46        11.80        20.25        13.38        15.06 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 
       33.76        28.47        25.74        27.48        14.66         0.36 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
       13.84         3.65         6.90        15.95        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
       37.71        11.84        33.57        13.84        19.04        15.48 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 
       10.75         7.96         1.84         7.13        17.98        15.78 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 
       47.01        19.00        18.97         2.04        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       13.15        21.07        21.47        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
        5.62        14.76        12.20        17.82        15.32         8.32 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A718 
        6.87        15.91        32.45        13.71         3.12        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

$`DEL PEAK 24(9P21.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-CN-6023 
        9.30        37.28        20.48        68.48        28.11        52.08 
TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-A4C7 TCGA-DQ-7593 TCGA-4P-AA8J 
       19.82        48.20        70.13        11.61        40.24         3.35 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6873 
       23.74        42.35        57.93        23.84        65.59         4.01 
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       105.90         4.80        18.38        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        48.76        52.14        12.99        14.33        73.61 
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        50.07 
TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       23.90        28.04        34.13        38.89         3.68        17.42 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       25.41        23.57        29.72        21.21         7.40        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
       16.57         4.41         2.70        23.44        20.88        19.53 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 
       70.45        62.37        45.99        11.21         4.24        32.38 
TCGA-CQ-6229 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       38.76        44.48        33.60        29.49        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-6480 TCGA-CR-6481 TCGA-CR-6482 
       50.01        39.52        36.99        11.90        10.22        11.34 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 
       11.64         7.69        15.75         9.27        47.34        35.84 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7385 
        3.45         3.09         9.17        34.06        19.92        32.78 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       47.01        12.89        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
       30.58        29.95        48.39       107.51        94.88        76.50 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
       91.53        23.05        60.49         7.07        54.74        21.07 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 
        4.73        21.90       140.78        19.79        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 
        6.08        53.95        65.82         8.42         2.50         4.14 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7100 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7248 
      172.67        18.81         9.01        71.21       130.88        17.13 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7414 
       95.34        47.97        57.47        17.85       210.97         0.46 
TCGA-CV-7416 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P 
       25.08        14.89        54.94        16.64        27.98        21.01 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A468 
      180.16       159.65         1.05        45.96        48.20        15.25 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6K0 TCGA-D6-6515 
        5.98        35.34        29.79         6.48        19.92        13.25 
TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM 
       25.41         2.53        16.14        18.67        28.77         7.63 
TCGA-D6-A6EN TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       22.59        58.45        33.86        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 
       40.04        41.59        21.63        31.13        18.94        17.85 
TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8314 
       12.43        15.16        20.94        21.93        27.48        22.03 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L 
        4.27        34.75        37.41         0.07         5.29        13.68 
TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN 
       19.27        14.37        30.05        12.62         6.25        15.42 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
       16.08        29.92        71.74        51.25        10.85        36.82 
TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       75.55        12.99        21.21        23.15         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-TN-A7HI 
       12.72        27.39        12.72        16.96         7.10        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A7JO 
       13.25        20.35        20.75 

  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                       169.38                        210.97 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                        20.52                         22.03 
[1] "0.1 - 169.4 (20.5)" "0.1 - 211.0 (22.0)"
[1] "hr=" "1.4"
D52V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 24(9P21.3) MUTATED        14       42        44       163         7
  DEL PEAK 24(9P21.3) WILD-TYPE      13       34        38        89         5
                               vv
clus                            STAGE IVC
  DEL PEAK 24(9P21.3) MUTATED           1
  DEL PEAK 24(9P21.3) WILD-TYPE         0
D52V3, multiclass
           clus
vv          DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  STAGE I                            14                            13
  STAGE II                           42                            34
  STAGE III                          44                            38
  STAGE IVA                         163                            89
  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 24(9P21.3) MUTATED      23  75  64 114
  DEL PEAK 24(9P21.3) WILD-TYPE    27  62  36  59
D52V4, multiclass
       clus
vv      DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  T0+T1                          23                            27
  T2                             75                            62
  T3                             64                            36
  T4                            114                            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 24(9P21.3) MUTATED   113  38 104   4
  DEL PEAK 24(9P21.3) WILD-TYPE  66  30  64   4
D52V5, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  N0                         113                            66
  N1                          38                            30
  N2                         104                            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 24(9P21.3) MUTATED   108   1
  DEL PEAK 24(9P21.3) WILD-TYPE  82   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED    108    1
  DEL PEAK 24(9P21.3) WILD-TYPE   82    0
   clus
vv  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  0                         108                            82
  1                           1                             0
[1] 2 2
[1] FALSE
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED    81 221
  DEL PEAK 24(9P21.3) WILD-TYPE  59 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     81  221
  DEL PEAK 24(9P21.3) WILD-TYPE   59  161
        clus
vv       DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  FEMALE                          81                            59
  MALE                           221                           161
[1] 2 2
[1] FALSE
D52V8, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED    92 172
  DEL PEAK 24(9P21.3) WILD-TYPE  70 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     92  172
  DEL PEAK 24(9P21.3) WILD-TYPE   70  129
     clus
vv    DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  NO                           92                            70
  YES                         172                           129
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.3) MUTATED                                   297
  DEL PEAK 24(9P21.3) WILD-TYPE                                 214
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 24(9P21.3) MUTATED                                                   4
  DEL PEAK 24(9P21.3) WILD-TYPE                                                 6
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 24(9P21.3) MUTATED                                                           1
  DEL PEAK 24(9P21.3) WILD-TYPE                                                         0
D52V9, multiclass
                                                           clus
vv                                                          DEL PEAK 24(9P21.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               297
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           1
                                                           clus
vv                                                          DEL PEAK 24(9P21.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 214
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
D52V11, continuous
D52V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(9P21.3) MUTATED                                  1     5
  DEL PEAK 24(9P21.3) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(9P21.3) MUTATED                          35   252
  DEL PEAK 24(9P21.3) WILD-TYPE                        13   194
D52V13, multiclass
                                  clus
vv                                 DEL PEAK 24(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 35
  WHITE                                                    252
                                  clus
vv                                 DEL PEAK 24(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      194
[1] 4 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 24(9P21.3) MUTATED    16 259
  DEL PEAK 24(9P21.3) WILD-TYPE  10 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     16  259
  DEL PEAK 24(9P21.3) WILD-TYPE   10  200
                        clus
vv                       DEL PEAK 24(9P21.3) MUTATED
  HISPANIC OR LATINO                              16
  NOT HISPANIC OR LATINO                         259
                        clus
vv                       DEL PEAK 24(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           200
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 25(9Q21.11) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(9Q21.11) MUTATED    59  48
  DEL PEAK 25(9Q21.11) WILD-TYPE 242 171
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           107                            413 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            48                            171 
$`DEL PEAK 25(9Q21.11) MUTATED`
TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CQ-7067 TCGA-CR-6472 TCGA-DQ-5629 
        3.55        30.18        25.71        16.73        34.52        30.94 
TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-6870 
       46.32        21.11        22.85         2.96        15.19        14.83 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-A5HZ 
       12.62        41.85        20.48        16.41        66.28        27.19 
TCGA-CN-4730 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5367 TCGA-CN-6018 TCGA-CN-6020 
       26.86        27.58        46.32        11.57        19.07         6.74 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CQ-5332 TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-7072 
       10.45        32.22        10.42        14.99        41.88        77.56 
TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 
       29.36        11.77        18.54        22.78        47.18        39.16 
TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CV-5430 TCGA-CV-5435 
       35.84        24.95         0.99        31.96       139.43        76.24 
TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7091 
       94.88        86.83        20.52        11.24        12.03       111.16 
TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7252 TCGA-CV-7254 
       18.81         1.84        77.16        31.36         4.96        47.97 
TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7432 TCGA-CV-7435 
        9.67        25.08         0.07       100.57        84.49       153.86 
TCGA-CV-7440 TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A6JU TCGA-CX-7086 
       22.19         6.51        88.87        56.61         3.62        18.84 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EO TCGA-D6-A6EP 
       23.05        11.44        25.32        17.72        24.95        13.94 
TCGA-D6-A6ES TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 
       12.79        18.02        37.18         3.02         0.46        20.25 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67D 
       28.47        14.66         3.65        19.04        15.48         1.84 
TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 
        7.13        17.98        15.78        47.01        18.97         2.04 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       12.72        21.07        19.73         5.62        14.76        12.20 
TCGA-QK-A8ZB TCGA-T2-A6WZ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7JD 
       17.82        15.91        64.80        54.67         2.83        24.30 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66T 
       18.05        13.94        17.03        20.55        18.15 

$`DEL PEAK 25(9Q21.11) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-CN-4727 
        9.30        37.28        20.48        68.48        28.11        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
        9.07         9.24        52.08        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
       19.82        24.39        48.20        32.88        70.13        43.04 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7593 
       11.61         6.02         0.36        34.36        14.04        40.24 
TCGA-HD-8634 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 
       12.66        48.03         3.35        13.64         9.07        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 
       15.52        21.17         4.01        29.42        20.45        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38         6.15       105.90         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       44.98        24.66        38.40        71.05        20.52        10.55 
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        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        12.89        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
       57.11        12.99        20.55        14.33        45.83        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       13.05        42.02         8.58        12.39        71.31         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        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       56.94        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
       28.04        34.13        38.89         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        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
        7.40        31.69        22.32        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
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        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 
       13.25         4.24        38.76        64.87        53.52        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       44.48        23.24        33.60        29.49        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-6480 TCGA-CR-6481 
       50.01        39.52        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-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        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         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       140.78 
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       172.67        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        89.65        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        49.71        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        21.01       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        28.01        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       22.52        10.42        10.55        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB 
        9.60         2.53        16.14        18.67        24.95        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 
       28.77         7.63        22.59        12.10        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
       37.25        33.86        46.45        20.45        37.58        40.04 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
       39.12        41.59        32.71        21.63        20.25        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       18.94        24.95        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        27.48        22.03         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        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       11.84        37.41         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       13.84        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
       12.62         6.25        15.42        16.08        29.92        71.74 
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-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       12.99        16.01        13.15        21.07        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-AA3J 
        7.30        21.47         9.34        27.39        12.89        15.32 
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-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71B 
       13.71         3.12        13.55        13.25        20.35        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH 
       49.45        44.65        74.47        17.95        55.43        29.46 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        14.56        13.35 

  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                         19.07                          21.63 
[1] "0.1 - 153.9 (19.1)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.1"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 25(9Q21.11) MUTATED         4       16        19        51         2
  DEL PEAK 25(9Q21.11) WILD-TYPE      23       60        63       201        10
                                vv
clus                             STAGE IVC
  DEL PEAK 25(9Q21.11) MUTATED           1
  DEL PEAK 25(9Q21.11) WILD-TYPE         0
D53V3, multiclass
           clus
vv          DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  STAGE I                              4                             23
  STAGE II                            16                             60
  STAGE III                           19                             63
  STAGE IVA                           51                            201
  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(9Q21.11) MUTATED       9  32  17  39
  DEL PEAK 25(9Q21.11) WILD-TYPE    41 105  83 134
D53V4, multiclass
       clus
vv      DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  T0+T1                            9                             41
  T2                              32                            105
  T3                              17                             83
  T4                              39                            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 25(9Q21.11) MUTATED    40  18  33   1
  DEL PEAK 25(9Q21.11) WILD-TYPE 139  50 135   7
D53V5, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  N0                           40                            139
  N1                           18                             50
  N2                           33                            135
  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 25(9Q21.11) MUTATED    49   1
  DEL PEAK 25(9Q21.11) WILD-TYPE 141   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     49    1
  DEL PEAK 25(9Q21.11) WILD-TYPE  141    0
   clus
vv  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  0                           49                            141
  1                            1                              0
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED    25  83
  DEL PEAK 25(9Q21.11) WILD-TYPE 115 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     25   83
  DEL PEAK 25(9Q21.11) WILD-TYPE  115  299
        clus
vv       DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  FEMALE                           25                            115
  MALE                             83                            299
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED    32  62
  DEL PEAK 25(9Q21.11) WILD-TYPE 130 239
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     32   62
  DEL PEAK 25(9Q21.11) WILD-TYPE  130  239
     clus
vv    DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  NO                            32                            130
  YES                           62                            239
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9Q21.11) MUTATED                                   108
  DEL PEAK 25(9Q21.11) WILD-TYPE                                 403
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 25(9Q21.11) MUTATED                                                   0
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                10
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 25(9Q21.11) MUTATED                                                           0
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                         1
D53V9, multiclass
                                                           clus
vv                                                          DEL PEAK 25(9Q21.11) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                108
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 25(9Q21.11) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  403
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, continuous
D53V11, continuous
D53V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(9Q21.11) MUTATED                                  1     1
  DEL PEAK 25(9Q21.11) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(9Q21.11) MUTATED                          14    86
  DEL PEAK 25(9Q21.11) WILD-TYPE                        34   360
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 25(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                      86
                                  clus
vv                                 DEL PEAK 25(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    34
  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"
D53V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED     6  91
  DEL PEAK 25(9Q21.11) WILD-TYPE  20 368
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED      6   91
  DEL PEAK 25(9Q21.11) WILD-TYPE   20  368
                        clus
vv                       DEL PEAK 25(9Q21.11) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       DEL PEAK 25(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            368
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 26(9Q34.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 26(9Q34.3) MUTATED    43  35
  DEL PEAK 26(9Q34.3) WILD-TYPE 258 184
  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE 
                           78                           442 
  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE 
                           35                           184 
$`DEL PEAK 26(9Q34.3) MUTATED`
TCGA-BA-6871 TCGA-BB-A5HU TCGA-CQ-7067 TCGA-CR-6472 TCGA-H7-A6C5 TCGA-HD-8635 
        3.55        25.71        16.73        34.52        21.11        22.85 
TCGA-BA-7269 TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7864 TCGA-BB-7870 
       41.85        13.38         9.14         4.41        50.20        66.28 
TCGA-BB-A5HZ TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-A63U 
       27.19        57.11        27.58        19.07         6.74        31.69 
TCGA-CN-A63Y TCGA-CQ-5327 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-7072 
       16.57        54.58         4.24        14.99        41.88        77.56 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7374 
       14.14        11.77        18.54        47.18        24.95         0.99 
TCGA-CR-7389 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5441 
       12.89         5.95       139.43       108.95        76.24        94.88 
TCGA-CV-5973 TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6948 
       86.83         9.60        20.52        11.24        12.03        42.38 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7104 TCGA-CV-7243 
      172.67       111.16        18.81        12.66        12.92        31.36 
TCGA-CV-7252 TCGA-CV-7255 TCGA-CV-7413 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7435 
        4.96         2.10         9.67         0.07       100.57       153.86 
TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JU TCGA-DQ-5631 
       22.19       169.38        60.43        56.61         3.62        18.02 
TCGA-F7-7848 TCGA-F7-A50I TCGA-HD-7753 TCGA-IQ-7630 TCGA-IQ-A6SH TCGA-MZ-A5BI 
       37.18         3.02        28.47        15.95        15.48         7.13 
TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       71.74        18.97        12.72        21.07         5.62        12.20 
TCGA-QK-A8ZB TCGA-UF-A719 TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-KU-A66T 
       17.82        54.67        24.30        18.05        13.94        18.15 

$`DEL PEAK 26(9Q34.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48        68.48        28.11        30.18 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       51.29         9.07         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 
       43.04        11.61         6.02         0.36        34.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV 
       14.04        46.32        40.24        12.66        48.03         2.96 
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-5558 TCGA-BA-6868 
       42.35        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IH 
       21.17        14.83        12.62         4.01        29.42        20.45 
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       105.90 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 
        4.80        18.38        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        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       12.99        20.55        14.33        45.83        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
       42.02        46.32         8.58        12.39        71.31         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 
       52.08        56.94        50.07        30.67        48.00        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
       47.44        28.04        34.13        10.45        32.22        38.89 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       17.29        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       52.37        21.50         2.93        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 
       56.58        13.25        38.76        64.87        53.52        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH 
       44.48        23.24        29.36        33.60        29.49        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-6480 TCGA-CR-6481 
       50.01        39.52        36.99        16.90        11.90        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        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        9.27        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
        3.09        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-7390 
       26.17        17.13        32.78        47.01        27.06        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
        5.13        35.41        29.95        48.39        17.16       129.21 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
       19.20        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-5978 
       17.92        13.35        23.05        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-6942 
        9.70         5.46         4.73        21.90        26.43       140.78 
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-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-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 
       64.83         7.99         9.01         5.26         1.84        52.31 
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-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       89.65        36.00        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        49.71        18.41        57.47        35.54 
TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
       17.85       210.97        89.33         0.46        22.85        25.08 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
       25.94        34.09        14.89        56.48       156.49        54.94 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 
        3.52        16.27        84.49        19.76         7.17        16.64 
TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
        6.38        27.98        21.01       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 
        1.05        45.96         6.51        88.87        48.20        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        28.01        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       22.52        10.42        10.55        18.84        51.12        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        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
        7.63        22.59        24.95        13.94        12.10        12.79 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
       23.34        58.45        37.25        33.86        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       37.58        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25        31.13        18.94        24.95         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-7229 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       20.94        33.76        25.74        21.93        27.48        27.48 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
       14.66        22.03         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-A61G 
        6.90        34.75        38.53        14.50        37.71        11.84 
TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O 
       37.41         0.07        33.57         5.29        13.68        13.84 
TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       19.04        19.27        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 
        1.84        12.62         6.25        15.42        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       29.92        15.78        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55         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        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J 
        9.34        27.39        19.73        12.89        14.76        15.32 
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-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       64.80         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       17.95        55.43        29.46        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       17.03        20.55        14.56        13.35 

  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE 
                       172.67                        210.97 
  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE 
                       19.020                        21.225 
[1] "0.1 - 172.7 (19.0)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D54V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 26(9Q34.3) MUTATED         5       15        12        35         2
  DEL PEAK 26(9Q34.3) WILD-TYPE      22       61        70       217        10
                               vv
clus                            STAGE IVC
  DEL PEAK 26(9Q34.3) MUTATED           1
  DEL PEAK 26(9Q34.3) WILD-TYPE         0
D54V3, multiclass
           clus
vv          DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE
  STAGE I                             5                            22
  STAGE II                           15                            61
  STAGE III                          12                            70
  STAGE IVA                          35                           217
  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 26(9Q34.3) MUTATED       8  24  14  25
  DEL PEAK 26(9Q34.3) WILD-TYPE    42 113  86 148
D54V4, multiclass
       clus
vv      DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE
  T0+T1                           8                            42
  T2                             24                           113
  T3                             14                            86
  T4                             25                           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 26(9Q34.3) MUTATED    29  10  25   1
  DEL PEAK 26(9Q34.3) WILD-TYPE 150  58 143   7
D54V5, multiclass
    clus
vv   DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE
  N0                          29                           150
  N1                          10                            58
  N2                          25                           143
  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 26(9Q34.3) MUTATED    27   1
  DEL PEAK 26(9Q34.3) WILD-TYPE 163   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 26(9Q34.3) MUTATED     27    1
  DEL PEAK 26(9Q34.3) WILD-TYPE  163    0
   clus
vv  DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE
  0                          27                           163
  1                           1                             0
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 26(9Q34.3) MUTATED    22  57
  DEL PEAK 26(9Q34.3) WILD-TYPE 118 325
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 26(9Q34.3) MUTATED     22   57
  DEL PEAK 26(9Q34.3) WILD-TYPE  118  325
        clus
vv       DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE
  FEMALE                          22                           118
  MALE                            57                           325
[1] 2 2
[1] FALSE
D54V8, binary
                               cls
clus                              0   1
  DEL PEAK 26(9Q34.3) MUTATED    24  47
  DEL PEAK 26(9Q34.3) WILD-TYPE 138 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 26(9Q34.3) MUTATED     24   47
  DEL PEAK 26(9Q34.3) WILD-TYPE  138  254
     clus
vv    DEL PEAK 26(9Q34.3) MUTATED DEL PEAK 26(9Q34.3) WILD-TYPE
  NO                           24                           138
  YES                          47                           254
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(9Q34.3) MUTATED                                    79
  DEL PEAK 26(9Q34.3) WILD-TYPE                                 432
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 26(9Q34.3) MUTATED                                                   0
  DEL PEAK 26(9Q34.3) WILD-TYPE                                                10
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 26(9Q34.3) MUTATED                                                           0
  DEL PEAK 26(9Q34.3) WILD-TYPE                                                         1
D54V9, multiclass
                                                           clus
vv                                                          DEL PEAK 26(9Q34.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                79
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 26(9Q34.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 432
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, continuous
D54V11, continuous
D54V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(9Q34.3) MUTATED                                  0     2
  DEL PEAK 26(9Q34.3) WILD-TYPE                                2     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(9Q34.3) MUTATED                          10    60
  DEL PEAK 26(9Q34.3) WILD-TYPE                        38   386
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 26(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     60
                                  clus
vv                                 DEL PEAK 26(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      386
[1] 4 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 26(9Q34.3) MUTATED     5  65
  DEL PEAK 26(9Q34.3) WILD-TYPE  21 394
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 26(9Q34.3) MUTATED      5   65
  DEL PEAK 26(9Q34.3) WILD-TYPE   21  394
                        clus
vv                       DEL PEAK 26(9Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       DEL PEAK 26(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                21
  NOT HISPANIC OR LATINO                           394
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 27(10P15.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10P15.3) MUTATED    85  85
  DEL PEAK 27(10P15.3) WILD-TYPE 216 134
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                           170                            350 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                            85                            134 
$`DEL PEAK 27(10P15.3) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BB-A5HU TCGA-CQ-5323 TCGA-CQ-7067 TCGA-CQ-A4C7 
        9.30        68.48        25.71        48.20        16.73        11.61 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-HD-8635 TCGA-UF-A71D TCGA-BA-4076 
       34.36        30.94        14.04        22.85        48.03        13.64 
TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
        9.07        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DI TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 
       41.85        29.42        11.05        66.28        24.66        20.52 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4737 
       10.55         6.28        55.86        38.04         4.67        20.55 
TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 
       42.02        12.39        71.31         8.32        56.94        30.67 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       48.00        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63W TCGA-CQ-5326 TCGA-CQ-6223 TCGA-CQ-6224 
       17.42        11.74        12.39         2.93        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CR-6474 
       13.25        14.99        64.87        41.88        77.56        18.54 
TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
       11.64        39.16        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
        3.09        24.95        29.23         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 TCGA-CV-5435 
       26.17        17.13        47.01        12.89         5.13        76.24 
TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6933 
      107.51        80.12        17.92        60.49        43.23        90.12 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6950 TCGA-CV-6952 
        2.14         5.46        26.43       140.78        15.09         6.08 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7097 
       65.82         2.50         4.14        64.83       172.67        12.66 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7235 
        9.01         5.26         1.84        21.80        71.21        77.16 
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-A45X 
       84.49         7.17         6.38        35.47        45.96         6.51 
TCGA-CV-A465 TCGA-CV-A6JD TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-D6-6517 
        7.07         5.98        28.01        21.24        22.52         9.60 
TCGA-D6-6826 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-DQ-7590 TCGA-F7-8489 TCGA-F7-A50G 
       11.44        13.94        18.02        46.45        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A620 TCGA-HD-7831 TCGA-HD-A4C1 TCGA-HD-A633 
        3.02        24.95        17.85        21.93         0.36        13.84 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A6SH TCGA-KU-A6H7 
       11.84        37.41        33.57         5.29        15.48        19.27 
TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
        7.96        15.42        47.01        75.55        18.97         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 
       29.00        13.15        21.07        23.15        21.47        27.39 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-T2-A6WX TCGA-T2-A6WZ 
       14.76        12.20        17.82         8.32         6.87        15.91 
TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71A 
        7.10        13.71         3.12        13.25        64.80         2.83 
TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-WA-A7GZ 
       49.51        17.95        24.30        18.05        13.94        20.55 
TCGA-WA-A7H4 TCGA-KU-A66T 
       14.56        18.15 

$`DEL PEAK 27(10P15.3) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       37.28        20.48         3.55        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
        9.07         9.24        52.08        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 
       19.82        24.39        32.88        70.13        43.04        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        6.02         0.36        46.32        40.24        21.11        12.66 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        2.96         3.35        15.19        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-A4IH TCGA-BA-A6D8 
       57.93        17.10        23.84        65.59        20.45        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       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HZ TCGA-BB-A6UM 
       50.20        44.98        38.40        71.05        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        8.81        12.69        48.76        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        57.11        12.99        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5364 
       27.58        73.61        13.05        46.32         8.58        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        52.08 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6994 TCGA-CN-6995 
       50.07        23.90        47.44        28.04        38.89         3.68 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        25.41        23.57        17.29        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
        7.40        31.69        22.32        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        2.70        23.44        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 
        4.24        41.19        32.38         4.24        38.76        53.52 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.10        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
       14.14        12.46        31.23        84.23        11.77        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-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
       16.90        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 
       22.78        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        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         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        89.65 
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        49.71        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 
       21.01       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-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        10.42        10.55        18.84        51.12        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-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       24.95        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       33.86        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A622 
       37.18        32.71        31.13        18.94         0.46        11.80 
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        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       33.76        28.47        25.74        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
       22.03         4.27         3.65         6.90        34.75        15.95 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O 
       38.53        14.50        37.71         0.07        13.68        13.84 
TCGA-IQ-A6SG TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       19.04        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 
        6.25         7.13        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T6 
       71.74        51.25        10.85        36.82        19.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB 
       16.01        21.21         7.30         9.34        12.72        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP 
       19.73        12.89         5.62        15.32        12.72        16.96 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 
       32.45        13.55        20.35        54.67        49.45        44.65 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       74.47        55.43        29.46        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-KU-A66S 
       17.03        13.35 

  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                          0.36                           0.07 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                        172.67                         210.97 
  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE 
                         18.97                          22.39 
[1] "0.4 - 172.7 (19.0)" "0.1 - 211.0 (22.4)"
[1] "hr=" "1.4"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 27(10P15.3) MUTATED         5       23        23        95         3
  DEL PEAK 27(10P15.3) WILD-TYPE      22       53        59       157         9
                                vv
clus                             STAGE IVC
  DEL PEAK 27(10P15.3) MUTATED           0
  DEL PEAK 27(10P15.3) WILD-TYPE         1
D55V3, multiclass
           clus
vv          DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  STAGE I                              5                             22
  STAGE II                            23                             53
  STAGE III                           23                             59
  STAGE IVA                           95                            157
  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 27(10P15.3) MUTATED       8  44  32  67
  DEL PEAK 27(10P15.3) WILD-TYPE    42  93  68 106
D55V4, multiclass
       clus
vv      DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  T0+T1                            8                             42
  T2                              44                             93
  T3                              32                             68
  T4                              67                            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 27(10P15.3) MUTATED    48  23  67   1
  DEL PEAK 27(10P15.3) WILD-TYPE 131  45 101   7
D55V5, multiclass
    clus
vv   DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  N0                           48                            131
  N1                           23                             45
  N2                           67                            101
  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 27(10P15.3) MUTATED    58   0
  DEL PEAK 27(10P15.3) WILD-TYPE 132   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED     58    0
  DEL PEAK 27(10P15.3) WILD-TYPE  132    1
   clus
vv  DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  0                           58                            132
  1                            0                              1
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED    41 129
  DEL PEAK 27(10P15.3) WILD-TYPE  99 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED     41  129
  DEL PEAK 27(10P15.3) WILD-TYPE   99  253
        clus
vv       DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  FEMALE                           41                             99
  MALE                            129                            253
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED    49 101
  DEL PEAK 27(10P15.3) WILD-TYPE 113 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED     49  101
  DEL PEAK 27(10P15.3) WILD-TYPE  113  200
     clus
vv    DEL PEAK 27(10P15.3) MUTATED DEL PEAK 27(10P15.3) WILD-TYPE
  NO                            49                            113
  YES                          101                            200
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.3) MUTATED                                   170
  DEL PEAK 27(10P15.3) WILD-TYPE                                 341
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 27(10P15.3) MUTATED                                                   0
  DEL PEAK 27(10P15.3) WILD-TYPE                                                10
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 27(10P15.3) MUTATED                                                           0
  DEL PEAK 27(10P15.3) WILD-TYPE                                                         1
D55V9, multiclass
                                                           clus
vv                                                          DEL PEAK 27(10P15.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                170
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 27(10P15.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  341
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, continuous
D55V11, continuous
D55V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(10P15.3) MUTATED                                  0     3
  DEL PEAK 27(10P15.3) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10P15.3) MUTATED                          24   140
  DEL PEAK 27(10P15.3) WILD-TYPE                        24   306
D55V13, multiclass
                                  clus
vv                                 DEL PEAK 27(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     140
                                  clus
vv                                 DEL PEAK 27(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    24
  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"
D55V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.3) MUTATED     7 150
  DEL PEAK 27(10P15.3) WILD-TYPE  19 309
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.3) MUTATED      7  150
  DEL PEAK 27(10P15.3) WILD-TYPE   19  309
                        clus
vv                       DEL PEAK 27(10P15.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          150
                        clus
vv                       DEL PEAK 27(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            309
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 28(10P11.21) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10P11.21) MUTATED    86  77
  DEL PEAK 28(10P11.21) WILD-TYPE 215 142
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                            163                             357 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                             77                             142 
$`DEL PEAK 28(10P11.21) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BB-A5HU TCGA-CQ-5323 TCGA-CQ-7067 TCGA-CQ-A4C7 
        9.30        68.48        25.71        48.20        16.73        11.61 
TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7593 TCGA-BA-4074 
        6.02        34.36        30.94        14.04        40.24        15.19 
TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        9.07        15.52        14.83        12.62         4.01        41.85 
TCGA-BA-A6D8 TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 
       27.95        11.05        16.41        66.28        38.40        20.52 
TCGA-BB-A5HY TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5360 
       10.55         6.28        55.86        20.55        42.02        71.31 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
        8.32        16.21        56.94        30.67        48.00        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A 
       34.13         6.74        10.45        17.42        11.74        17.29 
TCGA-CN-A63W TCGA-CN-A6V6 TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 
       12.39        20.88         2.93        10.42        41.19        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7072 
       56.58        13.25        14.99        64.87        41.88        77.56 
TCGA-CQ-A4CI TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       31.23        18.54        11.64        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7380 
       35.84         3.45        24.95        29.23         0.99        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7398 
       26.17        17.13        47.01        12.89        49.58         5.13 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-5977 
       17.16        76.24        80.12        17.92        86.83        60.49 
TCGA-CV-5979 TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       43.23        90.12         5.46        26.43        11.24       140.78 
TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 
       42.38        15.09        65.82         2.50         4.14       172.67 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7242 
       12.66         9.01         5.26         1.84        71.21        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7263 
       31.36        26.20        18.97        17.13         4.96        18.41 
TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 
        0.46        25.94       100.57        14.89        54.94        84.49 
TCGA-CV-7434 TCGA-CV-7438 TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A465 TCGA-CV-A6JD 
        7.17         6.38        35.47        45.96         7.07         5.98 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4ZB 
       21.24        22.52         9.60        23.05        11.44        12.36 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5631 TCGA-DQ-7590 TCGA-F7-A50G TCGA-F7-A50I 
       13.94        12.10        18.02        46.45        20.25         3.02 
TCGA-F7-A61V TCGA-F7-A61W TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-A633 TCGA-IQ-A61G 
       24.95         0.46        28.47        21.93        13.84        11.84 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H7 
       37.41        33.57         5.29        13.84        15.48        19.27 
TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T5 
        7.96        17.98        71.74        75.55         2.04        29.00 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       13.15        21.07        21.47        27.39        14.76        12.20 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-UF-A718 
       17.82         8.32         7.10        13.71        13.25        64.80 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-WA-A7GZ TCGA-WA-A7H4 
        2.83        49.51        17.95        24.30        20.55        14.56 
TCGA-KU-A66T 
       18.15 

$`DEL PEAK 28(10P11.21) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       37.28        20.48         3.55        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
        9.07         9.24        52.08        11.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 
       19.82        24.39        32.88        70.13        43.04        34.52 
TCGA-CX-7082 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D 
        0.36        46.32        21.11        12.66        22.85        48.03 
TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
        2.96         3.35        13.64        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-A4IF 
       57.93        17.10        23.84        65.59        21.17        29.42 
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-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        2.27        13.38        20.48         6.15       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         4.41        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A5HZ TCGA-BB-A6UM 
       50.20        44.98        24.66        71.05        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        8.81        12.69        48.76        38.04         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       12.89        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
       14.33        45.83        27.58        73.61        13.05        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
        8.58        12.39        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        8.52        52.08        50.07        23.90        47.44        28.04 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       32.22        38.89         3.68        35.01        25.41        23.57 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 
        4.41        12.07         2.70        23.44        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       21.50        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7071 
        4.24        32.38         4.24        38.76        53.52        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        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-6473 TCGA-CR-6477 TCGA-CR-6480 
       58.42        50.01        39.52        36.99        16.90        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        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        9.27        47.18         3.09        31.96         9.17        34.06 
TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       32.78        27.06        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       30.58        24.79         5.95        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
      139.43       129.21       108.95        19.20        17.95       107.51 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
       94.88        76.50        91.53        13.35        23.05        48.59 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        7.07        54.74        21.07        62.43         9.60         2.14 
TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6945 
        9.70        20.52         4.73        21.90        19.79        12.03 
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 
       89.65        95.34        11.87        47.97         2.10        49.71 
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        21.01       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-7085 
       28.01         3.62        23.47        19.92        10.42        10.55 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 
       18.84        51.12        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        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       22.59        24.95        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       33.86        20.45        37.58        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 
       37.18        32.71        21.63        31.13        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-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       20.94        33.76        25.74        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         0.36         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61L 
       15.95        38.53        14.50        37.71         0.07        13.68 
TCGA-IQ-A6SG TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
       19.04        10.75        14.37        30.05         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        6.25        15.42         7.13        16.08        29.92        15.78 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T3 
       51.25        10.85        36.82        47.01        19.00        18.97 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       12.99        16.01        21.21        23.15         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3J 
       12.72        21.07        19.73        12.89         5.62        15.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92N 
       12.72        16.96         6.87        15.91        32.45         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       13.55        20.35        54.67        49.45        44.65        74.47 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS 
       55.43        29.46        18.05        13.94        20.75        22.36 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-KU-A66S 
       32.65        17.03        13.35 

  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                           0.46                            0.07 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                         172.67                          210.97 
  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE 
                          18.54                           22.32 
[1] "0.5 - 172.7 (18.5)" "0.1 - 211.0 (22.3)"
[1] "hr=" "1.3"
D56V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 28(10P11.21) MUTATED         8       19        23        88
  DEL PEAK 28(10P11.21) WILD-TYPE      19       57        59       164
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 28(10P11.21) MUTATED           6         0
  DEL PEAK 28(10P11.21) WILD-TYPE         6         1
D56V3, multiclass
           clus
vv          DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  STAGE I                               8                              19
  STAGE II                             19                              57
  STAGE III                            23                              59
  STAGE IVA                            88                             164
  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 28(10P11.21) MUTATED      10  42  30  64
  DEL PEAK 28(10P11.21) WILD-TYPE    40  95  70 109
D56V4, multiclass
       clus
vv      DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  T0+T1                            10                              40
  T2                               42                              95
  T3                               30                              70
  T4                               64                             109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 28(10P11.21) MUTATED    49  22  60   3
  DEL PEAK 28(10P11.21) WILD-TYPE 130  46 108   5
D56V5, multiclass
    clus
vv   DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  N0                            49                             130
  N1                            22                              46
  N2                            60                             108
  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"
D56V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    56   0
  DEL PEAK 28(10P11.21) WILD-TYPE 134   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     56    0
  DEL PEAK 28(10P11.21) WILD-TYPE  134    1
   clus
vv  DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  0                            56                             134
  1                             0                               1
[1] 2 2
[1] FALSE
D56V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    36 127
  DEL PEAK 28(10P11.21) WILD-TYPE 104 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     36  127
  DEL PEAK 28(10P11.21) WILD-TYPE  104  255
        clus
vv       DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  FEMALE                            36                             104
  MALE                             127                             255
[1] 2 2
[1] FALSE
D56V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10P11.21) MUTATED    42 102
  DEL PEAK 28(10P11.21) WILD-TYPE 120 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED     42  102
  DEL PEAK 28(10P11.21) WILD-TYPE  120  199
     clus
vv    DEL PEAK 28(10P11.21) MUTATED DEL PEAK 28(10P11.21) WILD-TYPE
  NO                             42                             120
  YES                           102                             199
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10P11.21) MUTATED                                   161
  DEL PEAK 28(10P11.21) WILD-TYPE                                 350
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 28(10P11.21) MUTATED                                                   1
  DEL PEAK 28(10P11.21) WILD-TYPE                                                 9
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 28(10P11.21) MUTATED                                                           1
  DEL PEAK 28(10P11.21) WILD-TYPE                                                         0
D56V9, multiclass
                                                           clus
vv                                                          DEL PEAK 28(10P11.21) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 161
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
                                                           clus
vv                                                          DEL PEAK 28(10P11.21) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   350
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, continuous
D56V11, continuous
D56V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(10P11.21) MUTATED                                  0     5
  DEL PEAK 28(10P11.21) WILD-TYPE                                2     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(10P11.21) MUTATED                          25   131
  DEL PEAK 28(10P11.21) WILD-TYPE                        23   315
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 28(10P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      131
                                  clus
vv                                 DEL PEAK 28(10P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     23
  WHITE                                                        315
[1] 4 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 28(10P11.21) MUTATED     9 142
  DEL PEAK 28(10P11.21) WILD-TYPE  17 317
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10P11.21) MUTATED      9  142
  DEL PEAK 28(10P11.21) WILD-TYPE   17  317
                        clus
vv                       DEL PEAK 28(10P11.21) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           142
                        clus
vv                       DEL PEAK 28(10P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  17
  NOT HISPANIC OR LATINO                             317
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 29(10Q23.31) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(10Q23.31) MUTATED    77  61
  DEL PEAK 29(10Q23.31) WILD-TYPE 224 158
  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE 
                            138                             382 
  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE 
                             61                             158 
$`DEL PEAK 29(10Q23.31) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6024 
        9.30        68.48        28.11        51.29         9.07        11.08 
TCGA-CQ-6221 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-BA-4074 TCGA-BA-4078 
       32.88        14.04        46.32        40.24        15.19         9.07 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A6D8 TCGA-BA-A6DI TCGA-BA-A8YP 
       42.35        17.10        21.17        27.95        11.05        16.41 
TCGA-BB-7861 TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-5355 
       22.42        66.28        20.52         6.28        38.04        42.02 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
       12.39        71.31        56.94        48.00        19.07        34.13 
TCGA-CN-6020 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A6V6 
        6.74        11.74        23.57        17.29        31.69        20.88 
TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 
       19.53        10.42        13.25        14.99        64.87        77.56 
TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-7365 
       50.01        18.54        16.90        11.90        11.64        39.16 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       40.93        35.84         3.45        24.95        29.23         0.99 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
       17.13        47.01         5.13        17.16       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6933 
       76.24        19.20        86.83         7.07        43.23        90.12 
TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6960 
        9.70        26.43        11.24        12.03        15.09        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 
        2.50         4.14       172.67        12.66         5.26        52.31 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 
       36.00        31.36        26.20        17.13        18.41        57.47 
TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7438 
        0.46        25.94       100.57        14.89        84.49         6.38 
TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JY TCGA-D6-6823 TCGA-D6-A4ZB 
       45.96        60.43         7.07        21.24        23.05        12.36 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7590 
       13.94        12.10        12.79        23.34        18.02        46.45 
TCGA-DQ-7596 TCGA-H7-A76A TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
       41.59        20.94         3.65        11.84        37.41        33.57 
TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MT-A7BN TCGA-MZ-A5BI 
        5.29        19.04        19.27         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 
       21.47        27.39        21.07        14.76        12.20         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        64.80        54.67        49.51 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       44.65        17.95        17.03        20.55        14.56        18.15 

$`DEL PEAK 29(10Q23.31) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6022 
       37.28        20.48         3.55        30.18        25.71         9.24 
TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       52.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 
       70.13        16.73        43.04        11.61        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
        0.36        34.36        30.94        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 
       48.03         2.96         3.35        13.64        26.50        23.74 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
       57.93        23.84        65.59        15.52        14.83        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DB 
        4.01        41.85        29.42        20.45        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A480 
       71.05        10.55        27.19        12.92         8.81        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       48.76        55.86         4.67        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.81        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        46.32         8.58 
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-6013 TCGA-CN-6016 
        8.52        52.08        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       28.04        10.45        32.22        38.89         3.68        17.42 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       35.01        25.41        29.72        21.21         7.40        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
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        46.95 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       56.58         4.24        38.76        53.52        41.88        43.10 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       44.48        23.24        29.36        33.60        29.49        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-6471 TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6482 
       26.27        58.42        39.52        36.99        10.22        11.34 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
        7.69        12.46        22.78        15.75         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       47.34         3.09        31.96         9.17        34.06        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        49.58        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
       46.85        32.65        44.25        30.58        24.79         5.95 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5440 
       35.41        29.95        48.39       139.43        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-6003 TCGA-CV-6433 TCGA-CV-6436 
       23.05        48.59        60.49        54.74        21.07        62.43 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        9.60         2.14         5.46        20.52         4.73        21.90 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
      140.78        19.79        42.38        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-7089 TCGA-CV-7091 
       65.82        10.98         7.13         8.42        64.83       111.16 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7177 
       18.81         7.99         9.01         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        89.65 
TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 
       18.97        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 
       49.71        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-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
       54.94         3.52        16.27        19.76         7.17       153.86 
TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R 
       16.64        22.19        27.98        21.01       169.38       180.16 
TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      159.65        35.47         1.05         6.51        88.87        48.20 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
       67.86         0.76        56.61        15.25         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
        6.38        29.79         6.48        28.01         3.62        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60         2.53        16.14        11.44 
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        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7591 
       22.59        24.95        58.45        37.25        33.86        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       37.58        40.04        39.12        37.18        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       15.06        33.76        28.47        25.74        21.93        27.48 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        14.66        22.03         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        38.53        14.50        37.71 
TCGA-IQ-A61I TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W 
        0.07        13.68        13.84        15.48        10.75        14.37 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5Q6 
       30.05         1.84        12.62         6.25        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 
       71.74        10.85        36.82        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        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        7.30         9.34        12.72        19.73        12.89         5.62 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 
       17.82        15.32        12.72        16.96         6.87        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71E 
       13.71         3.12        13.55        20.35         2.83        49.45 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-KU-A66S 
       20.75        22.36        32.65        13.35 

  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE 
                           0.46                            0.07 
  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE 
                         172.67                          210.97 
  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE 
                          19.40                           21.85 
[1] "0.5 - 172.7 (19.4)" "0.1 - 211.0 (21.9)"
[1] "hr=" "1.1"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 29(10Q23.31) MUTATED         3       21        23        63
  DEL PEAK 29(10Q23.31) WILD-TYPE      24       55        59       189
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 29(10Q23.31) MUTATED           4         0
  DEL PEAK 29(10Q23.31) WILD-TYPE         8         1
D57V3, multiclass
           clus
vv          DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE
  STAGE I                               3                              24
  STAGE II                             21                              55
  STAGE III                            23                              59
  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
  DEL PEAK 29(10Q23.31) MUTATED       8  39  29  42
  DEL PEAK 29(10Q23.31) WILD-TYPE    42  98  71 131
D57V4, multiclass
       clus
vv      DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE
  T0+T1                             8                              42
  T2                               39                              98
  T3                               29                              71
  T4                               42                             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
  DEL PEAK 29(10Q23.31) MUTATED    47  15  45   2
  DEL PEAK 29(10Q23.31) WILD-TYPE 132  53 123   6
D57V5, multiclass
    clus
vv   DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE
  N0                            47                             132
  N1                            15                              53
  N2                            45                             123
  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 29(10Q23.31) MUTATED    47   0
  DEL PEAK 29(10Q23.31) WILD-TYPE 143   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(10Q23.31) MUTATED     47    0
  DEL PEAK 29(10Q23.31) WILD-TYPE  143    1
   clus
vv  DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE
  0                            47                             143
  1                             0                               1
[1] 2 2
[1] FALSE
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 29(10Q23.31) MUTATED    27 111
  DEL PEAK 29(10Q23.31) WILD-TYPE 113 271
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(10Q23.31) MUTATED     27  111
  DEL PEAK 29(10Q23.31) WILD-TYPE  113  271
        clus
vv       DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE
  FEMALE                            27                             113
  MALE                             111                             271
[1] 2 2
[1] FALSE
D57V8, binary
                                 cls
clus                                0   1
  DEL PEAK 29(10Q23.31) MUTATED    35  82
  DEL PEAK 29(10Q23.31) WILD-TYPE 127 219
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(10Q23.31) MUTATED     35   82
  DEL PEAK 29(10Q23.31) WILD-TYPE  127  219
     clus
vv    DEL PEAK 29(10Q23.31) MUTATED DEL PEAK 29(10Q23.31) WILD-TYPE
  NO                             35                             127
  YES                            82                             219
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(10Q23.31) MUTATED                                   137
  DEL PEAK 29(10Q23.31) WILD-TYPE                                 374
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 29(10Q23.31) MUTATED                                                   1
  DEL PEAK 29(10Q23.31) WILD-TYPE                                                 9
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 29(10Q23.31) MUTATED                                                           0
  DEL PEAK 29(10Q23.31) WILD-TYPE                                                         1
D57V9, multiclass
                                                           clus
vv                                                          DEL PEAK 29(10Q23.31) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 137
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
                                                           clus
vv                                                          DEL PEAK 29(10Q23.31) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   374
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
D57V11, continuous
D57V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(10Q23.31) MUTATED                                  0     3
  DEL PEAK 29(10Q23.31) WILD-TYPE                                2     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(10Q23.31) MUTATED                          17   116
  DEL PEAK 29(10Q23.31) WILD-TYPE                        31   330
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 29(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      116
                                  clus
vv                                 DEL PEAK 29(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     31
  WHITE                                                        330
[1] 4 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 29(10Q23.31) MUTATED    10 118
  DEL PEAK 29(10Q23.31) WILD-TYPE  16 341
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(10Q23.31) MUTATED     10  118
  DEL PEAK 29(10Q23.31) WILD-TYPE   16  341
                        clus
vv                       DEL PEAK 29(10Q23.31) MUTATED
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           118
                        clus
vv                       DEL PEAK 29(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  16
  NOT HISPANIC OR LATINO                             341
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 30(11P15.5) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(11P15.5) MUTATED    89  73
  DEL PEAK 30(11P15.5) WILD-TYPE 212 146
  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE 
                           162                            358 
  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE 
                            73                            146 
$`DEL PEAK 30(11P15.5) MUTATED`
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6997 
        3.55        28.11        30.18         9.07        35.05        32.48 
TCGA-CQ-6221 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-8635 
       32.88         6.02         0.36        30.94        46.32        22.85 
TCGA-UF-A71D TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
       48.03         9.07        17.10        15.52        14.83        12.62 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE 
       41.85        20.45        27.95        11.54         5.69        14.47 
TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-A6UO TCGA-CN-4725 
       16.41         4.41        66.28        71.05         8.81        38.04 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 
       56.68        12.89        57.11        12.99        45.83        27.58 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5374 
       46.32        12.39         8.32        11.54        11.84        56.94 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       30.67        48.00        34.13         6.74        10.45        32.22 
TCGA-CN-6998 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A6UY TCGA-CQ-5326 
       11.74        21.21        31.69        16.57        23.44         2.93 
TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       10.42         4.24        23.24        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-7374 
       54.67        16.90        10.22        11.34        11.64         0.99 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7399 TCGA-CR-7404 
       17.13        32.78        27.06        12.89         5.95        48.39 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6933 
      139.43       129.21        17.95         7.07         9.60        90.12 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 
        5.46        20.52        26.43       140.78        12.03        42.38 
TCGA-CV-6956 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 
        7.13         4.14       111.16        18.81        12.66         9.01 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7245 
        5.26         1.84        52.31        21.80        77.16        26.20 
TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7415 TCGA-CV-7416 
       11.87        49.71        18.41        35.54        22.85        25.08 
TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45U 
        0.07       100.57        16.27       153.86       180.16        35.47 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JU TCGA-D6-8568 TCGA-D6-A4ZB 
       88.87        48.20        60.43         3.62        24.95        12.36 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7594 TCGA-DQ-7596 
       13.94        12.79        23.34        58.45        40.04        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7753 
       37.18        32.71        20.25         3.02        20.25        28.47 
TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A6HZ TCGA-IQ-7632 
       21.93        27.48        14.66        22.03         3.65        14.50 
TCGA-IQ-A61G TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 
       11.84         6.25        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 
       23.15        21.47        12.89        14.76        12.20        15.32 
TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 
        8.32        15.91         3.12        13.25        64.80        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JH TCGA-KU-A66T 
        2.83        49.51        49.45        74.47        29.46        18.15 

$`DEL PEAK 30(11P15.5) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BB-A5HU TCGA-CN-4727 
        9.30        37.28        20.48        68.48        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
        9.24        52.08        11.08        19.82        24.39        48.20 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 
       70.13        16.73        43.04        11.61        34.52        34.36 
TCGA-DQ-7588 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A7JV TCGA-4P-AA8J 
       14.04        40.24        21.11        12.66         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
       15.19        13.64        26.50        23.74        42.35        57.93 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DB 
       23.84        65.59        21.17         4.01        29.42         7.10 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
        7.82         2.27        11.05        13.38        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         4.80        18.38        22.42        36.72 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 
       33.70        50.20        44.98        24.66        38.40        20.52 
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        48.76 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4737 
       55.86         4.67        26.86        32.81        52.14        20.55 
TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       14.33        73.61        13.05        42.02         8.58        71.31 
TCGA-CN-5364 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       16.21        11.57        12.49         8.52        52.08        50.07 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6995 
       23.90        47.44        28.04        19.07        38.89         3.68 
TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       17.42        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
        7.40        22.32        12.39         4.41        12.07         2.70 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        19.53        52.37        21.50        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       62.37        45.99        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-7064 
       46.95        56.58        13.25        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       53.52        41.88        43.10        77.56        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 TCGA-CR-5250 
       33.60        29.49        14.14        12.46        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
       58.42        50.01        39.52        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        22.78        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        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 
       44.25        30.58        24.79         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       172.67 
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 
       89.65        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        21.01 
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        28.01        21.24        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
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        28.77         7.63 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       22.59        24.95        12.10        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50J 
       46.45        20.45        37.58        39.12        21.63        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        11.80        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
       13.38        15.16        15.06        20.94        33.76        25.74 
TCGA-HD-7832 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       27.48         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J 
       15.95        38.53        37.71        37.41         0.07        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 
        5.29        13.68        13.84        19.04        15.48        19.27 
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-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX 
       17.98        29.92        71.74        51.25        10.85        47.01 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG 
       75.55        18.97        16.01        21.07        21.21         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        27.39        21.07        19.73         5.62 
TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       17.82        12.72        16.96         6.87         7.10        32.45 
TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
       13.71        13.55        20.35        44.65        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT 
       55.43        18.05        13.94        20.75        22.36        32.65 
TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       17.03        20.55        14.56        13.35 

  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE 
                        19.625                         21.370 
[1] "0.1 - 180.2 (19.6)" "0.1 - 211.0 (21.4)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 30(11P15.5) MUTATED         5       19        20        78         8
  DEL PEAK 30(11P15.5) WILD-TYPE      22       57        62       174         4
                                vv
clus                             STAGE IVC
  DEL PEAK 30(11P15.5) MUTATED           0
  DEL PEAK 30(11P15.5) WILD-TYPE         1
D58V3, multiclass
           clus
vv          DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE
  STAGE I                              5                             22
  STAGE II                            19                             57
  STAGE III                           20                             62
  STAGE IVA                           78                            174
  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 30(11P15.5) MUTATED      14  36  28  58
  DEL PEAK 30(11P15.5) WILD-TYPE    36 101  72 115
D58V4, multiclass
       clus
vv      DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE
  T0+T1                           14                             36
  T2                              36                            101
  T3                              28                             72
  T4                              58                            115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 30(11P15.5) MUTATED    45  18  51   6
  DEL PEAK 30(11P15.5) WILD-TYPE 134  50 117   2
D58V5, multiclass
    clus
vv   DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE
  N0                           45                            134
  N1                           18                             50
  N2                           51                            117
  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 30(11P15.5) MUTATED    51   0
  DEL PEAK 30(11P15.5) WILD-TYPE 139   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11P15.5) MUTATED     51    0
  DEL PEAK 30(11P15.5) WILD-TYPE  139    1
   clus
vv  DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE
  0                           51                            139
  1                            0                              1
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11P15.5) MUTATED    39 124
  DEL PEAK 30(11P15.5) WILD-TYPE 101 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11P15.5) MUTATED     39  124
  DEL PEAK 30(11P15.5) WILD-TYPE  101  258
        clus
vv       DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE
  FEMALE                           39                            101
  MALE                            124                            258
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(11P15.5) MUTATED    37  99
  DEL PEAK 30(11P15.5) WILD-TYPE 125 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11P15.5) MUTATED     37   99
  DEL PEAK 30(11P15.5) WILD-TYPE  125  202
     clus
vv    DEL PEAK 30(11P15.5) MUTATED DEL PEAK 30(11P15.5) WILD-TYPE
  NO                            37                            125
  YES                           99                            202
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11P15.5) MUTATED                                   156
  DEL PEAK 30(11P15.5) WILD-TYPE                                 355
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 30(11P15.5) MUTATED                                                   7
  DEL PEAK 30(11P15.5) WILD-TYPE                                                 3
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 30(11P15.5) MUTATED                                                           0
  DEL PEAK 30(11P15.5) WILD-TYPE                                                         1
D58V9, multiclass
                                                           clus
vv                                                          DEL PEAK 30(11P15.5) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                156
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 30(11P15.5) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  355
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
D58V11, continuous
D58V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(11P15.5) MUTATED                                  1     1
  DEL PEAK 30(11P15.5) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(11P15.5) MUTATED                          22   136
  DEL PEAK 30(11P15.5) WILD-TYPE                        26   310
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 30(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     136
                                  clus
vv                                 DEL PEAK 30(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(11P15.5) MUTATED    11 136
  DEL PEAK 30(11P15.5) WILD-TYPE  15 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11P15.5) MUTATED     11  136
  DEL PEAK 30(11P15.5) WILD-TYPE   15  323
                        clus
vv                       DEL PEAK 30(11P15.5) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK 30(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            323
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 31(11Q23.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(11Q23.1) MUTATED   141 103
  DEL PEAK 31(11Q23.1) WILD-TYPE 160 116
  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE 
                           244                            276 
  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE 
                           103                            116 
$`DEL PEAK 31(11Q23.1) MUTATED`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        68.48         3.55        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 TCGA-CQ-5323 TCGA-CQ-6221 
       51.29         9.07        11.08        35.05        48.20        32.88 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 
       16.73        11.61        34.52         6.02         0.36        34.36 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-BA-4074 TCGA-BA-4076 
       14.04        46.32        40.24        21.11        15.19        13.64 
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 
        9.07        26.50        57.93        17.10        15.52        14.83 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD 
       12.62         4.01        41.85        20.45        11.54         5.69 
TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 
        2.27        20.48         6.15       105.90         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A6UM 
       22.42        44.98        66.28        24.66        71.05        12.92 
TCGA-BB-A6UO TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4741 
        8.81        56.68        12.89        57.11        45.83        73.61 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       12.39        71.31         8.32        11.54        11.84        11.57 
TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
        8.52        56.94        30.67        48.00        23.90         6.74 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
       32.22        38.89         3.68        11.74        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63Y TCGA-CN-A641 
       17.29        29.72        21.21         7.40        16.57        12.07 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6224 
       23.44        20.88        19.53        10.42        32.38        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CR-5243 
        4.24        14.99        38.76        29.36        33.60        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       36.99        18.54        16.90        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        22.78         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 
      140.78        12.03         8.42         2.50       172.67       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-7086 
       45.96        88.87        60.43        35.34        29.79        18.84 
TCGA-CX-A4AQ TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-D6-A6ES 
       51.12        23.05        16.14        17.72        13.94        12.79 
TCGA-D6-A74Q TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 
       23.34        46.45        20.45        40.04        41.59        37.18 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A76A 
       32.71        20.25         3.02        20.25        15.06        20.94 
TCGA-HD-7753 TCGA-HD-8314 TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
       28.47        22.03        34.75        11.84        37.41        33.57 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
       13.68        13.84        19.27        14.37         7.96         1.84 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SW 
        6.25         7.13        17.98        71.74        10.85        36.82 
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-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 
       23.15         7.30        21.47        27.39        21.07        12.89 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ 
       14.76        12.20        15.32         8.32        16.96        15.91 
TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A719 
        7.10        13.71         3.12        13.25        20.35        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        2.83        49.51        49.45        74.47        17.95        24.30 
TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UP-A6WW TCGA-KU-A66T 
       29.46        22.36        17.03        18.15 

$`DEL PEAK 31(11Q23.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5557 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A6V1 
        9.30        20.48         9.24        52.08        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-DQ-5629 TCGA-HD-8634 TCGA-HD-8635 
       24.39        70.13        43.04        30.94        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 
       48.03         2.96         3.35        23.74        42.35        23.84 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
       65.59        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         4.80 
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        48.76        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
        4.67        26.86        32.81        52.14        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        42.02        46.32         8.58 
TCGA-CN-5364 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 
       16.21        12.49        52.08        50.07        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A63U 
       19.07        34.13        10.45        17.42        35.01        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5325 
       22.32        12.39         4.41         2.70        52.37        21.50 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        2.93        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-7064 TCGA-CQ-7065 
        4.24        41.19        46.95        13.25        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
       41.88        43.10        77.56        44.48        23.24        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-6471 TCGA-CR-6492 TCGA-CR-7364 
       14.14        12.46        31.23        39.52        15.75        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
       39.16        47.34        40.93        24.95        29.23         0.99 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 
       31.96        34.06        26.17        47.01        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        5.13        35.41        29.95       108.95        76.24        19.20 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6436 
       76.50        80.12        17.92        23.05         7.07        62.43 
TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6950 
        2.14         4.73        11.24        19.79        42.38        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-6962 TCGA-CV-7089 TCGA-CV-7099 TCGA-CV-7103 TCGA-CV-7178 
       28.34         4.14        64.83         7.99        52.31        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
       10.75       130.88         4.73        89.65        36.00        31.36 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       26.20        17.13        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
        2.10        49.71        17.85       210.97        89.33         9.67 
TCGA-CV-7416 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 
       25.08        14.89        56.48       156.49         3.52        16.27 
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        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A461 
      169.38       159.65         1.05         6.51        48.20        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-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        6.48        28.01         3.62        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       22.52        10.42        10.55        13.25        25.41         9.60 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB 
        2.53        11.44        18.67        24.95        25.32        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5624 
       28.77         7.63        22.59        24.95        12.10        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-8489 
       37.25        33.86        18.02        37.58        39.12        21.63 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        17.85        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       12.43        13.38        15.16        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       27.48        27.48        14.66         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        3.65         6.90        15.95        38.53        14.50        37.71 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A67A 
        0.07         5.29        19.04        15.48        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        21.21         9.34 
TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-T2-A6WX 
       12.72        19.73         5.62        17.82        12.72         6.87 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-UF-A718 TCGA-UF-A7J9 TCGA-UF-A7JF TCGA-UF-A7JJ 
       32.45        13.55        64.80        44.65        55.43        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       13.94        20.75        32.65        20.55        14.56        13.35 

  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE 
                         20.50                          21.78 
[1] "0.1 - 180.2 (20.5)" "0.1 - 211.0 (21.8)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 31(11Q23.1) MUTATED        11       33        32       116         6
  DEL PEAK 31(11Q23.1) WILD-TYPE      16       43        50       136         6
                                vv
clus                             STAGE IVC
  DEL PEAK 31(11Q23.1) MUTATED           0
  DEL PEAK 31(11Q23.1) WILD-TYPE         1
D59V3, multiclass
           clus
vv          DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE
  STAGE I                             11                             16
  STAGE II                            33                             43
  STAGE III                           32                             50
  STAGE IVA                          116                            136
  STAGE IVB                            6                              6
  STAGE IVC                            0                              1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T0+T1 T2 T3 T4
  DEL PEAK 31(11Q23.1) MUTATED      23 64 45 74
  DEL PEAK 31(11Q23.1) WILD-TYPE    27 73 55 99
D59V4, multiclass
       clus
vv      DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE
  T0+T1                           23                             27
  T2                              64                             73
  T3                              45                             55
  T4                              74                             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 31(11Q23.1) MUTATED    65  26  96   3
  DEL PEAK 31(11Q23.1) WILD-TYPE 114  42  72   5
D59V5, multiclass
    clus
vv   DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE
  N0                           65                            114
  N1                           26                             42
  N2                           96                             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 31(11Q23.1) MUTATED    80   0
  DEL PEAK 31(11Q23.1) WILD-TYPE 110   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11Q23.1) MUTATED     80    0
  DEL PEAK 31(11Q23.1) WILD-TYPE  110    1
   clus
vv  DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE
  0                           80                            110
  1                            0                              1
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(11Q23.1) MUTATED    43 203
  DEL PEAK 31(11Q23.1) WILD-TYPE  97 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11Q23.1) MUTATED     43  203
  DEL PEAK 31(11Q23.1) WILD-TYPE   97  179
        clus
vv       DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE
  FEMALE                           43                             97
  MALE                            203                            179
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(11Q23.1) MUTATED    59 158
  DEL PEAK 31(11Q23.1) WILD-TYPE 103 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11Q23.1) MUTATED     59  158
  DEL PEAK 31(11Q23.1) WILD-TYPE  103  143
     clus
vv    DEL PEAK 31(11Q23.1) MUTATED DEL PEAK 31(11Q23.1) WILD-TYPE
  NO                            59                            103
  YES                          158                            143
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(11Q23.1) MUTATED                                   239
  DEL PEAK 31(11Q23.1) WILD-TYPE                                 272
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 31(11Q23.1) MUTATED                                                   6
  DEL PEAK 31(11Q23.1) WILD-TYPE                                                 4
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 31(11Q23.1) MUTATED                                                           1
  DEL PEAK 31(11Q23.1) WILD-TYPE                                                         0
D59V9, multiclass
                                                           clus
vv                                                          DEL PEAK 31(11Q23.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                239
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          DEL PEAK 31(11Q23.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  272
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
D59V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(11Q23.1) MUTATED                                  1     1
  DEL PEAK 31(11Q23.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(11Q23.1) MUTATED                          25   213
  DEL PEAK 31(11Q23.1) WILD-TYPE                        23   233
D59V13, multiclass
                                  clus
vv                                 DEL PEAK 31(11Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     213
                                  clus
vv                                 DEL PEAK 31(11Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    23
  WHITE                                                       233
[1] 4 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 31(11Q23.1) MUTATED    15 213
  DEL PEAK 31(11Q23.1) WILD-TYPE  11 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(11Q23.1) MUTATED     15  213
  DEL PEAK 31(11Q23.1) WILD-TYPE   11  246
                        clus
vv                       DEL PEAK 31(11Q23.1) MUTATED
  HISPANIC OR LATINO                               15
  NOT HISPANIC OR LATINO                          213
                        clus
vv                       DEL PEAK 31(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            246
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 32(12Q24.33) MUTATION ANALYSIS
D60V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(12Q24.33) MUTATED    36  27
  DEL PEAK 32(12Q24.33) WILD-TYPE 265 192
  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE 
                             63                             457 
  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE 
                             27                             192 
$`DEL PEAK 32(12Q24.33) MUTATED`
TCGA-BA-4075 TCGA-CN-4727 TCGA-CN-6024 TCGA-CX-7219 TCGA-DQ-5629 TCGA-H7-A6C5 
        9.30        51.29        11.08        34.36        30.94        21.11 
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH 
       15.52        14.83         4.01        41.85        29.42        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-8596 TCGA-CN-4726 TCGA-CN-4728 
       27.95        14.47        16.41        71.05         4.67        56.68 
TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6988 TCGA-CN-6994 
       45.83        42.02        12.39        56.94        10.45        38.89 
TCGA-CN-A49B TCGA-CQ-5332 TCGA-CR-6493 TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7390 
       29.72        10.42         9.27         3.45        17.13        49.58 
TCGA-CV-5430 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-6948 
      139.43        17.92        48.59        54.74         9.70        42.38 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7254 TCGA-CV-7255 
      172.67       111.16         5.26         1.84        47.97         2.10 
TCGA-CV-7263 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A6JY TCGA-D6-A4Z9 TCGA-D6-A6EP 
       18.41        84.49       153.86        21.24        17.72        13.94 
TCGA-F7-7848 TCGA-IQ-A61G TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MZ-A5BI TCGA-P3-A5Q6 
       37.18        11.84        19.04        15.48         7.13        15.78 
TCGA-P3-A5QA TCGA-P3-A6T5 TCGA-QK-A8Z7 TCGA-T2-A6WZ TCGA-T3-A92M TCGA-UF-A719 
       71.74        29.00        12.89        15.91        13.71        54.67 
TCGA-UF-A7JF TCGA-WA-A7GZ TCGA-KU-A66T 
       55.43        20.55        18.15 

$`DEL PEAK 32(12Q24.33) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       25.71         9.07         9.24        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 
       19.82        24.39        48.20        32.88        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-7588 
       43.04        11.61        34.52         6.02         0.36        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
       46.32        40.24        12.66        22.85        48.03         2.96 
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-5558 TCGA-BA-6869 
       42.35        57.93        17.10        23.84        65.59        21.17 
TCGA-BA-6872 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       12.62        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       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        4.80         4.41        18.38        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-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-4725 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
       48.76        55.86        38.04        12.89        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
       52.14        57.11        12.99        20.55        14.33        27.58 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       73.61        13.05        46.32         8.58        71.31         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-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        50.07        30.67        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6995 
       28.04        19.07        34.13         6.74        32.22         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       17.42        11.74        35.01        25.41        23.57        17.29 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
       21.21         7.40        31.69        22.32        12.39        16.57 
TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
        4.41        12.07         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
       52.37        21.50         2.93        54.58        70.45        62.37 
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        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        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-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        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        22.78 
TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       15.75        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-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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       24.79         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-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
      107.51        94.88        76.50        91.53        80.12        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
       23.05        86.83        60.49         7.07        43.23        21.07 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6937 
       62.43         9.60        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       140.78        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-6962 
       10.98         7.13         8.42        28.34         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 
       64.83        18.81        12.66         7.99         9.01        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        89.65        36.00        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 TCGA-CV-7406 
       17.13        95.34         4.96        11.87        49.71        57.47 
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-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-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 
       21.01       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-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-A6JZ 
        6.38        29.79         6.48        28.01         3.62        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
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-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
       11.44        18.67        24.95        25.32        12.36        28.77 
TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
        7.63        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       37.58        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         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-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 
       15.06        20.94        33.76        28.47        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         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        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       14.50        37.71        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
       13.68        13.84        19.27        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         6.25        15.42        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       17.98        29.92        51.25        10.85        36.82        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 
       19.00        75.55        18.97         2.04        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        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        27.39        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO 
       14.76        12.20        17.82        15.32         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI 
       16.96         6.87         7.10        32.45         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        20.35        64.80         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ 
       44.65        74.47        17.95        24.30        29.46        18.05 
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 
TCGA-KU-A66S 
       13.35 

  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE 
                           1.84                            0.07 
  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE 
                         172.67                          210.97 
  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE 
                          20.45                           21.21 
[1] "1.8 - 172.7 (20.4)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.1"
D60V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 32(12Q24.33) MUTATED         3        8         8        33
  DEL PEAK 32(12Q24.33) WILD-TYPE      24       68        74       219
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 32(12Q24.33) MUTATED           2         0
  DEL PEAK 32(12Q24.33) WILD-TYPE        10         1
D60V3, multiclass
           clus
vv          DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE
  STAGE I                               3                              24
  STAGE II                              8                              68
  STAGE III                             8                              74
  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 32(12Q24.33) MUTATED       3  15  12  27
  DEL PEAK 32(12Q24.33) WILD-TYPE    47 122  88 146
D60V4, multiclass
       clus
vv      DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE
  T0+T1                             3                              47
  T2                               15                             122
  T3                               12                              88
  T4                               27                             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 32(12Q24.33) MUTATED    20   7  22   2
  DEL PEAK 32(12Q24.33) WILD-TYPE 159  61 146   6
D60V5, multiclass
    clus
vv   DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE
  N0                            20                             159
  N1                             7                              61
  N2                            22                             146
  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 32(12Q24.33) MUTATED    21   0
  DEL PEAK 32(12Q24.33) WILD-TYPE 169   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.33) MUTATED     21    0
  DEL PEAK 32(12Q24.33) WILD-TYPE  169    1
   clus
vv  DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE
  0                            21                             169
  1                             0                               1
[1] 2 2
[1] FALSE
D60V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.33) MUTATED    15  48
  DEL PEAK 32(12Q24.33) WILD-TYPE 125 334
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.33) MUTATED     15   48
  DEL PEAK 32(12Q24.33) WILD-TYPE  125  334
        clus
vv       DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE
  FEMALE                            15                             125
  MALE                              48                             334
[1] 2 2
[1] FALSE
D60V8, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.33) MUTATED    16  38
  DEL PEAK 32(12Q24.33) WILD-TYPE 146 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.33) MUTATED     16   38
  DEL PEAK 32(12Q24.33) WILD-TYPE  146  263
     clus
vv    DEL PEAK 32(12Q24.33) MUTATED DEL PEAK 32(12Q24.33) WILD-TYPE
  NO                             16                             146
  YES                            38                             263
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(12Q24.33) MUTATED                                    61
  DEL PEAK 32(12Q24.33) WILD-TYPE                                 450
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 32(12Q24.33) MUTATED                                                   2
  DEL PEAK 32(12Q24.33) WILD-TYPE                                                 8
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 32(12Q24.33) MUTATED                                                           0
  DEL PEAK 32(12Q24.33) WILD-TYPE                                                         1
D60V9, multiclass
                                                           clus
vv                                                          DEL PEAK 32(12Q24.33) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  61
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
                                                           clus
vv                                                          DEL PEAK 32(12Q24.33) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   450
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
D60V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(12Q24.33) MUTATED                                  0     0
  DEL PEAK 32(12Q24.33) WILD-TYPE                                2    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(12Q24.33) MUTATED                          12    49
  DEL PEAK 32(12Q24.33) WILD-TYPE                        36   397
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 32(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       49
                                  clus
vv                                 DEL PEAK 32(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                     36
  WHITE                                                        397
[1] 4 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 32(12Q24.33) MUTATED     5  53
  DEL PEAK 32(12Q24.33) WILD-TYPE  21 406
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.33) MUTATED      5   53
  DEL PEAK 32(12Q24.33) WILD-TYPE   21  406
                        clus
vv                       DEL PEAK 32(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       DEL PEAK 32(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                  21
  NOT HISPANIC OR LATINO                             406
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 33(13Q12.11) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(13Q12.11) MUTATED   133  99
  DEL PEAK 33(13Q12.11) WILD-TYPE 168 120
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            232                             288 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                             99                             120 
$`DEL PEAK 33(13Q12.11) MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 
       68.48         3.55        28.11        30.18        25.71         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 
        9.24        11.08        32.48        32.88        16.73        11.61 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
       34.52         6.02        34.36        30.94        14.04        46.32 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5149 
       21.11        22.85        48.03        15.19         9.07        26.50 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       42.35        17.10        15.52        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DI 
       41.85        20.45        11.54         5.69        14.47        11.05 
TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 
       20.48         9.14         4.41        36.72        50.20        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z 
       24.66        71.05        20.52        10.55        27.19         6.28 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 
       55.86        38.04        12.89        26.86        20.55        45.83 
TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5373 
       27.58        46.32        71.31         8.32        11.57        52.08 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 
       56.94        50.07        30.67        48.00        19.07         6.74 
TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       10.45        38.89        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V7 
       17.29        21.21         7.40        31.69        12.39        19.53 
TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7065 
       62.37        32.38        13.25         4.24        64.87        53.52 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 
       77.56        23.24        29.36        29.49        31.23        84.23 
TCGA-CR-5247 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 
       11.77        10.22         7.69        12.46         9.27        47.18 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 
       39.16        47.34         3.09        24.95         0.99        34.06 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 
       32.78        47.01        49.58        24.79         5.95        29.95 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5966 
      139.43       129.21       108.95       107.51        94.88        17.92 
TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6441 
       13.35        48.59        60.49         7.07        43.23         9.60 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
        2.14         9.70        21.90        26.43        11.24       140.78 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6960 
       12.03        42.38        15.09        30.08        65.82        28.34 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        4.14        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-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7255 TCGA-CV-7263 
       77.16        36.00        26.20        17.13         2.10        18.41 
TCGA-CV-7406 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
       57.47         0.46        22.85        25.94         0.07        34.09 
TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A461 
        3.52       153.86       180.16        45.96        88.87        67.86 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JU 
       56.61         7.07        35.34         6.38        29.79         3.62 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 
       18.84        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        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5630 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G 
       33.86        37.58        39.12        41.59        37.18        20.25 
TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 
        3.02         0.46        20.25        33.76        28.47        21.93 
TCGA-HD-8224 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61O 
       14.66        13.84         3.65        14.50        11.84        13.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 
       19.04        15.48         6.25         7.13        16.08        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6IH 
       71.74        47.01        18.97         2.04         7.30        21.47 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       27.39        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ 
        8.32        12.72        15.91        13.71         3.12        13.25 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 
       20.35        64.80        54.67         2.83        49.45        44.65 
TCGA-UF-A7JC TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JS 
       17.95        29.46        13.94        22.36 

$`DEL PEAK 33(13Q12.11) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6992 
        9.30        37.28        20.48        51.29        52.08        35.05 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CX-7082 
       19.82        24.39        48.20        70.13        43.04         0.36 
TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5151 
       40.24        12.66         2.96         3.35        13.64        23.74 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
       57.93        23.84        65.59        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 
      105.90         4.80        18.38        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        48.76         4.67 
TCGA-CN-4728 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
       56.68        32.81        52.14        57.11        12.99        14.33 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 
       73.61        13.05        42.02         8.58        12.39        16.21 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 
       11.54        11.84        12.49         8.52        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A49B 
       28.04        34.13        32.22         3.68        17.42        29.72 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        52.37        21.50         2.93        54.58        70.45 
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        46.95 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       56.58        14.99        38.76        41.88        43.10        44.48 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
       33.60        14.14        12.46        54.67        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-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7368 
       11.90        11.34        11.64        22.78        15.75        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7380 
       35.84         3.45        29.23        31.96         9.17        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
       26.17        17.13        27.06        12.89        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 
       32.65        44.25        30.58         5.13        35.41        48.39 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 
       17.16        76.24        19.20        17.95        76.50        91.53 
TCGA-CV-5444 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
       80.12        23.05        86.83        54.74        21.07        62.43 
TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6952 
       90.12         5.46        20.52         4.73        19.79         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       172.67 
TCGA-CV-7101 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
        5.26        71.21       130.88         4.73        89.65        31.36 
TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       18.97        95.34         4.96        11.87        47.97        49.71 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7416 
       35.54        17.85       210.97        89.33         9.67        25.08 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
      100.57        14.89        56.48       156.49        54.94        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-A45T TCGA-CV-A45U TCGA-CV-A45V 
       27.98        21.01       169.38       159.65        35.47         1.05 
TCGA-CV-A45X TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A468 TCGA-CV-A6JD 
        6.51        48.20        60.43         0.76        15.25         5.98 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        6.48        28.01        21.24        23.47        19.92        22.52 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        10.55        51.12        13.25        25.41         9.60 
TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
        2.53        18.67        25.32        12.36        28.77        22.59 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
       58.45        37.25        18.02        46.45        20.45        40.04 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
       32.71        21.63        31.13        18.94        24.95        17.85 
TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       11.80        12.43        13.38        15.16        15.06        20.94 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 
       25.74        27.48        27.48        22.03         0.36         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        38.53        37.71        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H7 TCGA-KU-A6H8 
        0.07        33.57         5.29        13.68        19.27        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-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       17.98        29.92        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-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC 
       21.21        23.15         9.34        12.72        21.07        19.73 
TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       15.32        16.96         6.87         7.10        32.45        13.55 
TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO 
       49.51        74.47        24.30        55.43        18.05        20.75 
TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       32.65        17.03        20.55        14.56        13.35        18.15 

  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                         180.16                          210.97 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                          21.14                           21.07 
[1] "0.1 - 180.2 (21.1)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D61V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 33(13Q12.11) MUTATED         8       25        37       121
  DEL PEAK 33(13Q12.11) WILD-TYPE      19       51        45       131
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 33(13Q12.11) MUTATED           6         1
  DEL PEAK 33(13Q12.11) WILD-TYPE         6         0
D61V3, multiclass
           clus
vv          DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  STAGE I                               8                              19
  STAGE II                             25                              51
  STAGE III                            37                              45
  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 33(13Q12.11) MUTATED      16 56 47 86
  DEL PEAK 33(13Q12.11) WILD-TYPE    34 81 53 87
D61V4, multiclass
       clus
vv      DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  T0+T1                            16                              34
  T2                               56                              81
  T3                               47                              53
  T4                               86                              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 33(13Q12.11) MUTATED    68  34  85   3
  DEL PEAK 33(13Q12.11) WILD-TYPE 111  34  83   5
D61V5, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  N0                            68                             111
  N1                            34                              34
  N2                            85                              83
  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 33(13Q12.11) MUTATED    84   1
  DEL PEAK 33(13Q12.11) WILD-TYPE 106   0
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     84    1
  DEL PEAK 33(13Q12.11) WILD-TYPE  106    0
   clus
vv  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  0                            84                             106
  1                             1                               0
[1] 2 2
[1] FALSE
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    52 181
  DEL PEAK 33(13Q12.11) WILD-TYPE  88 201
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     52  181
  DEL PEAK 33(13Q12.11) WILD-TYPE   88  201
        clus
vv       DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  FEMALE                            52                              88
  MALE                             181                             201
[1] 2 2
[1] FALSE
D61V8, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    69 135
  DEL PEAK 33(13Q12.11) WILD-TYPE  93 166
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     69  135
  DEL PEAK 33(13Q12.11) WILD-TYPE   93  166
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  NO                             69                              93
  YES                           135                             166
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q12.11) MUTATED                                   228
  DEL PEAK 33(13Q12.11) WILD-TYPE                                 283
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 33(13Q12.11) MUTATED                                                   4
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                 6
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 33(13Q12.11) MUTATED                                                           1
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                         0
D61V9, multiclass
                                                           clus
vv                                                          DEL PEAK 33(13Q12.11) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 228
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
                                                           clus
vv                                                          DEL PEAK 33(13Q12.11) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   283
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, continuous
D61V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(13Q12.11) MUTATED                                  2     3
  DEL PEAK 33(13Q12.11) WILD-TYPE                                0     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q12.11) MUTATED                          29   190
  DEL PEAK 33(13Q12.11) WILD-TYPE                        19   256
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 33(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      190
                                  clus
vv                                 DEL PEAK 33(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     19
  WHITE                                                        256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    15 194
  DEL PEAK 33(13Q12.11) WILD-TYPE  11 265
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     15  194
  DEL PEAK 33(13Q12.11) WILD-TYPE   11  265
                        clus
vv                       DEL PEAK 33(13Q12.11) MUTATED
  HISPANIC OR LATINO                                15
  NOT HISPANIC OR LATINO                           194
                        clus
vv                       DEL PEAK 33(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             265
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 34(13Q14.2) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(13Q14.2) MUTATED   130  86
  DEL PEAK 34(13Q14.2) WILD-TYPE 171 133
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           216                            304 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                            86                            133 
$`DEL PEAK 34(13Q14.2) MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-6021 
       68.48         3.55        28.11        30.18        25.71         9.07 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-5323 TCGA-CQ-7067 TCGA-CR-6472 TCGA-CR-6478 
        9.24        11.08        48.20        16.73        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-HD-8635 TCGA-UF-A71D 
        0.36        34.36        14.04        46.32        22.85        48.03 
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-6869 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
       21.17         4.01        41.85        20.45        27.95        11.54 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4224 
        7.10         5.69        11.05        20.48       105.90         9.14 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 
        4.41        18.38        22.42        36.72        50.20        66.28 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z 
       24.66        71.05        20.52        10.55        27.19         6.28 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 
       55.86        38.04        26.86        45.83        27.58        46.32 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
       71.31         8.32        11.54        11.57        52.08        56.94 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 
       30.67        48.00        19.07         6.74        10.45        38.89 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C 
       11.74        35.01        25.41        23.57        17.29        21.21 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5330 TCGA-CQ-6220 
        7.40        12.39        20.88        19.53        62.37        32.38 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-A4CD 
       56.58        13.25        14.99        64.87        53.52        33.60 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
       29.49        31.23        84.23        11.77        54.67        37.87 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7364 
       58.42        50.01        16.90        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 
       24.79         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       140.78        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-7086 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
       35.34        29.79        18.84        16.14        11.44        18.67 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7592 
       24.95        17.72        13.94        33.86        46.45        37.58 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W 
       39.12        41.59        37.18        20.25         3.02         0.46 
TCGA-F7-A623 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8224 
       20.25        20.94        28.47        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61I TCGA-IQ-A61O TCGA-IQ-A6SG 
       22.03        13.84         3.65         0.07        13.84        19.04 
TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q6 
       15.48        19.27         6.25         7.13        16.08        15.78 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T7 
       71.74        51.25        10.85        47.01         2.04        16.01 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 
        7.30        21.47        27.39        12.89         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
       12.20        17.82         8.32        16.96        15.91         7.10 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
       13.71         3.12        20.35        64.80        54.67         2.83 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JS TCGA-UP-A6WW TCGA-KU-A66T 
       49.45        44.65        17.95        22.36        17.03        18.15 

$`DEL PEAK 34(13Q14.2) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6992 
        9.30        37.28        20.48        51.29        52.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
       32.48        19.82        24.39        32.88        70.13        43.04 
TCGA-CQ-A4C7 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-UF-A7JV 
       11.61        30.94        40.24        21.11        12.66         2.96 
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
        3.35        13.64        23.74        23.84        65.59        15.52 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG 
       14.83        12.62        29.42        14.47         7.82         2.27 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-7863 TCGA-BB-7866 
       13.38        16.41         6.15         4.80        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        48.76         4.67 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        12.89        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       20.55        14.33        73.61        13.05        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-6010 
       12.39        16.21        11.84        12.49         8.52        50.07 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6995 
       23.90        47.44        28.04        34.13        32.22         3.68 
TCGA-CN-6996 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       17.42        29.72        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
       12.07         2.70        23.44        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
       54.58        70.45        45.99        10.42        11.21         4.24 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7069 TCGA-CQ-7071 
       41.19        46.95         4.24        38.76        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CH 
       77.56        44.48        23.24        29.36        14.14        12.46 
TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 
       26.27        39.52        36.99        18.54        11.90        11.34 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 
       11.64        12.46        22.78        15.75         9.27        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-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-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        5.13        35.41        17.16        76.24        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
      107.51        76.50        91.53        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
       23.05        86.83        48.59        43.23        54.74        21.07 
TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
       62.43        90.12         2.14         9.70         5.46        20.52 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6953 
        4.73        21.90        19.79        12.03         6.08        53.95 
TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
       10.98         7.13         8.42         2.50       172.67        12.66 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
        5.26         1.84        71.21       130.88         4.73        89.65 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 
       31.36        18.97        95.34         4.96        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
        2.10        49.71        35.54        17.85       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 
        9.67         0.46        25.08       100.57        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-7437 TCGA-CV-7438 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
       16.64         6.38        27.98        21.01       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-A6JM TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
       15.25         5.98         6.38         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO 
       25.32        12.36        28.77         7.63        22.59        24.95 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 
       12.10        12.79        23.34        58.45        37.25        18.02 
TCGA-DQ-7591 TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S 
       20.45        40.04        32.71        21.63        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       24.95        17.85        11.80        12.43        13.38        15.16 
TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-A4C1 TCGA-HD-A634 
       15.06        33.76        25.74        27.48         0.36         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        38.53        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H8 
       11.84        37.41        33.57         5.29        13.68        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-A7D7 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       17.98        29.92        36.82        19.00        75.55        18.97 
TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
       29.00        12.99        13.15        21.07        21.21        23.15 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-AA3J TCGA-RS-A6TO 
        9.34        12.72        21.07        19.73        15.32        12.72 
TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-UF-A71B TCGA-UF-A7JA 
        6.87        32.45        13.55        13.25        49.51        74.47 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       32.65        20.55        14.56        13.35 

  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                          0.07                           0.36 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                         22.11                          20.55 
[1] "0.1 - 180.2 (22.1)" "0.4 - 211.0 (20.6)"
[1] "hr=" "1.1"
D62V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 34(13Q14.2) MUTATED        11       24        36       101         6
  DEL PEAK 34(13Q14.2) WILD-TYPE      16       52        46       151         6
                                vv
clus                             STAGE IVC
  DEL PEAK 34(13Q14.2) MUTATED           1
  DEL PEAK 34(13Q14.2) WILD-TYPE         0
D62V3, multiclass
           clus
vv          DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  STAGE I                             11                             16
  STAGE II                            24                             52
  STAGE III                           36                             46
  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 34(13Q14.2) MUTATED      22  58  39  67
  DEL PEAK 34(13Q14.2) WILD-TYPE    28  79  61 106
D62V4, multiclass
       clus
vv      DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  T0+T1                           22                             28
  T2                              58                             79
  T3                              39                             61
  T4                              67                            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 34(13Q14.2) MUTATED    63  29  75   4
  DEL PEAK 34(13Q14.2) WILD-TYPE 116  39  93   4
D62V5, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  N0                           63                            116
  N1                           29                             39
  N2                           75                             93
  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 34(13Q14.2) MUTATED    74   1
  DEL PEAK 34(13Q14.2) WILD-TYPE 116   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     74    1
  DEL PEAK 34(13Q14.2) WILD-TYPE  116    0
   clus
vv  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  0                           74                            116
  1                            1                              0
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED    48 169
  DEL PEAK 34(13Q14.2) WILD-TYPE  92 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     48  169
  DEL PEAK 34(13Q14.2) WILD-TYPE   92  213
        clus
vv       DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  FEMALE                           48                             92
  MALE                            169                            213
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED    61 130
  DEL PEAK 34(13Q14.2) WILD-TYPE 101 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     61  130
  DEL PEAK 34(13Q14.2) WILD-TYPE  101  171
     clus
vv    DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  NO                            61                            101
  YES                          130                            171
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                   210
  DEL PEAK 34(13Q14.2) WILD-TYPE                                 301
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 34(13Q14.2) MUTATED                                                   6
  DEL PEAK 34(13Q14.2) WILD-TYPE                                                 4
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 34(13Q14.2) MUTATED                                                           1
  DEL PEAK 34(13Q14.2) WILD-TYPE                                                         0
D62V9, multiclass
                                                           clus
vv                                                          DEL PEAK 34(13Q14.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                210
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          DEL PEAK 34(13Q14.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  301
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
D62V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(13Q14.2) MUTATED                                  2     3
  DEL PEAK 34(13Q14.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(13Q14.2) MUTATED                          28   178
  DEL PEAK 34(13Q14.2) WILD-TYPE                        20   268
D62V13, multiclass
                                  clus
vv                                 DEL PEAK 34(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     178
                                  clus
vv                                 DEL PEAK 34(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       268
[1] 4 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 34(13Q14.2) MUTATED    14 183
  DEL PEAK 34(13Q14.2) WILD-TYPE  12 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     14  183
  DEL PEAK 34(13Q14.2) WILD-TYPE   12  276
                        clus
vv                       DEL PEAK 34(13Q14.2) MUTATED
  HISPANIC OR LATINO                               14
  NOT HISPANIC OR LATINO                          183
                        clus
vv                       DEL PEAK 34(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            276
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 35(14Q11.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(14Q11.2) MUTATED    46  29
  DEL PEAK 35(14Q11.2) WILD-TYPE 255 190
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                            75                            445 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                            29                            190 
$`DEL PEAK 35(14Q11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-CQ-6221 TCGA-CR-6472 TCGA-DQ-5629 TCGA-H7-A6C5 
        9.30         3.55        32.88        34.52        30.94        21.11 
TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-A4IH 
       48.03         3.35         9.07        42.35        21.17        20.45 
TCGA-BA-A6D8 TCGA-BB-7862 TCGA-BB-A6UM TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4735 
       27.95        36.72        12.92        38.04        12.89        57.11 
TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A63U 
       30.67        34.13         6.74         3.68        17.29        31.69 
TCGA-CQ-5332 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6493 
       10.42        77.56        11.77        11.64        22.78         9.27 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7388 TCGA-CR-7398 TCGA-CR-7399 
       39.16        47.34         3.45        27.06         5.13         5.95 
TCGA-CV-5435 TCGA-CV-5966 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6940 
       76.24        17.92        90.12         9.70        21.90        26.43 
TCGA-CV-6945 TCGA-CV-7177 TCGA-CV-7180 TCGA-CV-7263 TCGA-CV-7413 TCGA-CV-7423 
       12.03        21.80        10.75        18.41         9.67       100.57 
TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6K1 
       84.49       153.86        48.20        60.43        21.24        22.52 
TCGA-CX-A4AQ TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EP 
       51.12        11.44        25.32        17.72         7.63        13.94 
TCGA-F7-7848 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-8224 TCGA-HD-A633 TCGA-IQ-A6SH 
       37.18        20.94        33.76        14.66        13.84        15.48 
TCGA-MT-A7BN TCGA-P3-A6T0 TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B 
       15.42        19.00        12.89        15.32        54.67        49.51 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-WA-A7GZ 
       74.47        55.43        20.55 

$`DEL PEAK 35(14Q11.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
       37.28        20.48        68.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       51.29         9.07         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7067 
       32.48        19.82        24.39        48.20        70.13        16.73 
TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-7588 
       43.04        11.61         6.02         0.36        34.36        14.04 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-BA-4074 
       46.32        40.24        12.66        22.85         2.96        15.19 
TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
       13.64        26.50        23.74        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       65.59        15.52        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       29.42        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 
      105.90         9.14         4.80         4.41        18.38        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-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       71.05        20.52        10.55        27.19         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
       12.69        48.76        55.86         4.67        56.68        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         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-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6988 
       48.00        23.90        47.44        28.04        19.07        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       32.22        38.89        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
       23.57        29.72        21.21         7.40        22.32        12.39 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       62.37        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       64.87        53.52        41.88        43.10        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        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-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 
       39.52        36.99        18.54        16.90        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 
       11.34         7.69        12.46        15.75        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-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-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       47.01        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
       44.25        30.58        24.79        35.41        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 
      139.43        17.16       129.21       108.95        19.20        17.95 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
      107.51        94.88        76.50        91.53        80.12        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        48.59        60.49         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
       54.74        21.07        62.43         9.60         2.14         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6948 
       20.52         4.73        11.24       140.78        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-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
        7.13         8.42        28.34         2.50         4.14        64.83 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
      172.67       111.16        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-7183 
        5.26         1.84        52.31        12.92        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        89.65        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-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
        2.10        49.71        57.47        35.54        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
       89.33         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-7429 
       34.09        14.89        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       16.27        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        21.01       169.38       180.16       159.65        35.47 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A463 
        1.05        45.96         6.51        88.87        67.86         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-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01         3.62        23.47        19.92 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
       10.42        10.55        18.84        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-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       28.77        22.59        24.95        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       58.45        37.25        33.86        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       37.58        40.04        39.12        41.59        32.71        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
       20.25         3.02        31.13        18.94        24.95         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-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 
       15.06        28.47        25.74        21.93        27.48        27.48 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         0.36         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
        0.07        33.57         5.29        13.68        13.84        19.04 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        10.75        14.37         7.96        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
       12.62         6.25         7.13        16.08        17.98        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       15.78        71.74        51.25        10.85        36.82        47.01 
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        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z8 
        9.34        12.72        27.39        21.07        19.73         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       14.76        12.20        17.82         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
        6.87        15.91         7.10        32.45        13.71         3.12 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71E 
       13.55        13.25        20.35        64.80         2.83        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       44.65        17.95        24.30        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        17.03        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                          3.35                           0.07 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                         21.17                          21.07 
[1] "3.4 - 153.9 (21.2)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D63V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 35(14Q11.2) MUTATED         1       14        11        37         1
  DEL PEAK 35(14Q11.2) WILD-TYPE      26       62        71       215        11
                                vv
clus                             STAGE IVC
  DEL PEAK 35(14Q11.2) MUTATED           0
  DEL PEAK 35(14Q11.2) WILD-TYPE         1
D63V3, multiclass
           clus
vv          DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  STAGE I                              1                             26
  STAGE II                            14                             62
  STAGE III                           11                             71
  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 35(14Q11.2) MUTATED       4  23  13  26
  DEL PEAK 35(14Q11.2) WILD-TYPE    46 114  87 147
D63V4, multiclass
       clus
vv      DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  T0+T1                            4                             46
  T2                              23                            114
  T3                              13                             87
  T4                              26                            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 35(14Q11.2) MUTATED    28  11  23   0
  DEL PEAK 35(14Q11.2) WILD-TYPE 151  57 145   8
D63V5, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  N0                           28                            151
  N1                           11                             57
  N2                           23                            145
  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 35(14Q11.2) MUTATED    30   0
  DEL PEAK 35(14Q11.2) WILD-TYPE 160   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED     30    0
  DEL PEAK 35(14Q11.2) WILD-TYPE  160    1
   clus
vv  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  0                           30                            160
  1                            0                              1
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED    15  60
  DEL PEAK 35(14Q11.2) WILD-TYPE 125 322
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED     15   60
  DEL PEAK 35(14Q11.2) WILD-TYPE  125  322
        clus
vv       DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  FEMALE                           15                            125
  MALE                             60                            322
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED    16  51
  DEL PEAK 35(14Q11.2) WILD-TYPE 146 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED     16   51
  DEL PEAK 35(14Q11.2) WILD-TYPE  146  250
     clus
vv    DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  NO                            16                            146
  YES                           51                            250
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q11.2) MUTATED                                    72
  DEL PEAK 35(14Q11.2) WILD-TYPE                                 439
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 35(14Q11.2) MUTATED                                                   3
  DEL PEAK 35(14Q11.2) WILD-TYPE                                                 7
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 35(14Q11.2) MUTATED                                                           0
  DEL PEAK 35(14Q11.2) WILD-TYPE                                                         1
D63V9, multiclass
                                                           clus
vv                                                          DEL PEAK 35(14Q11.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 72
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 35(14Q11.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  439
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
D63V11, continuous
D63V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(14Q11.2) MUTATED                                  0     1
  DEL PEAK 35(14Q11.2) WILD-TYPE                                2    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(14Q11.2) MUTATED                          11    62
  DEL PEAK 35(14Q11.2) WILD-TYPE                        37   384
D63V13, multiclass
                                  clus
vv                                 DEL PEAK 35(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      62
                                  clus
vv                                 DEL PEAK 35(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       384
[1] 4 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 35(14Q11.2) MUTATED     0  65
  DEL PEAK 35(14Q11.2) WILD-TYPE  26 394
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED      0   65
  DEL PEAK 35(14Q11.2) WILD-TYPE   26  394
                        clus
vv                       DEL PEAK 35(14Q11.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       DEL PEAK 35(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 26
  NOT HISPANIC OR LATINO                            394
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 36(14Q32.32) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 36(14Q32.32) MUTATED    48  27
  DEL PEAK 36(14Q32.32) WILD-TYPE 253 192
  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE 
                             75                             445 
  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE 
                             27                             192 
$`DEL PEAK 36(14Q32.32) MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-6992 TCGA-CQ-6221 TCGA-CR-6472 TCGA-DQ-7593 
       68.48         3.55        35.05        32.88        34.52        40.24 
TCGA-H7-A6C5 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 
       21.11        48.03         3.35         9.07        42.35        57.93 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IH TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 
       21.17        14.83        20.45        16.41       105.90         4.80 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-A6UM TCGA-CN-4728 TCGA-CN-4735 
       18.38        36.72        44.98        12.92        56.68        57.11 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A63U TCGA-CN-A63Y 
       34.13         6.74         3.68        35.01        31.69        16.57 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       23.44        20.88        11.77        26.27        58.42        50.01 
TCGA-CR-6480 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5434 TCGA-CV-5442 TCGA-CV-5443 
       11.90         5.13         5.95       108.95        76.50        91.53 
TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6962 
       17.92         7.07        21.07         9.70        21.90         4.14 
TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7423 
       18.97        17.13        18.41        57.47        34.09       100.57 
TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-A4AQ 
      153.86        48.20        60.43        21.24        22.52        51.12 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7596 TCGA-H7-A76A 
       25.32         7.63        18.02        46.45        41.59        20.94 
TCGA-HD-8224 TCGA-HD-A6HZ TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A6T0 
       14.66         3.65        15.42         7.13        16.08        19.00 
TCGA-T2-A6X0 TCGA-UF-A71E TCGA-UF-A7J9 
        7.10        49.45        44.65 

$`DEL PEAK 36(14Q32.32) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        37.28        20.48        28.11        30.18        25.71 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 
       51.29         9.07         9.24        52.08        11.08        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       19.82        24.39        48.20        70.13        16.73        43.04 
TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 
       11.61         6.02         0.36        34.36        30.94        14.04 
TCGA-DQ-7589 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 
       46.32        12.66        22.85         2.96        15.19        13.64 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       26.50        23.74        17.10        23.84        65.59        15.52 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
       12.62         4.01        41.85        29.42        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-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7861 
       13.38        20.48         6.15         9.14         4.41        22.42 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       33.70        50.20        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-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
       48.76        55.86        38.04         4.67        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        12.99        20.55        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
       27.58        73.61        13.05        42.02        46.32         8.58 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       12.39        71.31         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-6010 
       11.57        12.49         8.52        52.08        56.94        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
       10.45        32.22        38.89        17.42        11.74        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
       23.57        17.29        29.72        21.21         7.40        22.32 
TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.39         4.41        12.07         2.70        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       10.42        11.21         4.24        41.19        32.38        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       56.58        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
       53.52        41.88        43.10        77.56        44.48        23.24 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
       29.36        33.60        29.49        14.14        12.46        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
       84.23        54.67        37.87        39.52        36.99        18.54 
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 
       22.78        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-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-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
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-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-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-6436 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6934 TCGA-CV-6936 
       54.74        62.43         9.60        90.12         2.14         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       140.78        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-7095 TCGA-CV-7097 TCGA-CV-7099 
       64.83       172.67       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        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       36.00        31.36        26.20        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        49.71        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-7421 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 
        0.07        14.89        56.48       156.49        54.94         3.52 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 
       16.27        84.49        19.76         7.17        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        21.01       169.38       180.16       159.65 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 
       35.47         1.05        45.96         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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
        6.38        29.79         6.48        28.01         3.62        23.47 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6515 TCGA-D6-6516 
       19.92        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-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       24.95        17.72        12.36        28.77        22.59        24.95 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
       13.94        12.10        12.79        23.34        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
       33.86        20.45        37.58        40.04        39.12        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
       32.71        21.63        20.25         3.02        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 
       24.95         0.46        17.85        11.80        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       13.38        15.16        15.06        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       21.93        27.48        27.48        22.03         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        38.53        14.50 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K 
       37.71        11.84        37.41         0.07        33.57         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 
       13.68        13.84        19.04        15.48        19.27        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         6.25 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       17.98        29.92        15.78        71.74        51.25        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       36.82        47.01        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        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ 
       15.32         8.32        12.72        16.96         6.87        15.91 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL 
       32.45        13.71         3.12        13.55        13.25        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC 
       64.80        54.67         2.83        49.51        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE 
                           3.35                            0.07 
  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE 
                         153.86                          210.97 
  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE 
                          21.24                           21.01 
[1] "3.4 - 153.9 (21.2)" "0.1 - 211.0 (21.0)"
[1] "hr=" "1.3"
D64V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 36(14Q32.32) MUTATED         0       11        10        31
  DEL PEAK 36(14Q32.32) WILD-TYPE      27       65        72       221
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 36(14Q32.32) MUTATED           2         0
  DEL PEAK 36(14Q32.32) WILD-TYPE        10         1
D64V3, multiclass
           clus
vv          DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE
  STAGE I                               0                              27
  STAGE II                             11                              65
  STAGE III                            10                              72
  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 36(14Q32.32) MUTATED       4  20  14  18
  DEL PEAK 36(14Q32.32) WILD-TYPE    46 117  86 155
D64V4, multiclass
       clus
vv      DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE
  T0+T1                             4                              46
  T2                               20                             117
  T3                               14                              86
  T4                               18                             155
[1] 4 2
[1] TRUE
[1] "dimension of 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(14Q32.32) MUTATED    20   8  21   2
  DEL PEAK 36(14Q32.32) WILD-TYPE 159  60 147   6
D64V5, multiclass
    clus
vv   DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE
  N0                            20                             159
  N1                             8                              60
  N2                            21                             147
  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 36(14Q32.32) MUTATED    19   0
  DEL PEAK 36(14Q32.32) WILD-TYPE 171   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(14Q32.32) MUTATED     19    0
  DEL PEAK 36(14Q32.32) WILD-TYPE  171    1
   clus
vv  DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE
  0                            19                             171
  1                             0                               1
[1] 2 2
[1] FALSE
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 36(14Q32.32) MUTATED    13  62
  DEL PEAK 36(14Q32.32) WILD-TYPE 127 320
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(14Q32.32) MUTATED     13   62
  DEL PEAK 36(14Q32.32) WILD-TYPE  127  320
        clus
vv       DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE
  FEMALE                            13                             127
  MALE                              62                             320
[1] 2 2
[1] FALSE
D64V8, binary
                                 cls
clus                                0   1
  DEL PEAK 36(14Q32.32) MUTATED    14  51
  DEL PEAK 36(14Q32.32) WILD-TYPE 148 250
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(14Q32.32) MUTATED     14   51
  DEL PEAK 36(14Q32.32) WILD-TYPE  148  250
     clus
vv    DEL PEAK 36(14Q32.32) MUTATED DEL PEAK 36(14Q32.32) WILD-TYPE
  NO                             14                             148
  YES                            51                             250
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(14Q32.32) MUTATED                                    73
  DEL PEAK 36(14Q32.32) WILD-TYPE                                 438
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 36(14Q32.32) MUTATED                                                   2
  DEL PEAK 36(14Q32.32) WILD-TYPE                                                 8
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 36(14Q32.32) MUTATED                                                           0
  DEL PEAK 36(14Q32.32) WILD-TYPE                                                         1
D64V9, multiclass
                                                           clus
vv                                                          DEL PEAK 36(14Q32.32) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  73
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
                                                           clus
vv                                                          DEL PEAK 36(14Q32.32) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   438
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
D64V11, continuous
D64V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(14Q32.32) MUTATED                                  0     0
  DEL PEAK 36(14Q32.32) WILD-TYPE                                2    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(14Q32.32) MUTATED                          10    64
  DEL PEAK 36(14Q32.32) WILD-TYPE                        38   382
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 36(14Q32.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       64
                                  clus
vv                                 DEL PEAK 36(14Q32.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                         11
  BLACK OR AFRICAN AMERICAN                                     38
  WHITE                                                        382
[1] 4 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 36(14Q32.32) MUTATED     2  65
  DEL PEAK 36(14Q32.32) WILD-TYPE  24 394
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 36(14Q32.32) MUTATED      2   65
  DEL PEAK 36(14Q32.32) WILD-TYPE   24  394
                        clus
vv                       DEL PEAK 36(14Q32.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            65
                        clus
vv                       DEL PEAK 36(14Q32.32) WILD-TYPE
  HISPANIC OR LATINO                                  24
  NOT HISPANIC OR LATINO                             394
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 37(15Q15.1) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(15Q15.1) MUTATED    65  59
  DEL PEAK 37(15Q15.1) WILD-TYPE 236 160
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                           124                            396 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                            59                            160 
$`DEL PEAK 37(15Q15.1) MUTATED`
TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6997 
       68.48        28.11        30.18         9.07        11.08        32.48 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6478 TCGA-CX-7219 TCGA-BA-5152 TCGA-BA-5153 
       16.73        11.61         6.02        34.36        42.35        57.93 
TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DE 
       17.10        15.52        21.17        41.85        29.42        14.47 
TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7866 TCGA-BB-7870 
       11.05        16.41       105.90         4.80        44.98        66.28 
TCGA-BB-7871 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-5359 TCGA-CN-5363 
       24.66        38.04        56.68        26.86        12.39         8.32 
TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 
        8.52        48.00        47.44        17.42        11.74        23.57 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6UY TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 
       12.39        12.07        23.44         2.93        62.37        10.42 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CE 
       56.58         4.24        38.76        77.56        44.48        29.49 
TCGA-CR-5243 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-7373 TCGA-CR-7402 TCGA-CV-5435 
       84.23        18.54        11.90        29.23        29.95        76.24 
TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       94.88        17.92        13.35        48.59        60.49        43.23 
TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6960 
        9.60        20.52        26.43        42.38        65.82        28.34 
TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7235 
        2.50         4.14        18.81        12.92        21.80        77.16 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 
       36.00        31.36        18.97        47.97        49.71        35.54 
TCGA-CV-7414 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-A45R 
        0.46        14.89        84.49       153.86         6.38       180.16 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-D6-6517 TCGA-D6-6823 
       60.43         7.07         6.38        23.47         9.60        23.05 
TCGA-D6-6826 TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5631 TCGA-F7-A50I 
       11.44        24.95        23.34        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        20.94        37.71        37.41 
TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-P3-A5QA TCGA-P3-A6T3 
       13.84        15.48        15.42         7.13        71.74        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        19.73        14.76        12.20 
TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A718 TCGA-UF-A719 
       12.72        15.91        13.71         3.12        64.80        54.67 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JO TCGA-KU-A66T 
       74.47        24.30        20.75        18.15 

$`DEL PEAK 37(15Q15.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-4727 
        9.30        37.28        20.48         3.55        25.71        51.29 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
        9.24        52.08        35.05        19.82        24.39        48.20 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 
       32.88        70.13        43.04        34.52         0.36        30.94 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 
       14.04        46.32        40.24        21.11        12.66        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       48.03         2.96         3.35        15.19        13.64         9.07 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6872 
       26.50        23.74        23.84        65.59        14.83        12.62 
TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
        4.01        20.45        27.95        11.54         7.10         5.69 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 
        7.82         2.27        13.38        20.48         6.15         9.14 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
        4.41        18.38        22.42        36.72        33.70        50.20 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM 
       38.40        71.05        20.52        10.55        27.19        12.92 
TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
        8.81         6.28        12.69        48.76        55.86         4.67 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
       14.33        45.83        27.58        73.61        13.05        42.02 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       46.32         8.58        71.31        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        52.08        56.94        50.07        30.67 
TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       23.90        28.04        19.07        34.13         6.74        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       32.22        38.89         3.68        35.01        25.41        17.29 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
       29.72        21.21         7.40        31.69        22.32        16.57 
TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 
        4.41         2.70        20.88        19.53        52.37        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       54.58        70.45        45.99        11.21         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 
       32.38        46.95        13.25        14.99        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
       41.88        43.10        23.24        29.36        33.60        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-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6481 
       58.42        50.01        39.52        36.99        16.90        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        22.78        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-7374 TCGA-CR-7376 TCGA-CR-7377 
        3.45         3.09        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-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
       44.25        30.58        24.79         5.13         5.95        35.41 
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-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5971 
       17.95       107.51        76.50        91.53        80.12        23.05 
TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 
       86.83         7.07        54.74        21.07        62.43        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 
        2.14         9.70         5.46         4.73        21.90        11.24 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
      140.78        19.79        12.03        15.09        30.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-7089 TCGA-CV-7090 
       53.95        10.98         7.13         8.42        64.83       172.67 
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-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 
       52.31        71.21        10.75       130.88         4.73        89.65 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 
       26.20        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-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-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-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64        22.19        27.98        21.01       169.38 
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-A468 TCGA-CV-A6JD 
       48.20        67.86         0.76        56.61        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        28.01         3.62        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ 
       19.92        22.52        10.42        10.55        18.84        51.12 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
       13.25        25.41         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-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 
       13.94        12.10        12.79        37.25        33.86        46.45 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       20.45        37.58        40.04        39.12        41.59        37.18 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
       32.71        21.63        20.25        31.13        24.95         0.46 
TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
       17.85        11.80        13.38        15.16        15.06        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         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-A61I 
       34.75        15.95        38.53        14.50        11.84         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-KU-A6H8 
       33.57         5.29        13.68        19.04        19.27        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         6.25 
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-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-A6IH TCGA-QK-A6II 
       13.15        21.07        21.21        23.15        21.47         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB 
       12.72        27.39        21.07        12.89         5.62        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       15.32         8.32        16.96         6.87         7.10        32.45 
TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.55        13.25        20.35         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       44.65        17.95        55.43        29.46        18.05        13.94 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 

  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                          0.46                           0.07 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                        180.16                         210.97 
  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE 
                        21.485                         21.070 
[1] "0.5 - 180.2 (21.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D65V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 37(15Q15.1) MUTATED         3       23        17        58         3
  DEL PEAK 37(15Q15.1) WILD-TYPE      24       53        65       194         9
                                vv
clus                             STAGE IVC
  DEL PEAK 37(15Q15.1) MUTATED           0
  DEL PEAK 37(15Q15.1) WILD-TYPE         1
D65V3, multiclass
           clus
vv          DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  STAGE I                              3                             24
  STAGE II                            23                             53
  STAGE III                           17                             65
  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
  DEL PEAK 37(15Q15.1) MUTATED       6  37  25  39
  DEL PEAK 37(15Q15.1) WILD-TYPE    44 100  75 134
D65V4, multiclass
       clus
vv      DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  T0+T1                            6                             44
  T2                              37                            100
  T3                              25                             75
  T4                              39                            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 37(15Q15.1) MUTATED    37  15  42   3
  DEL PEAK 37(15Q15.1) WILD-TYPE 142  53 126   5
D65V5, multiclass
    clus
vv   DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  N0                           37                            142
  N1                           15                             53
  N2                           42                            126
  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 37(15Q15.1) MUTATED    36   0
  DEL PEAK 37(15Q15.1) WILD-TYPE 154   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED     36    0
  DEL PEAK 37(15Q15.1) WILD-TYPE  154    1
   clus
vv  DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  0                           36                            154
  1                            0                              1
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED    29  95
  DEL PEAK 37(15Q15.1) WILD-TYPE 111 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED     29   95
  DEL PEAK 37(15Q15.1) WILD-TYPE  111  287
        clus
vv       DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  FEMALE                           29                            111
  MALE                             95                            287
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED    33  73
  DEL PEAK 37(15Q15.1) WILD-TYPE 129 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED     33   73
  DEL PEAK 37(15Q15.1) WILD-TYPE  129  228
     clus
vv    DEL PEAK 37(15Q15.1) MUTATED DEL PEAK 37(15Q15.1) WILD-TYPE
  NO                            33                            129
  YES                           73                            228
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(15Q15.1) MUTATED                                   123
  DEL PEAK 37(15Q15.1) WILD-TYPE                                 388
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 37(15Q15.1) MUTATED                                                   0
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                10
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 37(15Q15.1) MUTATED                                                           1
  DEL PEAK 37(15Q15.1) WILD-TYPE                                                         0
D65V9, multiclass
                                                           clus
vv                                                          DEL PEAK 37(15Q15.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                123
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          DEL PEAK 37(15Q15.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  388
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, continuous
D65V11, continuous
D65V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(15Q15.1) MUTATED                                  0     2
  DEL PEAK 37(15Q15.1) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(15Q15.1) MUTATED                          14   103
  DEL PEAK 37(15Q15.1) WILD-TYPE                        34   343
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 37(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     103
                                  clus
vv                                 DEL PEAK 37(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q15.1) MUTATED     9 104
  DEL PEAK 37(15Q15.1) WILD-TYPE  17 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q15.1) MUTATED      9  104
  DEL PEAK 37(15Q15.1) WILD-TYPE   17  355
                        clus
vv                       DEL PEAK 37(15Q15.1) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 37(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            355
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 38(16Q23.1) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16Q23.1) MUTATED    58  40
  DEL PEAK 38(16Q23.1) WILD-TYPE 243 179
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            98                            422 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            40                            179 
$`DEL PEAK 38(16Q23.1) MUTATED`
TCGA-BA-5559 TCGA-CN-6021 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-7588 
       68.48         9.07        11.61        34.52         0.36        14.04 
TCGA-DQ-7589 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-A4IH TCGA-BB-4225 
       46.32        13.64         9.07        57.93        20.45         4.80 
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        46.32        71.31         8.32 
TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6996 TCGA-CN-A497 TCGA-CN-A499 
       56.94        48.00         6.74        17.42        35.01        23.57 
TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CQ-6224 TCGA-CR-5243 
       17.29         7.40        31.69        23.44        56.58        84.23 
TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 
       58.42        36.99        10.22        11.64        40.93         3.45 
TCGA-CR-7374 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
        0.99         5.13        29.95        94.88        91.53        80.12 
TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6962 TCGA-CV-7235 
       17.92         7.07        26.43        11.24         4.14        77.16 
TCGA-CV-7236 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7418 
        4.73        95.34        49.71        35.54         0.46        25.94 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W 
       14.89        54.94         3.52        84.49         6.38        45.96 
TCGA-CV-A460 TCGA-CV-A6JN TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6827 TCGA-D6-A4Z9 
       60.43        29.79        18.84        51.12        18.67        17.72 
TCGA-D6-A6EM TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50I TCGA-F7-A622 
        7.63        46.45        20.45        37.58         3.02        11.80 
TCGA-HD-7832 TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A6SG 
       27.48        14.66        37.71        37.41         0.07        19.04 
TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A6IF TCGA-QK-A8ZA 
       19.27         7.13        51.25        36.82        23.15        12.20 
TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71E 
       12.72         3.12        13.25        54.67         2.83        49.45 
TCGA-UF-A7J9 TCGA-UP-A6WW 
       44.65        17.03 

$`DEL PEAK 38(16Q23.1) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       25.71        51.29         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 
       16.73        43.04         6.02        34.36        30.94        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 
       15.19        26.50        23.74        42.35        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
       65.59        15.52        21.17        14.83        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
       41.85        29.42        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-4228 TCGA-BB-7863 
       16.41         6.15       105.90         9.14        18.38        33.70 
TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       50.20        24.66        38.40        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        48.76        55.86        38.04         4.67 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
       56.68        26.86        32.81        52.14        57.11        12.99 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
       20.55        14.33        45.83        27.58        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 
       42.02         8.58        12.39        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        52.08        50.07        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 
       23.90        47.44        28.04        19.07        34.13        10.45 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
       32.22        38.89         3.68        11.74        25.41        29.72 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
       21.21        22.32        12.39        16.57         4.41        12.07 
TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 
        2.70        20.88        19.53        52.37        21.50         2.93 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
       54.58        70.45        62.37        45.99        10.42        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        46.95        13.25         4.24 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
       14.99        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       77.56        44.48        23.24        29.36        33.60        29.49 
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-6470 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       26.27        50.01        39.52        18.54        16.90        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        22.78        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-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-7388 TCGA-CR-7389 TCGA-CR-7390 
       17.13        32.78        47.01        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
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-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
      108.95        76.24        19.20        17.95       107.51        76.50 
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-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-6942 
        9.70         5.46        20.52         4.73        21.90       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 
       19.79        12.03        42.38        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-6961 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        2.50        64.83       172.67       111.16        18.81        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-7238 TCGA-CV-7242 
       21.80        71.21        10.75       130.88        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        18.97        17.13         4.96        11.87 
TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
       47.97         2.10        18.41        57.47        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 
       89.33         9.67        22.85        25.08         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
      100.57        56.48       156.49        16.27        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
      153.86        16.64        22.19        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
      180.16       159.65        35.47         1.05         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-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        5.98        35.34         6.38         6.48        28.01         3.62 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
       21.24        23.47        19.92        22.52        10.42        10.55 
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-A6EN 
       11.44        24.95        25.32        12.36        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       37.25        33.86        18.02        40.04        39.12        41.59 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
       37.18        32.71        21.63        20.25        31.13        18.94 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       24.95         0.46        17.85        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
       15.16        15.06        20.94        33.76        28.47        25.74 
TCGA-HD-7831 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       21.93        27.48        22.03         0.36        13.84         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        38.53        14.50 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH 
       11.84        33.57         5.29        13.68        13.84        15.48 
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-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        6.25        15.42        16.08        17.98        29.92        15.78 
TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 
       71.74        10.85        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-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
       21.07        19.73        12.89         5.62        14.76        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       15.32         8.32        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B 
       32.45        13.71        13.55        20.35        64.80        49.51 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       74.47        17.95        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 
       13.94        20.75        22.36        32.65        20.55        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                         95.34                         210.97 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                         21.47                          21.09 
[1] "0.1 - 95.3 (21.5)"  "0.1 - 211.0 (21.1)"
[1] "hr=" "1"  
D66V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 38(16Q23.1) MUTATED         2        9        17        41         4
  DEL PEAK 38(16Q23.1) WILD-TYPE      25       67        65       211         8
                                vv
clus                             STAGE IVC
  DEL PEAK 38(16Q23.1) MUTATED           0
  DEL PEAK 38(16Q23.1) WILD-TYPE         1
D66V3, multiclass
           clus
vv          DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  STAGE I                              2                             25
  STAGE II                             9                             67
  STAGE III                           17                             65
  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 38(16Q23.1) MUTATED       6  24  20  26
  DEL PEAK 38(16Q23.1) WILD-TYPE    44 113  80 147
D66V4, multiclass
       clus
vv      DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  T0+T1                            6                             44
  T2                              24                            113
  T3                              20                             80
  T4                              26                            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 38(16Q23.1) MUTATED    22  15  30   3
  DEL PEAK 38(16Q23.1) WILD-TYPE 157  53 138   5
D66V5, multiclass
    clus
vv   DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  N0                           22                            157
  N1                           15                             53
  N2                           30                            138
  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 38(16Q23.1) MUTATED    26   0
  DEL PEAK 38(16Q23.1) WILD-TYPE 164   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     26    0
  DEL PEAK 38(16Q23.1) WILD-TYPE  164    1
   clus
vv  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  0                           26                            164
  1                            0                              1
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    21  77
  DEL PEAK 38(16Q23.1) WILD-TYPE 119 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     21   77
  DEL PEAK 38(16Q23.1) WILD-TYPE  119  305
        clus
vv       DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  FEMALE                           21                            119
  MALE                             77                            305
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    25  64
  DEL PEAK 38(16Q23.1) WILD-TYPE 137 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     25   64
  DEL PEAK 38(16Q23.1) WILD-TYPE  137  237
     clus
vv    DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  NO                            25                            137
  YES                           64                            237
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                                    94
  DEL PEAK 38(16Q23.1) WILD-TYPE                                 417
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 38(16Q23.1) MUTATED                                                   4
  DEL PEAK 38(16Q23.1) WILD-TYPE                                                 6
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 38(16Q23.1) MUTATED                                                           0
  DEL PEAK 38(16Q23.1) WILD-TYPE                                                         1
D66V9, multiclass
                                                           clus
vv                                                          DEL PEAK 38(16Q23.1) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 94
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 38(16Q23.1) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  417
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, continuous
D66V11, continuous
D66V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(16Q23.1) MUTATED                                  1     2
  DEL PEAK 38(16Q23.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16Q23.1) MUTATED                          11    82
  DEL PEAK 38(16Q23.1) WILD-TYPE                        37   364
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 38(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      82
                                  clus
vv                                 DEL PEAK 38(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    37
  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"
D66V14, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED     5  88
  DEL PEAK 38(16Q23.1) WILD-TYPE  21 371
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED      5   88
  DEL PEAK 38(16Q23.1) WILD-TYPE   21  371
                        clus
vv                       DEL PEAK 38(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       DEL PEAK 38(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 21
  NOT HISPANIC OR LATINO                            371
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 39(16Q23.3) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(16Q23.3) MUTATED    63  42
  DEL PEAK 39(16Q23.3) WILD-TYPE 238 177
  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE 
                           105                            415 
  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE 
                            42                            177 
$`DEL PEAK 39(16Q23.3) MUTATED`
TCGA-BA-5559 TCGA-CN-6021 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-7588 
       68.48         9.07        11.61        34.52         0.36        14.04 
TCGA-DQ-7589 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-A4IH 
       46.32        13.64         9.07        23.74        57.93        20.45 
TCGA-BA-A6DA TCGA-BA-A6DF TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 
       11.54         7.82         4.80        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        46.32 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6996 TCGA-CN-A497 
       71.31         8.32        56.94        48.00        17.42        35.01 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CQ-5324 
       23.57        17.29         7.40        31.69        23.44        52.37 
TCGA-CQ-5327 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6473 
       54.58        41.19        56.58        84.23        58.42        36.99 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7398 TCGA-CR-7402 
       10.22        11.64        40.93         3.45         5.13        29.95 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
      139.43       129.21        94.88        91.53        80.12        17.92 
TCGA-CV-5978 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6962 TCGA-CV-7095 TCGA-CV-7097 
        7.07        26.43        11.24         4.14        18.81        12.66 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7418 
       77.16         4.73        49.71        35.54         0.46        25.94 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45W 
       14.89        54.94         3.52        84.49         6.38        45.96 
TCGA-CV-A460 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM 
       60.43        18.84        51.12        18.67        17.72         7.63 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50I TCGA-F7-A622 TCGA-HD-8224 
       46.45        20.45        37.58         3.02        11.80        14.66 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-MZ-A5BI 
       37.71        37.41         0.07        19.04        19.27         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A8Z9 
       17.98        51.25        36.82        13.15        23.15        14.76 
TCGA-QK-A8ZA TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71A 
       12.20        12.72         3.12        13.25        54.67         2.83 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UP-A6WW 
       49.45        44.65        17.03 

$`DEL PEAK 39(16Q23.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        37.28        20.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       25.71        51.29         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 
       32.48        19.82        24.39        48.20        32.88        70.13 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 
       16.73        43.04         6.02        34.36        30.94        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       15.19        26.50        42.35        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       15.52        21.17        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DG 
       29.42        27.95         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       105.90 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 
        9.14         4.41        18.38        33.70        50.20        24.66 
TCGA-BB-7872 TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 
       38.40        27.19        12.92         8.81         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 
       48.76        55.86        38.04         4.67        56.68        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
       32.81        52.14        57.11        12.99        20.55        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       45.83        27.58        73.61        13.05        42.02         8.58 
TCGA-CN-5359 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
       12.39        16.21        11.54        11.84        11.57        12.49 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        8.52        52.08        50.07        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C 
       38.89         3.68        11.74        25.41        29.72        21.21 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 
       20.88        19.53        21.50         2.93        70.45        62.37 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-6223 
       45.99        10.42        11.21         4.24        32.38        46.95 
TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 
       13.25         4.24        14.99        38.76        64.87        53.52 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
       33.60        29.49        14.14        12.46        31.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6474 
       54.67        37.87        26.27        50.01        39.52        18.54 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
       16.90        11.90        11.34         7.69        12.46        22.78 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 
       15.75         9.27        47.18        39.16        47.34        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-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       27.06        12.89        49.58        30.02        46.85        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 
       44.25        30.58        24.79         5.95        35.41        48.39 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
       17.16       108.95        76.24        19.20        17.95       107.51 
TCGA-CV-5442 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       76.50        13.35        23.05        86.83        48.59        60.49 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
       43.23        54.74        21.07        62.43         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
        2.14         9.70         5.46        20.52         4.73        21.90 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 
      140.78        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-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 
       28.34         2.50        64.83       172.67       111.16         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-7238 TCGA-CV-7242 TCGA-CV-7243 
       71.21        10.75       130.88        89.65        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-7263 TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7410 
       47.97         2.10        18.41        57.47        17.85       210.97 
TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7422 
       89.33         9.67        22.85        25.08         0.07        34.09 
TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
      100.57        56.48       156.49        16.27        19.76         7.17 
TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q 
      153.86        16.64        22.19        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y 
      180.16       159.65        35.47         1.05         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        28.01 
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-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
       16.14        11.44        24.95        25.32        12.36        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7594 TCGA-DQ-7595 
       58.45        37.25        33.86        18.02        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
       41.59        37.18        32.71        21.63        20.25        31.13 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-F7-A624 
       18.94        24.95         0.46        17.85        20.25        12.43 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
       13.38        15.16        15.06        20.94        33.76        28.47 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        21.93        27.48        27.48        22.03         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-A61G TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       38.53        14.50        11.84        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
       13.84        15.48        10.75        14.37         7.96        30.05 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-P3-A5Q5 
        1.84        12.62         6.25        15.42        16.08        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       15.78        71.74        10.85        47.01        19.00        75.55 
TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z 
       18.97         2.04        29.00        12.99        16.01        21.07 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21         7.30        21.47         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J 
       21.07        19.73        12.89         5.62        17.82        15.32 
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-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7JA 
       13.71        13.55        20.35        64.80        49.51        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
       17.95        24.30        55.43        29.46        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       20.75        22.36        32.65        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE 
                        139.43                         210.97 
  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE 
                         20.52                          21.11 
[1] "0.1 - 139.4 (20.5)" "0.1 - 211.0 (21.1)"
[1] "hr=" "1.1"
D67V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 39(16Q23.3) MUTATED         2       11        18        47         4
  DEL PEAK 39(16Q23.3) WILD-TYPE      25       65        64       205         8
                                vv
clus                             STAGE IVC
  DEL PEAK 39(16Q23.3) MUTATED           0
  DEL PEAK 39(16Q23.3) WILD-TYPE         1
D67V3, multiclass
           clus
vv          DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE
  STAGE I                              2                             25
  STAGE II                            11                             65
  STAGE III                           18                             64
  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 39(16Q23.3) MUTATED       6  25  25  29
  DEL PEAK 39(16Q23.3) WILD-TYPE    44 112  75 144
D67V4, multiclass
       clus
vv      DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE
  T0+T1                            6                             44
  T2                              25                            112
  T3                              25                             75
  T4                              29                            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 39(16Q23.3) MUTATED    24  14  36   3
  DEL PEAK 39(16Q23.3) WILD-TYPE 155  54 132   5
D67V5, multiclass
    clus
vv   DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE
  N0                           24                            155
  N1                           14                             54
  N2                           36                            132
  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 39(16Q23.3) MUTATED    29   0
  DEL PEAK 39(16Q23.3) WILD-TYPE 161   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.3) MUTATED     29    0
  DEL PEAK 39(16Q23.3) WILD-TYPE  161    1
   clus
vv  DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE
  0                           29                            161
  1                            0                              1
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.3) MUTATED    25  80
  DEL PEAK 39(16Q23.3) WILD-TYPE 115 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.3) MUTATED     25   80
  DEL PEAK 39(16Q23.3) WILD-TYPE  115  302
        clus
vv       DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE
  FEMALE                           25                            115
  MALE                             80                            302
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.3) MUTATED    27  68
  DEL PEAK 39(16Q23.3) WILD-TYPE 135 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.3) MUTATED     27   68
  DEL PEAK 39(16Q23.3) WILD-TYPE  135  233
     clus
vv    DEL PEAK 39(16Q23.3) MUTATED DEL PEAK 39(16Q23.3) WILD-TYPE
  NO                            27                            135
  YES                           68                            233
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(16Q23.3) MUTATED                                   101
  DEL PEAK 39(16Q23.3) WILD-TYPE                                 410
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 39(16Q23.3) MUTATED                                                   4
  DEL PEAK 39(16Q23.3) WILD-TYPE                                                 6
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 39(16Q23.3) MUTATED                                                           0
  DEL PEAK 39(16Q23.3) WILD-TYPE                                                         1
D67V9, multiclass
                                                           clus
vv                                                          DEL PEAK 39(16Q23.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                101
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 39(16Q23.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  410
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, continuous
D67V11, continuous
D67V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(16Q23.3) MUTATED                                  1     3
  DEL PEAK 39(16Q23.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(16Q23.3) MUTATED                          11    87
  DEL PEAK 39(16Q23.3) WILD-TYPE                        37   359
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 39(16Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      87
                                  clus
vv                                 DEL PEAK 39(16Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       359
[1] 4 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 39(16Q23.3) MUTATED     7  93
  DEL PEAK 39(16Q23.3) WILD-TYPE  19 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.3) MUTATED      7   93
  DEL PEAK 39(16Q23.3) WILD-TYPE   19  366
                        clus
vv                       DEL PEAK 39(16Q23.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       DEL PEAK 39(16Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 19
  NOT HISPANIC OR LATINO                            366
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 40(17P11.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P11.2) MUTATED    53  46
  DEL PEAK 40(17P11.2) WILD-TYPE 248 173
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                            99                            421 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                            46                            173 
$`DEL PEAK 40(17P11.2) MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II TCGA-BB-A5HU 
        9.30        20.48        68.48         3.55        30.18        25.71 
TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-7588 
       32.88        16.73        11.61        34.52        34.36        14.04 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A4IH 
       21.11        22.85        26.50        15.52        14.83        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7866 
       27.95        14.47        16.41       105.90        36.72        44.98 
TCGA-BB-7871 TCGA-BB-8601 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-5374 
       24.66        20.52        38.04        26.86        45.83        56.94 
TCGA-CN-6988 TCGA-CN-A63W TCGA-CQ-6220 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-A4C9 
       10.45        12.39        32.38        13.25        14.99        23.24 
TCGA-CQ-A4CI TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7369 TCGA-CR-7371 
       31.23        11.64        12.46        47.18        35.84         3.09 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       49.58         5.13        17.95        80.12        17.92        13.35 
TCGA-CV-6441 TCGA-CV-6937 TCGA-CV-6948 TCGA-CV-6961 TCGA-CV-7102 TCGA-CV-7180 
        9.60        20.52        42.38         2.50         1.84        10.75 
TCGA-CV-7245 TCGA-CV-7254 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7421 TCGA-CV-7423 
       26.20        47.97        18.41        57.47         0.07       100.57 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-A45W TCGA-CV-A460 TCGA-CV-A465 
       14.89        54.94       153.86        45.96        60.43         7.07 
TCGA-CV-A6JU TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM 
        3.62        18.84        51.12        11.44        25.32         7.63 
TCGA-DQ-7591 TCGA-DQ-7595 TCGA-F7-A620 TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7831 
       20.45        39.12        17.85        20.25        28.47        21.93 
TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-MT-A67D TCGA-MT-A67G TCGA-MT-A7BN 
       15.95        11.84        37.41         1.84         6.25        15.42 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z 
       15.78        71.74        47.01        16.01        13.15        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
       19.73        12.89         5.62        14.76        12.20        17.82 
TCGA-T2-A6WZ TCGA-T3-A92N TCGA-UF-A7JH 
       15.91         3.12        29.46 

$`DEL PEAK 40(17P11.2) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-A4IG TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
       37.28        28.11        51.29         9.07         9.24        52.08 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       11.08        35.05        32.48        19.82        24.39        48.20 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7589 
       70.13        43.04         6.02         0.36        30.94        46.32 
TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       40.24        12.66        48.03         2.96         3.35        15.19 
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
       13.64         9.07        23.74        42.35        57.93        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       23.84        65.59        21.17        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       29.42        11.54         7.10         5.69         7.82         2.27 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 
       11.05        13.38        20.48         6.15         9.14         4.80 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 
        4.41        18.38        22.42        33.70        50.20        66.28 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       38.40        71.05        10.55        27.19        12.92         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
        6.28        12.69        48.76        55.86         4.67        56.68 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
       12.89        32.81        52.14        57.11        12.99        20.55 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       14.33        27.58        73.61        13.05        42.02        46.32 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
        8.58        12.39        71.31         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        52.08        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       30.67        48.00        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 
       34.13         6.74        32.22        38.89         3.68        17.42 
TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
       11.74        35.01        25.41        23.57        17.29        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        22.32        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5324 
       12.07         2.70        23.44        20.88        19.53        52.37 
TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
       21.50         2.93        54.58        70.45        62.37        45.99 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
       10.42        11.21         4.24        41.19        46.95        56.58 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 
        4.24        38.76        64.87        53.52        41.88        43.10 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       77.56        44.48        29.36        33.60        29.49        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-6473 TCGA-CR-6474 TCGA-CR-6477 
       58.42        50.01        39.52        36.99        18.54        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        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7372 
        9.27        39.16        47.34        40.93         3.45        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-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
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-5440 TCGA-CV-5441 
      129.21       108.95        76.24        19.20       107.51        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
       76.50        91.53        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-6933 
        7.07        43.23        54.74        21.07        62.43        90.12 
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-6945 TCGA-CV-6950 TCGA-CV-6951 
       11.24       140.78        19.79        12.03        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-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
       28.34         4.14        64.83       172.67       111.16        18.81 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7104 
       12.66         7.99         9.01         5.26        52.31        12.92 
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        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
       36.00        31.36        18.97        17.13        95.34         4.96 
TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 
       11.87         2.10        49.71        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-7425 TCGA-CV-7427 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       34.09        56.48       156.49         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 
       21.01       169.38       180.16       159.65        35.47         1.05 
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-A6JM TCGA-CV-A6JN TCGA-CV-A6JO 
       15.25         5.98        35.34         6.38        29.79         6.48 
TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
       28.01        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-D6-6825 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        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
       22.59        24.95        13.94        12.10        12.79        23.34 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 
       58.45        37.25        33.86        18.02        46.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
       40.04        41.59        37.18        32.71        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A622 
        3.02        31.13        18.94        24.95         0.46        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        20.94        33.76 
TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 
       25.74        27.48        27.48        14.66        22.03         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        38.53 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        37.71         0.07        33.57         5.29        13.68 
TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       13.84        19.04        15.48        19.27        10.75        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 
        7.96        30.05        12.62         7.13        16.08        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-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-QK-A652 TCGA-QK-A6IF 
       18.97         2.04        29.00        12.99        21.21        23.15 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB 
        7.30        21.47         9.34        12.72        27.39        21.07 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       15.32         8.32        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       32.45        13.71        13.55        13.25        20.35        64.80 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
       54.67         2.83        49.51        49.45        44.65        74.47 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       17.95        24.30        55.43        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        17.03        20.55        14.56        13.35 
TCGA-KU-A66T 
       18.15 

  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                        153.86                         210.97 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                         20.25                          21.63 
[1] "0.1 - 153.9 (20.2)" "0.1 - 211.0 (21.6)"
[1] "hr=" "1.2"
D68V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 40(17P11.2) MUTATED         3       19        17        43         3
  DEL PEAK 40(17P11.2) WILD-TYPE      24       57        65       209         9
                                vv
clus                             STAGE IVC
  DEL PEAK 40(17P11.2) MUTATED           1
  DEL PEAK 40(17P11.2) WILD-TYPE         0
D68V3, multiclass
           clus
vv          DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  STAGE I                              3                             24
  STAGE II                            19                             57
  STAGE III                           17                             65
  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 40(17P11.2) MUTATED       9  30  20  30
  DEL PEAK 40(17P11.2) WILD-TYPE    41 107  80 143
D68V4, multiclass
       clus
vv      DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  T0+T1                            9                             41
  T2                              30                            107
  T3                              20                             80
  T4                              30                            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 40(17P11.2) MUTATED    29  17  34   2
  DEL PEAK 40(17P11.2) WILD-TYPE 150  51 134   6
D68V5, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  N0                           29                            150
  N1                           17                             51
  N2                           34                            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"
D68V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    35   1
  DEL PEAK 40(17P11.2) WILD-TYPE 155   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     35    1
  DEL PEAK 40(17P11.2) WILD-TYPE  155    0
   clus
vv  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  0                           35                            155
  1                            1                              0
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    24  75
  DEL PEAK 40(17P11.2) WILD-TYPE 116 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     24   75
  DEL PEAK 40(17P11.2) WILD-TYPE  116  307
        clus
vv       DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  FEMALE                           24                            116
  MALE                             75                            307
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    36  52
  DEL PEAK 40(17P11.2) WILD-TYPE 126 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     36   52
  DEL PEAK 40(17P11.2) WILD-TYPE  126  249
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  NO                            36                            126
  YES                           52                            249
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                    96
  DEL PEAK 40(17P11.2) WILD-TYPE                                 415
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 40(17P11.2) MUTATED                                                   3
  DEL PEAK 40(17P11.2) WILD-TYPE                                                 7
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 40(17P11.2) MUTATED                                                           0
  DEL PEAK 40(17P11.2) WILD-TYPE                                                         1
D68V9, multiclass
                                                           clus
vv                                                          DEL PEAK 40(17P11.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 96
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 40(17P11.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  415
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, continuous
D68V11, continuous
D68V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(17P11.2) MUTATED                                  0     2
  DEL PEAK 40(17P11.2) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17P11.2) MUTATED                          19    75
  DEL PEAK 40(17P11.2) WILD-TYPE                        29   371
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 40(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                      75
                                  clus
vv                                 DEL PEAK 40(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       371
[1] 4 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 40(17P11.2) MUTATED     8  84
  DEL PEAK 40(17P11.2) WILD-TYPE  18 375
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED      8   84
  DEL PEAK 40(17P11.2) WILD-TYPE   18  375
                        clus
vv                       DEL PEAK 40(17P11.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 40(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            375
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 41(17Q25.3) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(17Q25.3) MUTATED    44  27
  DEL PEAK 41(17Q25.3) WILD-TYPE 257 192
  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE 
                            71                            449 
  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE 
                            27                            192 
$`DEL PEAK 41(17Q25.3) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BA-A4II TCGA-CN-6992 TCGA-CQ-6221 TCGA-CQ-7067 
        9.30         3.55        30.18        35.05        32.88        16.73 
TCGA-DQ-7588 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4227 
       14.04        15.52        14.83        16.41       105.90         4.41 
TCGA-CN-4723 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-A63Y TCGA-CN-A6V6 
       55.86        45.83        56.94        30.67        16.57        20.88 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-A4C9 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-6471 
       10.42        56.58        23.24        54.67        37.87        39.52 
TCGA-CR-6474 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7404 
       18.54        10.22        11.64         0.99        32.78        48.39 
TCGA-CV-5430 TCGA-CV-5966 TCGA-CV-6948 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7095 
      139.43        17.92        42.38         4.14       111.16        18.81 
TCGA-CV-7101 TCGA-CV-7248 TCGA-CV-7409 TCGA-D6-6826 TCGA-D6-A74Q TCGA-DQ-5631 
        5.26        17.13        17.85        11.44        23.34        18.02 
TCGA-DQ-7594 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7754 TCGA-HD-7831 
       40.04        20.25         3.02        20.25        25.74        21.93 
TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O 
       14.66         3.65        15.95        11.84        37.41        13.84 
TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA 
       19.27         6.25        15.42        16.08        17.98        71.74 
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        14.76        12.20 
TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-UF-A719 TCGA-UP-A6WW TCGA-KU-A66T 
       16.96        15.91        54.67        17.03        18.15 

$`DEL PEAK 41(17Q25.3) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-4727 
       37.28        20.48        68.48        28.11        25.71        51.29 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07         9.24        52.08        11.08        32.48        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6472 
       24.39        48.20        70.13        43.04        11.61        34.52 
TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 
        6.02         0.36        34.36        30.94        46.32        40.24 
TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J 
       21.11        12.66        22.85        48.03         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 
       57.93        17.10        23.84        65.59        21.17        12.62 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA 
        4.01        41.85        29.42        20.45        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-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
       13.38        20.48         6.15         9.14         4.80        18.38 
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-A5HY TCGA-BB-A5HZ 
       24.66        38.40        71.05        20.52        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        48.76        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        4.67        56.68        12.89        26.86        32.81        52.14 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
       57.11        12.99        20.55        14.33        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
       13.05        42.02        46.32         8.58        12.39        71.31 
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-6012 TCGA-CN-6013 TCGA-CN-6016 
        8.52        52.08        50.07        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 
       38.89         3.68        17.42        11.74        35.01        25.41 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       23.57        17.29        29.72        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       22.32        12.39         4.41        12.07         2.70        23.44 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       19.53        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       62.37        45.99        11.21         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
       46.95        13.25         4.24        14.99        38.76        64.87 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       53.52        41.88        43.10        77.56        44.48        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
       33.60        29.49        14.14        12.46        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6477 
       11.77        26.27        58.42        50.01        36.99        16.90 
TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
       11.90        11.34         7.69        12.46        22.78        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-7376 TCGA-CR-7377 
        3.45         3.09        24.95        29.23        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 
       34.06        19.92        26.17        17.13        47.01        27.06 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         5.13         5.95        35.41        29.95 
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-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
      107.51        94.88        76.50        91.53        80.12        13.35 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
       23.05        86.83        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-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-6945 TCGA-CV-6950 TCGA-CV-6951 
       11.24       140.78        19.79        12.03        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-7089 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
       28.34         2.50        64.83       172.67        12.66         7.99 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        9.01         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
       10.75       130.88        77.16         4.73        89.65        36.00 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 
       31.36        26.20        18.97        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        49.71        18.41        57.47        35.54 
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-7432 TCGA-CV-7433 
      156.49        54.94         3.52        16.27        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 
       21.01       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-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        28.01         3.62        21.24 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
       23.47        19.92        22.52        10.42        10.55        18.84 
TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
       51.12        13.25        25.41         9.60        23.05         2.53 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       16.14        18.67        24.95        25.32        17.72        12.36 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
       28.77         7.63        22.59        24.95        13.94        12.10 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
       12.79        58.45        37.25        33.86        46.45        20.45 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
       37.58        39.12        41.59        37.18        32.71        21.63 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 
       31.13        18.94        24.95         0.46        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        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       28.47        27.48        27.48        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
        4.27         6.90        34.75        38.53        14.50        37.71 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07        33.57         5.29        13.68        19.04        15.48 
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-MZ-A5BI TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
        7.13        29.92        15.78        36.82        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        21.21        23.15         7.30        21.47         9.34 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB 
       27.39        21.07        19.73        12.89         5.62        17.82 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       15.32         8.32        12.72         6.87         7.10        32.45 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 
       13.71         3.12        13.55        13.25        20.35        64.80 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        2.83        49.51        49.45        44.65        74.47        17.95 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       24.30        55.43        29.46        18.05        13.94        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        20.55        14.56        13.35 

  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE 
                          0.99                           0.07 
  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE 
                        139.43                         210.97 
  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE 
                         17.98                          21.80 
[1] "1.0 - 139.4 (18.0)" "0.1 - 211.0 (21.8)"
[1] "hr=" "1"  
D69V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 41(17Q25.3) MUTATED         3        9         8        32         3
  DEL PEAK 41(17Q25.3) WILD-TYPE      24       67        74       220         9
                                vv
clus                             STAGE IVC
  DEL PEAK 41(17Q25.3) MUTATED           0
  DEL PEAK 41(17Q25.3) WILD-TYPE         1
D69V3, multiclass
           clus
vv          DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE
  STAGE I                              3                             24
  STAGE II                             9                             67
  STAGE III                            8                             74
  STAGE IVA                           32                            220
  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 41(17Q25.3) MUTATED       6  25   7  20
  DEL PEAK 41(17Q25.3) WILD-TYPE    44 112  93 153
D69V4, multiclass
       clus
vv      DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE
  T0+T1                            6                             44
  T2                              25                            112
  T3                               7                             93
  T4                              20                            153
[1] 4 2
[1] TRUE
[1] "dimension of 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(17Q25.3) MUTATED    17   8  24   3
  DEL PEAK 41(17Q25.3) WILD-TYPE 162  60 144   5
D69V5, multiclass
    clus
vv   DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE
  N0                           17                            162
  N1                            8                             60
  N2                           24                            144
  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 41(17Q25.3) MUTATED    23   0
  DEL PEAK 41(17Q25.3) WILD-TYPE 167   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q25.3) MUTATED     23    0
  DEL PEAK 41(17Q25.3) WILD-TYPE  167    1
   clus
vv  DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE
  0                           23                            167
  1                            0                              1
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q25.3) MUTATED    15  56
  DEL PEAK 41(17Q25.3) WILD-TYPE 125 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q25.3) MUTATED     15   56
  DEL PEAK 41(17Q25.3) WILD-TYPE  125  326
        clus
vv       DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE
  FEMALE                           15                            125
  MALE                             56                            326
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q25.3) MUTATED    18  46
  DEL PEAK 41(17Q25.3) WILD-TYPE 144 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q25.3) MUTATED     18   46
  DEL PEAK 41(17Q25.3) WILD-TYPE  144  255
     clus
vv    DEL PEAK 41(17Q25.3) MUTATED DEL PEAK 41(17Q25.3) WILD-TYPE
  NO                            18                            144
  YES                           46                            255
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(17Q25.3) MUTATED                                    69
  DEL PEAK 41(17Q25.3) WILD-TYPE                                 442
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 41(17Q25.3) MUTATED                                                   1
  DEL PEAK 41(17Q25.3) WILD-TYPE                                                 9
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 41(17Q25.3) MUTATED                                                           1
  DEL PEAK 41(17Q25.3) WILD-TYPE                                                         0
D69V9, multiclass
                                                           clus
vv                                                          DEL PEAK 41(17Q25.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 69
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            1
                                                           clus
vv                                                          DEL PEAK 41(17Q25.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  442
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, continuous
D69V11, continuous
D69V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(17Q25.3) MUTATED                                  0     1
  DEL PEAK 41(17Q25.3) WILD-TYPE                                2    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(17Q25.3) MUTATED                           8    58
  DEL PEAK 41(17Q25.3) WILD-TYPE                        40   388
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 41(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      58
                                  clus
vv                                 DEL PEAK 41(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       388
[1] 4 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 41(17Q25.3) MUTATED     8  57
  DEL PEAK 41(17Q25.3) WILD-TYPE  18 402
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q25.3) MUTATED      8   57
  DEL PEAK 41(17Q25.3) WILD-TYPE   18  402
                        clus
vv                       DEL PEAK 41(17Q25.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 41(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 18
  NOT HISPANIC OR LATINO                            402
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 42(18Q23) MUTATION ANALYSIS
D70V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 42(18Q23) MUTATED   161 126
  DEL PEAK 42(18Q23) WILD-TYPE 140  93
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         287                          233 
  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                         126                           93 
$`DEL PEAK 42(18Q23) MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6022 
        9.30        20.48         3.55        30.18        51.29         9.24 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CQ-6221 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CX-7082 
       11.08        35.05        32.88        16.73        11.61         0.36 
TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-H7-A6C5 TCGA-HD-8635 
       34.36        30.94        14.04        46.32        21.11        22.85 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 
       48.03         2.96         3.35        15.19        13.64        26.50 
TCGA-BA-5152 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       42.35        65.59        15.52        21.17        14.83        12.62 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
        4.01        29.42        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-7862 
       14.47        11.05        20.48        16.41         9.14        36.72 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       66.28        24.66        38.40        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
       27.19         8.81         6.28        12.69        55.86        38.04 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4737 
        4.67        56.68        12.89        26.86        57.11        20.55 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 
       45.83        27.58        13.05        42.02        12.39         8.32 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
       16.21        11.84        11.57         8.52        52.08        50.07 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 
       30.67        48.00        19.07        34.13         6.74        10.45 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A499 
       38.89         3.68        17.42        11.74        35.01        23.57 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A640 
       29.72        21.21         7.40        31.69        12.39         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-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
       46.95        56.58        13.25         4.24        14.99        38.76 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CG 
       64.87        53.52        77.56        44.48        29.36        14.14 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6488 
       31.23        11.77        18.54        11.90        11.64        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 
       22.78        15.75         9.27        39.16         3.45        24.95 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 
       29.23         0.99         9.17        34.06        17.13        47.01 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
        5.95        35.41        29.95        48.39       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 
       76.24        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-6935 TCGA-CV-6937 TCGA-CV-6940 
       54.74         9.60        90.12         9.70        20.52        26.43 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 
      140.78        12.03        42.38        65.82         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       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7180 
       18.81        12.66         5.26         1.84        12.92        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-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
       17.13        95.34        11.87        47.97         2.10        49.71 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 
       18.41        35.54        17.85         9.67        22.85        25.08 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
       34.09       100.57        14.89         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U 
       19.76       153.86         6.38        22.19       180.16        35.47 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JM 
       45.96         6.51        88.87        67.86         7.07         6.38 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-6517 
       28.01         3.62        23.47        22.52        18.84         9.60 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       23.05        16.14        24.95        25.32        17.72        12.36 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5630 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
       33.86        37.58        39.12        37.18        21.63        20.25 
TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 
        3.02         0.46        17.85        20.25        15.16        15.06 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-7630 
       33.76        28.47        27.48        14.66         3.65        15.95 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG 
       37.71        11.84        37.41        13.68        13.84        19.04 
TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A7BN TCGA-P3-A5Q6 
       15.48        14.37         7.96         1.84        15.42        15.78 
TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
       71.74        19.00         2.04        29.00        12.99        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-A8Z9 
       13.15        21.07        21.21        21.47         5.62        14.76 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ 
       12.20        17.82        15.32         8.32        12.72        15.91 
TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7J9 
       13.71         3.12        13.25        54.67        49.51        44.65 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
       74.47        17.95        24.30        55.43        18.05        13.94 
TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66T 
       20.75        22.36        32.65        14.56        18.15 

$`DEL PEAK 42(18Q23) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-6021 TCGA-CN-6023 
       37.28        68.48        28.11        25.71         9.07        52.08 
TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 
       32.48        19.82        24.39        48.20        70.13        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-DQ-7593 TCGA-HD-8634 TCGA-BA-4078 TCGA-BA-5151 
       34.52         6.02        40.24        12.66         9.07        23.74 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DF 
       57.93        17.10        23.84        41.85        20.45         7.82 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        2.27        13.38         6.15       105.90         4.80         4.41 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-A6UM 
       18.38        22.42        33.70        50.20        44.98        12.92 
TCGA-CN-4722 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 
       48.76        32.81        52.14        12.99        14.33        73.61 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5374 
       46.32         8.58        71.31        11.54        12.49        56.94 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6989 TCGA-CN-A498 TCGA-CN-A49A 
       23.90        47.44        28.04        32.22        25.41        17.29 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
       22.32        16.57         2.70        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
       52.37        54.58        70.45        62.37        45.99        11.21 
TCGA-CQ-5334 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE 
        4.24        41.88        43.10        23.24        33.60        29.49 
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-6473 TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6482 
       50.01        39.52        36.99        16.90        10.22        11.34 
TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        7.69        47.18        47.34        40.93        35.84         3.09 
TCGA-CR-7376 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 
       31.96        19.92        26.17        32.78        27.06        12.89 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
       49.58        30.02        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-5442 
       24.79         5.13       139.43        17.16        19.20        76.50 
TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 
       91.53        23.05        21.07        62.43         2.14         5.46 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 
        4.73        21.90        11.24        19.79        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7103 
        6.08        53.95        10.98         7.99         9.01        52.31 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7252 TCGA-CV-7406 
       21.80        71.21       130.88        89.65         4.96        57.47 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7425 
      210.97        89.33         0.46        25.94         0.07        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45P 
      156.49        54.94         7.17        16.64        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 
      169.38       159.65         1.05        48.20        60.43         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
       56.61        15.25         5.98        35.34        29.79         6.48 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       21.24        19.92        10.42        10.55        51.12        13.25 
TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM 
       25.41         2.53        11.44        18.67        28.77         7.63 
TCGA-D6-A6EN TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 
       22.59        37.25        18.02        46.45        20.45        40.04 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 
       41.59        32.71        31.13        18.94        24.95        11.80 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
       12.43        13.38        20.94        25.74        21.93        27.48 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       22.03         0.36        13.84         4.27         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-KU-A6H7 
       38.53        14.50         0.07        33.57         5.29        19.27 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
       10.75        30.05        12.62         6.25         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
       17.98        29.92        51.25        10.85        36.82        47.01 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
       75.55        18.97        23.15         7.30         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-RS-A6TP TCGA-T2-A6WX 
       27.39        21.07        19.73        12.89        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        20.35        64.80         2.83 
TCGA-UF-A71E TCGA-UF-A7JH TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66S 
       49.45        29.46        17.03        20.55        13.35 

  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE 
                        0.36                         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 
                       19.07                        23.24 
[1] "0.4 - 180.2 (19.1)" "0.1 - 211.0 (23.2)"
[1] "hr=" "1.2"
D70V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 42(18Q23) MUTATED        15       42        45       150         7
  DEL PEAK 42(18Q23) WILD-TYPE      12       34        37       102         5
                              vv
clus                           STAGE IVC
  DEL PEAK 42(18Q23) MUTATED           1
  DEL PEAK 42(18Q23) WILD-TYPE         0
D70V3, multiclass
           clus
vv          DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  STAGE I                           15                           12
  STAGE II                          42                           34
  STAGE III                         45                           37
  STAGE IVA                        150                          102
  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  71  58 110
  DEL PEAK 42(18Q23) WILD-TYPE    26  66  42  63
D70V4, multiclass
       clus
vv      DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  T0+T1                         24                           26
  T2                            71                           66
  T3                            58                           42
  T4                           110                           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   99 40 99  5
  DEL PEAK 42(18Q23) WILD-TYPE 80 28 69  3
D70V5, multiclass
    clus
vv   DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  N0                         99                           80
  N1                         40                           28
  N2                         99                           69
  N3                          5                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED   105   1
  DEL PEAK 42(18Q23) WILD-TYPE  85   0
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED    105    1
  DEL PEAK 42(18Q23) WILD-TYPE   85    0
   clus
vv  DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  0                        105                           85
  1                          1                            0
[1] 2 2
[1] FALSE
D70V7, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED    72 216
  DEL PEAK 42(18Q23) WILD-TYPE  68 166
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     72  216
  DEL PEAK 42(18Q23) WILD-TYPE   68  166
        clus
vv       DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  FEMALE                         72                           68
  MALE                          216                          166
[1] 2 2
[1] FALSE
D70V8, binary
                              cls
clus                             0   1
  DEL PEAK 42(18Q23) MUTATED    85 168
  DEL PEAK 42(18Q23) WILD-TYPE  77 133
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     85  168
  DEL PEAK 42(18Q23) WILD-TYPE   77  133
     clus
vv    DEL PEAK 42(18Q23) MUTATED DEL PEAK 42(18Q23) WILD-TYPE
  NO                          85                           77
  YES                        168                          133
[1] 2 2
[1] FALSE
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(18Q23) MUTATED                                   285
  DEL PEAK 42(18Q23) WILD-TYPE                                 226
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 42(18Q23) MUTATED                                                   2
  DEL PEAK 42(18Q23) WILD-TYPE                                                 8
                              vv
clus                           HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 42(18Q23) MUTATED                                                           1
  DEL PEAK 42(18Q23) WILD-TYPE                                                         0
D70V9, multiclass
                                                           clus
vv                                                          DEL PEAK 42(18Q23) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                              285
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                  2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                          1
                                                           clus
vv                                                          DEL PEAK 42(18Q23) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                226
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, continuous
D70V11, continuous
D70V12, 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                          36   233
  DEL PEAK 42(18Q23) WILD-TYPE                        12   213
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     8
  BLACK OR AFRICAN AMERICAN                                36
  WHITE                                                   233
                                  clus
vv                                 DEL PEAK 42(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     213
[1] 4 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 42(18Q23) MUTATED    18 246
  DEL PEAK 42(18Q23) WILD-TYPE   8 213
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(18Q23) MUTATED     18  246
  DEL PEAK 42(18Q23) WILD-TYPE    8  213
                        clus
vv                       DEL PEAK 42(18Q23) MUTATED
  HISPANIC OR LATINO                             18
  NOT HISPANIC OR LATINO                        246
                        clus
vv                       DEL PEAK 42(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          213
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 43(19P13.3) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(19P13.3) MUTATED    91  83
  DEL PEAK 43(19P13.3) WILD-TYPE 210 136
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                           174                            346 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            83                            136 
$`DEL PEAK 43(19P13.3) MUTATED`
TCGA-BA-4075 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-6022 TCGA-CN-A6V3 TCGA-CQ-5323 
        9.30         3.55        25.71         9.24        24.39        48.20 
TCGA-CQ-A4C7 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-5149 
       11.61        14.04        46.32        22.85         3.35        26.50 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
       42.35        57.93        15.52         4.01        41.85        29.42 
TCGA-BA-A6DA TCGA-BA-A6DL TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
       11.54        20.48         4.41        24.66        38.40        71.05 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4729 
       10.55        27.19         8.81         6.28        38.04        12.89 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 
       32.81        57.11        12.99        20.55        14.33        73.61 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 
       46.32        12.39         8.32        11.54         8.52        56.94 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6020 
       30.67        48.00        23.90        47.44        19.07         6.74 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A641 
       38.89         3.68        17.42        23.57         7.40        12.07 
TCGA-CN-A642 TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6225 
        2.70         2.93        62.37        32.38        46.95        13.25 
TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-6477 TCGA-CR-6484 
       64.87        41.88        23.24        33.60        16.90        11.64 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 
       47.18        39.16         3.09        29.23         0.99         9.17 
TCGA-CR-7386 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       47.01         5.13         5.95       129.21       108.95        76.24 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
       17.95       107.51        13.35        43.23        54.74         9.60 
TCGA-CV-6933 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6950 
       90.12         5.46        20.52        26.43        12.03        15.09 
TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        6.08         7.13         2.50       111.16        18.81        12.66 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 
        9.01         5.26         1.84        12.92        71.21        10.75 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 
       26.20        18.97        11.87        47.97        49.71        35.54 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
        9.67        22.85        25.08        54.94         3.52        16.27 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A461 TCGA-CV-A465 TCGA-CV-A6JN 
      153.86        22.19        35.47        67.86         7.07        29.79 
TCGA-CV-A6K1 TCGA-D6-6516 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM 
       22.52        25.41        16.14        11.44        25.32         7.63 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 
       12.10        12.79        58.45        20.45        37.58        39.12 
TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A623 
       37.18        20.25         3.02        31.13         0.46        20.25 
TCGA-HD-7753 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I 
       28.47         3.65        34.75        37.71        11.84         0.07 
TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A6SX 
       13.68        19.04        15.48         7.96        17.98        47.01 
TCGA-P3-A6T4 TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A6IJ 
        2.04        16.01        13.15        21.21         9.34        12.72 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K 
       12.89         5.62        14.76        12.20        17.82         8.32 
TCGA-RS-A6TO TCGA-T3-A92N TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A7JC 
       12.72         3.12        64.80        54.67         2.83        17.95 
TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UP-A6WW TCGA-WA-A7GZ TCGA-KU-A66T 
       29.46        13.94        20.75        17.03        20.55        18.15 

$`DEL PEAK 43(19P13.3) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       37.28        20.48        68.48        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 
        9.07        52.08        11.08        35.05        32.48        19.82 
TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6472 TCGA-CR-6478 
       32.88        70.13        16.73        43.04        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
        0.36        34.36        30.94        40.24        21.11        12.66 
TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
       48.03         2.96        15.19        13.64         9.07        23.74 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
       17.10        23.84        65.59        21.17        14.83        12.62 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        27.95         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       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        9.14         4.80        18.38        22.42        36.72        33.70 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A6UM TCGA-C9-A480 
       50.20        44.98        66.28        20.52        12.92        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 
       48.76        55.86         4.67        56.68        26.86        52.14 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       45.83        27.58        13.05        42.02         8.58        71.31 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6010 
       16.21        11.84        11.57        12.49        52.08        50.07 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6998 TCGA-CN-A497 
       28.04        34.13        10.45        32.22        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       25.41        17.29        29.72        21.21        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 
       12.39        16.57         4.41        23.44        20.88        19.53 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
       52.37        21.50        54.58        70.45        45.99        10.42 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
       11.21         4.24        41.19        56.58         4.24        14.99 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
       38.76        53.52        43.10        77.56        44.48        29.36 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       29.49        14.14        12.46        31.23        84.23        11.77 
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-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
       36.99        18.54        11.90        10.22        11.34         7.69 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 
       12.46        22.78        15.75         9.27        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7380 
       35.84         3.45        24.95        31.96        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
       26.17        17.13        32.78        27.06        12.89        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 
       35.41        29.95        48.39       139.43        17.16        19.20 
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-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
       86.83        48.59        60.49         7.07        21.07        62.43 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 
        2.14         9.70         4.73        21.90        11.24       140.78 
TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       19.79        42.38        30.08        53.95        65.82        10.98 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 
        8.42        28.34         4.14        64.83       172.67         7.99 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 
       52.31        21.80       130.88        77.16         4.73        89.65 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7255 
       36.00        31.36        17.13        95.34         4.96         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-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-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 
      156.49        84.49        19.76         7.17        16.64         6.38 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V 
       27.98        21.01       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-A463 
       45.96         6.51        88.87        48.20        60.43         0.76 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO 
       56.61        15.25         5.98        35.34         6.38         6.48 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 
       28.01         3.62        21.24        23.47        19.92        10.42 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 TCGA-D6-6823 
       10.55        18.84        51.12        13.25         9.60        23.05 
TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
        2.53        18.67        24.95        17.72        12.36        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 
       22.59        24.95        13.94        23.34        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
       18.02        46.45        40.04        41.59        32.71        21.63 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 TCGA-H7-7774 
       18.94        24.95        17.85        11.80        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7831 
       15.16        15.06        20.94        33.76        25.74        21.93 
TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 
       27.48        27.48        14.66        22.03         0.36        13.84 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61H 
        4.27         6.90        15.95        38.53        14.50        37.41 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57         5.29        13.84        19.27        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         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF 
       16.08        29.92        15.78        71.74        51.25        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-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB 
       21.07        23.15         7.30        21.47        27.39        21.07 
TCGA-QK-A6VC TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       19.73        15.32        16.96         6.87        15.91         7.10 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A71B 
       32.45        13.71        13.55        13.25        20.35        49.51 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
       49.45        44.65        74.47        24.30        55.43        18.05 
TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 TCGA-KU-A66S 
       22.36        32.65        14.56        13.35 

  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 
                         18.48                          22.34 
[1] "0.1 - 153.9 (18.5)" "0.1 - 211.0 (22.3)"
[1] "hr=" "1.5"
D71V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 43(19P13.3) MUTATED         6       19        34        92         3
  DEL PEAK 43(19P13.3) WILD-TYPE      21       57        48       160         9
                                vv
clus                             STAGE IVC
  DEL PEAK 43(19P13.3) MUTATED           1
  DEL PEAK 43(19P13.3) WILD-TYPE         0
D71V3, multiclass
           clus
vv          DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  STAGE I                              6                             21
  STAGE II                            19                             57
  STAGE III                           34                             48
  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  43  38  66
  DEL PEAK 43(19P13.3) WILD-TYPE    37  94  62 107
D71V4, multiclass
       clus
vv      DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  T0+T1                           13                             37
  T2                              43                             94
  T3                              38                             62
  T4                              66                            107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 43(19P13.3) MUTATED    52  30  64   3
  DEL PEAK 43(19P13.3) WILD-TYPE 127  38 104   5
D71V5, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  N0                           52                            127
  N1                           30                             38
  N2                           64                            104
  N3                            3                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    62   1
  DEL PEAK 43(19P13.3) WILD-TYPE 128   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     62    1
  DEL PEAK 43(19P13.3) WILD-TYPE  128    0
   clus
vv  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  0                           62                            128
  1                            1                              0
[1] 2 2
[1] FALSE
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    44 131
  DEL PEAK 43(19P13.3) WILD-TYPE  96 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     44  131
  DEL PEAK 43(19P13.3) WILD-TYPE   96  251
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  FEMALE                           44                             96
  MALE                            131                            251
[1] 2 2
[1] FALSE
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    55  93
  DEL PEAK 43(19P13.3) WILD-TYPE 107 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     55   93
  DEL PEAK 43(19P13.3) WILD-TYPE  107  208
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  NO                            55                            107
  YES                           93                            208
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                   174
  DEL PEAK 43(19P13.3) WILD-TYPE                                 337
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 43(19P13.3) MUTATED                                                   1
  DEL PEAK 43(19P13.3) WILD-TYPE                                                 9
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 43(19P13.3) MUTATED                                                           0
  DEL PEAK 43(19P13.3) WILD-TYPE                                                         1
D71V9, multiclass
                                                           clus
vv                                                          DEL PEAK 43(19P13.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                174
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 43(19P13.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  337
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      9
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, continuous
D71V11, continuous
D71V12, 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                          18   147
  DEL PEAK 43(19P13.3) WILD-TYPE                        30   299
D71V13, multiclass
                                  clus
vv                                 DEL PEAK 43(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     147
                                  clus
vv                                 DEL PEAK 43(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       299
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    11 152
  DEL PEAK 43(19P13.3) WILD-TYPE  15 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     11  152
  DEL PEAK 43(19P13.3) WILD-TYPE   15  307
                        clus
vv                       DEL PEAK 43(19P13.3) MUTATED
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          152
                        clus
vv                       DEL PEAK 43(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 15
  NOT HISPANIC OR LATINO                            307
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 44(19Q13.43) MUTATION ANALYSIS
D72V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(19Q13.43) MUTATED    53  44
  DEL PEAK 44(19Q13.43) WILD-TYPE 248 175
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             97                             423 
  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE 
                             44                             175 
$`DEL PEAK 44(19Q13.43) MUTATED`
TCGA-BA-4075 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-A4C7 TCGA-DQ-7588 
        9.30         9.07        35.05        32.48        11.61        14.04 
TCGA-UF-A71D TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 
       48.03        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-6989 TCGA-CN-6994 
       46.32        56.94        48.00        19.07        32.22        38.89 
TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A641 TCGA-CN-A6V7 TCGA-CQ-5326 
       17.42        17.29        31.69        12.07        19.53         2.93 
TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
       10.42        32.38        64.87        41.88        23.24        31.23 
TCGA-CR-5248 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7390 
       54.67        12.46        39.16        29.23         0.99        49.58 
TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5979 
        5.13        17.16       108.95        76.24        17.95        43.23 
TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6956 
       54.74        90.12        26.43        11.24        42.38         7.13 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7245 
       28.34         4.14        12.66        10.75        77.16        26.20 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7430 
       47.97        49.71        35.54        25.08         3.52        16.27 
TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8569 
        7.07        29.79        22.52         9.60        11.44        25.32 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-F7-A61W TCGA-HD-7753 TCGA-IQ-A61I 
        7.63        24.95        13.94         0.46        28.47         0.07 
TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-QK-A652 TCGA-QK-A6IH 
       13.68        19.04        15.48         7.96        21.21        21.47 
TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-T2-A6WZ TCGA-UF-A719 
       12.72        12.89        14.76        12.20        15.91        54.67 
TCGA-UF-A7JC 
       17.95 

$`DEL PEAK 44(19Q13.43) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
       37.28        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A6V1 
       25.71        51.29         9.24        52.08        11.08        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
       24.39        48.20        32.88        70.13        16.73        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 
       34.52         6.02         0.36        34.36        30.94        46.32 
TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-8635 TCGA-UF-A7JV TCGA-4P-AA8J 
       40.24        21.11        12.66        22.85         2.96         3.35 
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
       15.19         9.07        23.74        42.35        57.93        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 
       65.59        15.52        21.17        41.85        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI 
       11.54         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       105.90         9.14 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        4.80        18.38        22.42        33.70        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UM TCGA-BB-A6UO 
       66.28        38.40        10.55        27.19        12.92         8.81 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
       12.69        48.76        55.86        56.68        12.89        26.86 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
       32.81        52.14        57.11        12.99        14.33        45.83 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
       27.58        73.61        13.05        42.02         8.58        12.39 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
       71.31         8.32        16.21        11.54        11.84        11.57 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
       12.49         8.52        52.08        50.07        30.67        23.90 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6995 
       47.44        28.04        34.13         6.74        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        25.41        23.57        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A642 
        7.40        22.32        12.39        16.57         4.41         2.70 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
       23.44        20.88        52.37        21.50        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
       62.37        45.99        11.21         4.24        41.19        46.95 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 
       56.58        13.25         4.24        14.99        38.76        53.52 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.10        77.56        44.48        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 
       14.14        12.46        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-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        22.78 
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-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        3.45         3.09        24.95        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
       19.92        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        46.85        32.65        44.25        30.58 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
       24.79         5.95        35.41        29.95        48.39       139.43 
TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
      129.21        19.20       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-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
       60.49         7.07        21.07        62.43         9.60         2.14 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 
        9.70         5.46        20.52         4.73        21.90       140.78 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
       19.79        12.03        15.09        30.08         6.08        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7090 
       65.82        10.98         8.42         2.50        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
      111.16        18.81         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 
       52.31        12.92        21.80        71.21       130.88         4.73 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 
       89.65        36.00        31.36        18.97        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7409 
        4.96        11.87         2.10        18.41        57.47        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-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 
       54.94        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        21.01       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-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-A6JU 
        5.98        35.34         6.38         6.48        28.01         3.62 
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-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
       51.12        13.25        25.41        23.05         2.53        16.14 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
       18.67        24.95        17.72        12.36        28.77        22.59 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       12.10        12.79        23.34        58.45        37.25        33.86 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
       18.02        46.45        20.45        37.58        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
       41.59        37.18        32.71        21.63        20.25         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       31.13        18.94        24.95        17.85        11.80        20.25 
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        20.94        33.76 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       25.74        21.93        27.48        27.48        14.66        22.03 
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-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
       15.95        38.53        14.50        37.71        11.84        37.41 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
       33.57         5.29        13.84        19.27        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         6.25        15.42         7.13 
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        71.74        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-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-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC 
       23.15         7.30         9.34        27.39        21.07        19.73 
TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
        5.62        17.82        15.32         8.32        12.72        16.96 
TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-TN-A7HI 
        6.87         7.10        32.45        13.71         3.12        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        20.35        64.80         2.83        49.51        49.45 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
       44.65        74.47        24.30        55.43        29.46        18.05 
TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       13.94        20.75        22.36        32.65        17.03        20.55 
TCGA-WA-A7H4 TCGA-KU-A66S TCGA-KU-A66T 
       14.56        13.35        18.15 

  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 
                          19.53                           21.21 
[1] "0.1 - 109.0 (19.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1.3"
D72V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IVA
  DEL PEAK 44(19Q13.43) MUTATED         2       12        24        45
  DEL PEAK 44(19Q13.43) WILD-TYPE      25       64        58       207
                                 vv
clus                              STAGE IVB STAGE IVC
  DEL PEAK 44(19Q13.43) MUTATED           3         0
  DEL PEAK 44(19Q13.43) WILD-TYPE         9         1
D72V3, multiclass
           clus
vv          DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  STAGE I                               2                              25
  STAGE II                             12                              64
  STAGE III                            24                              58
  STAGE IVA                            45                             207
  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  26  29  28
  DEL PEAK 44(19Q13.43) WILD-TYPE    45 111  71 145
D72V4, multiclass
       clus
vv      DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  T0+T1                             5                              45
  T2                               26                             111
  T3                               29                              71
  T4                               28                             145
[1] 4 2
[1] TRUE
[1] "dimension of 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    30  15  35   1
  DEL PEAK 44(19Q13.43) WILD-TYPE 149  53 133   7
D72V5, multiclass
    clus
vv   DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  N0                            30                             149
  N1                            15                              53
  N2                            35                             133
  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"
D72V6, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED    31   0
  DEL PEAK 44(19Q13.43) WILD-TYPE 159   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     31    0
  DEL PEAK 44(19Q13.43) WILD-TYPE  159    1
   clus
vv  DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  0                            31                             159
  1                             0                               1
[1] 2 2
[1] FALSE
D72V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED    25  72
  DEL PEAK 44(19Q13.43) WILD-TYPE 115 310
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     25   72
  DEL PEAK 44(19Q13.43) WILD-TYPE  115  310
        clus
vv       DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  FEMALE                            25                             115
  MALE                              72                             310
[1] 2 2
[1] FALSE
D72V8, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED    31  56
  DEL PEAK 44(19Q13.43) WILD-TYPE 131 245
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED     31   56
  DEL PEAK 44(19Q13.43) WILD-TYPE  131  245
     clus
vv    DEL PEAK 44(19Q13.43) MUTATED DEL PEAK 44(19Q13.43) WILD-TYPE
  NO                             31                             131
  YES                            56                             245
[1] 2 2
[1] FALSE
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19Q13.43) MUTATED                                    95
  DEL PEAK 44(19Q13.43) WILD-TYPE                                 416
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 44(19Q13.43) MUTATED                                                   2
  DEL PEAK 44(19Q13.43) WILD-TYPE                                                 8
                                 vv
clus                              HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 44(19Q13.43) MUTATED                                                           0
  DEL PEAK 44(19Q13.43) WILD-TYPE                                                         1
D72V9, multiclass
                                                           clus
vv                                                          DEL PEAK 44(19Q13.43) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  95
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             0
                                                           clus
vv                                                          DEL PEAK 44(19Q13.43) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                   416
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                       8
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                               1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, continuous
D72V11, continuous
D72V12, 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                          12    81
  DEL PEAK 44(19Q13.43) WILD-TYPE                        36   365
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 44(19Q13.43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       81
                                  clus
vv                                 DEL PEAK 44(19Q13.43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               2
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     36
  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"
D72V14, binary
                                 cls
clus                                0   1
  DEL PEAK 44(19Q13.43) MUTATED     8  84
  DEL PEAK 44(19Q13.43) WILD-TYPE  18 375
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(19Q13.43) MUTATED      8   84
  DEL PEAK 44(19Q13.43) WILD-TYPE   18  375
                        clus
vv                       DEL PEAK 44(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                            84
                        clus
vv                       DEL PEAK 44(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             375
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 45(21Q22.3) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(21Q22.3) MUTATED   121  86
  DEL PEAK 45(21Q22.3) WILD-TYPE 180 133
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                           207                            313 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                            86                            133 
$`DEL PEAK 45(21Q22.3) MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-6021 
        9.30        68.48         3.55        28.11        25.71         9.07 
TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-7067 TCGA-CQ-A4C7 
        9.24        35.05        32.48        48.20        16.73        11.61 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8634 
        0.36        34.36        30.94        14.04        21.11        12.66 
TCGA-4P-AA8J TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A6D8 TCGA-BA-A6DA 
        3.35        65.59        15.52        14.83        27.95        11.54 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HY 
       36.72        50.20        24.66        71.05        20.52        10.55 
TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       27.19         6.28        38.04         4.67        56.68        12.89 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
       12.99        20.55        14.33        45.83        73.61        13.05 
TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 
       42.02        71.31         8.32        11.54         8.52        56.94 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6994 
       50.07        48.00        19.07        34.13        10.45        38.89 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W 
       17.42        11.74        23.57        29.72         7.40        12.39 
TCGA-CQ-5326 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
        2.93        62.37        10.42        32.38        46.95        56.58 
TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 
       13.25        38.76        64.87        53.52        41.88        77.56 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
       44.48        23.24        29.49        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        22.78        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 
      172.67       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        49.71        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-7086 
       45.96         7.07        29.79         6.48         3.62        18.84 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
       25.41        23.05        16.14        11.44        17.72        12.36 
TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7592 TCGA-F7-8298 
        7.63        12.10        23.34        58.45        37.58        32.71 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       20.25         3.02        31.13        24.95         0.46        17.85 
TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-A633 
       15.16        15.06        33.76        28.47        21.93        13.84 
TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
        3.65        37.71        11.84        37.41        33.57        13.68 
TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QF 
       15.48         7.96        17.98        15.78        71.74        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-A6T8 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A8Z7 
       13.15         7.30        21.47        12.72        21.07        12.89 
TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-T3-A92M TCGA-T3-A92N 
       14.76        15.32         8.32         7.10        13.71         3.12 
TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        2.83        49.45        44.65        17.95        24.30        29.46 
TCGA-UF-A7JK TCGA-WA-A7H4 TCGA-KU-A66T 
       13.94        14.56        18.15 

$`DEL PEAK 45(21Q22.3) WILD-TYPE`
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6023 TCGA-CN-6024 
       37.28        20.48        30.18        51.29        52.08        11.08 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 
       19.82        24.39        32.88        70.13        43.04        34.52 
TCGA-CR-6478 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV 
        6.02        46.32        40.24        22.85        48.03         2.96 
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
       15.19        13.64         9.07        26.50        23.74        42.35 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
       57.93        17.10        23.84        21.17        12.62         4.01 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE 
       41.85        29.42        20.45         7.10         5.69        14.47 
TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
        7.82         2.27        11.05        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       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A6UM 
       22.42        33.70        44.98        66.28        38.40        12.92 
TCGA-BB-A6UO TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4730 TCGA-CN-4731 
        8.81        12.69        48.76        55.86        26.86        32.81 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
       52.14        57.11        27.58        46.32         8.58        12.39 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6011 
       16.21        11.84        11.57        12.49        52.08        30.67 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6989 TCGA-CN-6995 
       23.90        47.44        28.04         6.74        32.22         3.68 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
       35.01        25.41        17.29        21.21        31.69        22.32 
TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
       16.57         4.41        12.07         2.70        23.44        20.88 
TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       19.53        52.37        21.50        54.58        70.45        45.99 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7071 
       11.21         4.24        41.19         4.24        14.99        43.10 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       29.36        33.60        14.14        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 
       11.90        10.22        11.34         7.69        15.75         9.27 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       47.18        40.93        24.95        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7390 
       19.92        26.17        17.13        32.78        47.01        49.58 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
       30.02        46.85        32.65        44.25        30.58        24.79 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.13        35.41        29.95        48.39       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
      108.95        76.24        19.20        94.88        76.50        91.53 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6933 TCGA-CV-6935 
       13.35        23.05        21.07        62.43        90.12         9.70 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 
        5.46         4.73        21.90        26.43       140.78        19.79 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       12.03        42.38        15.09         6.08        53.95        10.98 
TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
       28.34        18.81        12.66         7.99         9.01         1.84 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 
       21.80        71.21       130.88         4.73        89.65        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 
        4.96        11.87         2.10        57.47        35.54       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-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-A45O TCGA-CV-A45P TCGA-CV-A45Q 
        7.17        16.64         6.38        27.98        21.01       169.38 
TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z 
      180.16       159.65         1.05         6.51        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
       60.43        67.86         0.76        56.61        15.25         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       35.34         6.38        28.01        21.24        23.47        19.92 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6517 
       22.52        10.42        10.55        51.12        13.25         9.60 
TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EN 
        2.53        18.67        24.95        25.32        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       24.95        13.94        12.79        37.25        33.86        18.02 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       46.45        20.45        40.04        39.12        41.59        37.18 
TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       21.63        18.94        11.80        20.25        12.43        13.38 
TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
       20.94        25.74        27.48        27.48        14.66        22.03 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
        0.36         4.27         6.90        34.75        15.95        38.53 
TCGA-IQ-7632 TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-KU-A6H7 
       14.50         0.07         5.29        13.84        19.04        19.27 
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         6.25 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
       15.42         7.13        16.08        29.92        51.25        36.82 
TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II 
       12.99        16.01        21.07        21.21        23.15         9.34 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-RS-A6TO 
       27.39        19.73         5.62        12.20        17.82        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-A71B TCGA-UF-A7JA TCGA-UF-A7JF 
       20.35        64.80        54.67        49.51        74.47        55.43 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7GZ 
       18.05        20.75        22.36        32.65        17.03        20.55 
TCGA-KU-A66S 
       13.35 

  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                          0.36                           0.07 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                        172.67                         210.97 
  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE 
                         20.25                          21.50 
[1] "0.4 - 172.7 (20.2)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1"  
D73V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 45(21Q22.3) MUTATED        10       31        35       106         6
  DEL PEAK 45(21Q22.3) WILD-TYPE      17       45        47       146         6
                                vv
clus                             STAGE IVC
  DEL PEAK 45(21Q22.3) MUTATED           0
  DEL PEAK 45(21Q22.3) WILD-TYPE         1
D73V3, multiclass
           clus
vv          DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  STAGE I                             10                             17
  STAGE II                            31                             45
  STAGE III                           35                             47
  STAGE IVA                          106                            146
  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  58  47  72
  DEL PEAK 45(21Q22.3) WILD-TYPE    37  79  53 101
D73V4, multiclass
       clus
vv      DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  T0+T1                           13                             37
  T2                              58                             79
  T3                              47                             53
  T4                              72                            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  33  72   4
  DEL PEAK 45(21Q22.3) WILD-TYPE 112  35  96   4
D73V5, multiclass
    clus
vv   DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  N0                           67                            112
  N1                           33                             35
  N2                           72                             96
  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"
D73V6, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED    72   0
  DEL PEAK 45(21Q22.3) WILD-TYPE 118   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     72    0
  DEL PEAK 45(21Q22.3) WILD-TYPE  118    1
   clus
vv  DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  0                           72                            118
  1                            0                              1
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED    50 158
  DEL PEAK 45(21Q22.3) WILD-TYPE  90 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     50  158
  DEL PEAK 45(21Q22.3) WILD-TYPE   90  224
        clus
vv       DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  FEMALE                           50                             90
  MALE                            158                            224
[1] 2 2
[1] FALSE
D73V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q22.3) MUTATED    57 120
  DEL PEAK 45(21Q22.3) WILD-TYPE 105 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED     57  120
  DEL PEAK 45(21Q22.3) WILD-TYPE  105  181
     clus
vv    DEL PEAK 45(21Q22.3) MUTATED DEL PEAK 45(21Q22.3) WILD-TYPE
  NO                            57                            105
  YES                          120                            181
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(21Q22.3) MUTATED                                   204
  DEL PEAK 45(21Q22.3) WILD-TYPE                                 307
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 45(21Q22.3) MUTATED                                                   4
  DEL PEAK 45(21Q22.3) WILD-TYPE                                                 6
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 45(21Q22.3) MUTATED                                                           0
  DEL PEAK 45(21Q22.3) WILD-TYPE                                                         1
D73V9, multiclass
                                                           clus
vv                                                          DEL PEAK 45(21Q22.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                204
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 45(21Q22.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  307
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, continuous
D73V11, continuous
D73V12, 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                          28   166
  DEL PEAK 45(21Q22.3) WILD-TYPE                        20   280
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     166
                                  clus
vv                                 DEL PEAK 45(21Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       280
[1] 4 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 45(21Q22.3) MUTATED     9 183
  DEL PEAK 45(21Q22.3) WILD-TYPE  17 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q22.3) MUTATED      9  183
  DEL PEAK 45(21Q22.3) WILD-TYPE   17  276
                        clus
vv                       DEL PEAK 45(21Q22.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          183
                        clus
vv                       DEL PEAK 45(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 17
  NOT HISPANIC OR LATINO                            276
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 46(XP22.2) MUTATION ANALYSIS
D74V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 46(XP22.2) MUTATED    80  77
  DEL PEAK 46(XP22.2) WILD-TYPE 221 142
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          157                           363 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           77                           142 
$`DEL PEAK 46(XP22.2) MUTATED`
TCGA-BA-A4IG TCGA-BB-A5HU TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 
       28.11        25.71        52.08        11.08        35.05        32.48 
TCGA-CQ-6221 TCGA-CQ-A4C7 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 
       32.88        11.61        34.52         0.36        30.94        14.04 
TCGA-H7-A6C5 TCGA-HD-8635 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6868 
       21.11        22.85        13.64         9.07        26.50        15.52 
TCGA-BA-6872 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP 
       12.62        20.45        27.95        14.47        20.48        16.41 
TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A6UM TCGA-BB-A6UO TCGA-CN-4725 
       36.72        24.66        71.05        12.92         8.81        38.04 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5359 
       56.68        12.89        57.11        12.99        20.55        12.39 
TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6988 
       71.31        56.94        50.07        48.00        19.07        10.45 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A6V6 TCGA-CN-A6V7 
       32.22        17.42        17.29        29.72        20.88        19.53 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6227 TCGA-CQ-6229 
       62.37        10.42        41.19        32.38         4.24        38.76 
TCGA-CQ-7072 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6487 
       77.56        31.23        11.77        54.67        16.90         7.69 
TCGA-CR-6493 TCGA-CR-7374 TCGA-CR-7380 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 
        9.27         0.99        19.92        17.13        49.58        24.79 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
        5.13         5.95       139.43       108.95        76.24        17.95 
TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 
       13.35        48.59        60.49         9.60        90.12         9.70 
TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6959 TCGA-CV-6960 
        5.46        26.43        42.38        30.08         8.42        28.34 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7243 
       18.81         5.26         1.84        77.16         4.73        31.36 
TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7407 TCGA-CV-7409 
       26.20        18.97        47.97         2.10        35.54        17.85 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-7430 
        0.46        22.85        25.94        56.48         3.52        16.27 
TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A460 
       84.49         6.38       169.38        45.96         6.51        60.43 
TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-6516 
        7.07        29.79        21.24        22.52        18.84        25.41 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A74Q 
       11.44        18.67        24.95        12.36         7.63        23.34 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8489 
       37.25        18.02        20.45        37.58        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A620 TCGA-HD-7917 TCGA-IQ-A61G TCGA-IQ-A6SG 
       20.25         0.46        17.85        27.48        11.84        19.04 
TCGA-IQ-A6SH TCGA-MT-A7BN TCGA-P3-A5QE TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 
       15.48        15.42        51.25        18.97         2.04        29.00 
TCGA-P3-A6T6 TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-T3-A92M 
       12.99        21.47         5.62        15.32        15.91        13.71 
TCGA-T3-A92N TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JC 
        3.12        13.25        54.67        49.51        49.45        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW TCGA-WA-A7GZ 
       24.30        29.46        20.75        22.36        17.03        20.55 
TCGA-WA-A7H4 
       14.56 

$`DEL PEAK 46(XP22.2) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4II 
        9.30        37.28        20.48        68.48         3.55        30.18 
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
       51.29         9.07         9.24        19.82        24.39        48.20 
TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7589 
       70.13        16.73        43.04         6.02        34.36        46.32 
TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-4074 
       40.24        12.66        48.03         2.96         3.35        15.19 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       23.74        42.35        57.93        17.10        23.84        65.59 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA 
       21.17        14.83         4.01        41.85        29.42        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-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
        6.15       105.90         9.14         4.80         4.41        18.38 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
       22.42        33.70        50.20        44.98        66.28        38.40 
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        48.76 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4738 
       55.86         4.67        26.86        32.81        52.14        14.33 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
       45.83        27.58        73.61        13.05        42.02        46.32 
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-6011 TCGA-CN-6013 TCGA-CN-6016 
       12.49         8.52        52.08        30.67        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 
       28.04        34.13         6.74        38.89         3.68        11.74 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
       35.01        25.41        23.57        21.21         7.40        31.69 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 
       22.32        12.39        16.57         4.41        12.07         2.70 
TCGA-CN-A6UY TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       23.44        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 
       45.99        11.21         4.24        46.95        56.58        13.25 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
       14.99        64.87        53.52        41.88        43.10        44.48 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       23.24        29.36        33.60        29.49        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       36.99        18.54        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        22.78        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        46.85        32.65        44.25 
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       140.78        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       172.67       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 
       89.65        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 
       49.71        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        21.01       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        28.01         3.62 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       23.47        19.92        10.42        10.55        51.12        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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77        22.59        24.95        13.94        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       58.45        33.86        46.45        40.04        39.12        41.59 
TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 
       32.71         3.02        31.13        18.94        24.95        11.80 
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        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         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-A61H 
       34.75        15.95        38.53        14.50        37.71        37.41 
TCGA-IQ-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 
        0.07        33.57         5.29        13.68        13.84        19.27 
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-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
        6.25         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 
       71.74        10.85        36.82        47.01        19.00        75.55 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
       16.01        13.15        21.07        21.21        23.15         7.30 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
        9.34        12.72        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP 
       14.76        12.20        17.82         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        20.35        64.80 
TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK 
        2.83        44.65        74.47        55.43        18.05        13.94 
TCGA-UF-A7JT TCGA-KU-A66S TCGA-KU-A66T 
       32.65        13.35        18.15 

  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                         0.36                          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 
                        20.55                         21.50 
[1] "0.4 - 169.4 (20.6)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1.3"
D74V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 46(XP22.2) MUTATED         6       19        25        75         6
  DEL PEAK 46(XP22.2) WILD-TYPE      21       57        57       177         6
                               vv
clus                            STAGE IVC
  DEL PEAK 46(XP22.2) MUTATED           1
  DEL PEAK 46(XP22.2) WILD-TYPE         0
D74V3, multiclass
           clus
vv          DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  STAGE I                             6                            21
  STAGE II                           19                            57
  STAGE III                          25                            57
  STAGE IVA                          75                           177
  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  36  41  49
  DEL PEAK 46(XP22.2) WILD-TYPE    38 101  59 124
D74V4, multiclass
       clus
vv      DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  T0+T1                          12                            38
  T2                             36                           101
  T3                             41                            59
  T4                             49                           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    45  18  61   3
  DEL PEAK 46(XP22.2) WILD-TYPE 134  50 107   5
D74V5, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  N0                          45                           134
  N1                          18                            50
  N2                          61                           107
  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"
D74V6, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    48   1
  DEL PEAK 46(XP22.2) WILD-TYPE 142   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     48    1
  DEL PEAK 46(XP22.2) WILD-TYPE  142    0
   clus
vv  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  0                          48                           142
  1                           1                             0
[1] 2 2
[1] FALSE
D74V7, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    35 122
  DEL PEAK 46(XP22.2) WILD-TYPE 105 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     35  122
  DEL PEAK 46(XP22.2) WILD-TYPE  105  260
        clus
vv       DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  FEMALE                          35                           105
  MALE                           122                           260
[1] 2 2
[1] FALSE
D74V8, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    45  93
  DEL PEAK 46(XP22.2) WILD-TYPE 117 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     45   93
  DEL PEAK 46(XP22.2) WILD-TYPE  117  208
     clus
vv    DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  NO                           45                           117
  YES                          93                           208
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                                   152
  DEL PEAK 46(XP22.2) WILD-TYPE                                 359
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 46(XP22.2) MUTATED                                                   5
  DEL PEAK 46(XP22.2) WILD-TYPE                                                 5
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 46(XP22.2) MUTATED                                                           0
  DEL PEAK 46(XP22.2) WILD-TYPE                                                         1
D74V9, multiclass
                                                           clus
vv                                                          DEL PEAK 46(XP22.2) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               152
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 46(XP22.2) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 359
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, continuous
D74V11, continuous
D74V12, 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                          16   136
  DEL PEAK 46(XP22.2) WILD-TYPE                        32   310
D74V13, multiclass
                                  clus
vv                                 DEL PEAK 46(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    136
                                  clus
vv                                 DEL PEAK 46(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED     9 137
  DEL PEAK 46(XP22.2) WILD-TYPE  17 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED      9  137
  DEL PEAK 46(XP22.2) WILD-TYPE   17  322
                        clus
vv                       DEL PEAK 46(XP22.2) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       DEL PEAK 46(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           322
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 47(XP21.3) MUTATION ANALYSIS
D75V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 47(XP21.3) MUTATED    87  72
  DEL PEAK 47(XP21.3) WILD-TYPE 214 147
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                          159                           361 
  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE 
                           72                           147 
$`DEL PEAK 47(XP21.3) MUTATED`
TCGA-BB-A5HU TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-6221 TCGA-CQ-A4C7 
       25.71        11.08        35.05        32.48        32.88        11.61 
TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8635 
       34.52         0.36        30.94        14.04        21.11        22.85 
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-A6UM TCGA-BB-A6UO TCGA-CN-4725 TCGA-CN-4728 
       24.66        71.05        12.92         8.81        38.04        56.68 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5359 
       12.89        57.11        12.99        20.55        13.05        12.39 
TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
       71.31        56.94        50.07        30.67        48.00        19.07 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A6V7 
       10.45        32.22        17.42        17.29        29.72        19.53 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 
       54.58        62.37        45.99        10.42        41.19        32.38 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4CI 
        4.24        38.76        64.87        53.52        77.56        31.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7374 TCGA-CR-7380 
       11.77        54.67         7.69         9.27         0.99        19.92 
TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 
       17.13        49.58        24.79         5.13         5.95       139.43 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 
       76.24        17.95        80.12        13.35        48.59        60.49 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6951 
        9.60         9.70         5.46        26.43        42.38        30.08 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 
        8.42        28.34        18.81         5.26         1.84        77.16 
TCGA-CV-7236 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7254 TCGA-CV-7255 
        4.73        31.36        26.20        18.97        47.97         2.10 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7418 TCGA-CV-7425 TCGA-CV-7430 TCGA-CV-7432 
       35.54        17.85        25.94        56.48        16.27        84.49 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45W TCGA-CV-A45X 
       16.64         6.38       169.38       180.16        45.96         6.51 
TCGA-CV-A460 TCGA-CV-A465 TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-6516 
       60.43         7.07        21.24        22.52        18.84        25.41 
TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A74Q 
       23.05        11.44        24.95        17.72         7.63        23.34 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8489 
       37.25        18.02        20.45        37.58        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A620 TCGA-HD-7917 TCGA-HD-A4C1 TCGA-IQ-A61G 
       20.25         0.46        17.85        27.48         0.36        11.84 
TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MT-A7BN TCGA-P3-A5QE TCGA-P3-A6T3 
       19.04        15.48         7.96        15.42        51.25        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-QK-A6IH TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3J 
        2.04        12.99        21.47         5.62        17.82        15.32 
TCGA-T2-A6WZ TCGA-T3-A92M TCGA-TN-A7HJ TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E 
       15.91        13.71        13.25        54.67        49.51        49.45 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UP-A6WW 
       17.95        24.30        29.46        20.75        22.36        17.03 
TCGA-WA-A7GZ TCGA-WA-A7H4 TCGA-KU-A66T 
       20.55        14.56        18.15 

$`DEL PEAK 47(XP21.3) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG 
        9.30        37.28        20.48        68.48         3.55        28.11 
TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-A6V1 
       30.18        51.29         9.07         9.24        52.08        19.82 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CR-6478 
       24.39        48.20        70.13        16.73        43.04         6.02 
TCGA-CX-7219 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-HD-8634 TCGA-UF-A71D TCGA-UF-A7JV 
       34.36        46.32        40.24        12.66        48.03         2.96 
TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
        3.35        23.74        42.35        57.93        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 
       65.59        15.52        21.17        14.83         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG 
       29.42        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       105.90         9.14         4.80 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
       18.38        22.42        33.70        50.20        44.98        66.28 
TCGA-BB-7872 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 
       38.40        20.52        10.55        27.19         6.28        12.69 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       48.76        55.86         4.67        26.86        32.81        52.14 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
       14.33        45.83        27.58        73.61        42.02        46.32 
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-6013 TCGA-CN-6016 TCGA-CN-6017 
       12.49         8.52        52.08        23.90        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A497 
       34.13         6.74        38.89         3.68        11.74        35.01 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       25.41        23.57        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5333 
       20.88        52.37        21.50         2.93        70.45        11.21 
TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7069 
        4.24        46.95        56.58        13.25        14.99        41.88 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       43.10        44.48        23.24        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       14.14        12.46        84.23        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
       50.01        39.52        36.99        18.54        16.90        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        22.78        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 
       46.85        32.65        44.25        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       140.78 
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       172.67 
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        89.65        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        49.71        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        21.01       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        28.01         3.62 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       23.47        19.92        10.42        10.55        51.12        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-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
       28.77        22.59        24.95        13.94        12.10        12.79 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
       58.45        33.86        46.45        40.04        39.12        41.59 
TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A622 
       32.71         3.02        31.13        18.94        24.95        11.80 
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        20.94 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-8224 
       33.76        28.47        25.74        21.93        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
       22.03        13.84         4.27         3.65         6.90        34.75 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61I 
       15.95        38.53        14.50        37.71        37.41         0.07 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A6H7 TCGA-KU-A6H8 
       33.57         5.29        13.68        13.84        19.27        10.75 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI 
       14.37        30.05         1.84        12.62         6.25         7.13 
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        71.74        10.85 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T5 TCGA-P3-A6T7 
       36.82        47.01        19.00        75.55        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
       13.15        21.07        21.21        23.15         7.30         9.34 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 
       12.72        27.39        21.07        19.73        12.89        14.76 
TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 
       12.20         8.32        12.72        16.96         6.87         7.10 
TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A71A 
       32.45         3.12        13.55        20.35        64.80         2.83 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT 
       44.65        74.47        55.43        18.05        13.94        32.65 
TCGA-KU-A66S 
       13.35 

  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 
                        20.48                         21.50 
[1] "0.4 - 180.2 (20.5)" "0.1 - 211.0 (21.5)"
[1] "hr=" "1.1"
D75V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 47(XP21.3) MUTATED         5       22        25        78         6
  DEL PEAK 47(XP21.3) WILD-TYPE      22       54        57       174         6
                               vv
clus                            STAGE IVC
  DEL PEAK 47(XP21.3) MUTATED           1
  DEL PEAK 47(XP21.3) WILD-TYPE         0
D75V3, multiclass
           clus
vv          DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  STAGE I                             5                            22
  STAGE II                           22                            54
  STAGE III                          25                            57
  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  41  40  51
  DEL PEAK 47(XP21.3) WILD-TYPE    39  96  60 122
D75V4, multiclass
       clus
vv      DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  T0+T1                          11                            39
  T2                             41                            96
  T3                             40                            60
  T4                             51                           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    47  20  61   3
  DEL PEAK 47(XP21.3) WILD-TYPE 132  48 107   5
D75V5, multiclass
    clus
vv   DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  N0                          47                           132
  N1                          20                            48
  N2                          61                           107
  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 47(XP21.3) MUTATED    53   1
  DEL PEAK 47(XP21.3) WILD-TYPE 137   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     53    1
  DEL PEAK 47(XP21.3) WILD-TYPE  137    0
   clus
vv  DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  0                          53                           137
  1                           1                             0
[1] 2 2
[1] FALSE
D75V7, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED    38 121
  DEL PEAK 47(XP21.3) WILD-TYPE 102 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     38  121
  DEL PEAK 47(XP21.3) WILD-TYPE  102  261
        clus
vv       DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  FEMALE                          38                           102
  MALE                           121                           261
[1] 2 2
[1] FALSE
D75V8, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED    46  94
  DEL PEAK 47(XP21.3) WILD-TYPE 116 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     46   94
  DEL PEAK 47(XP21.3) WILD-TYPE  116  207
     clus
vv    DEL PEAK 47(XP21.3) MUTATED DEL PEAK 47(XP21.3) WILD-TYPE
  NO                           46                           116
  YES                          94                           207
[1] 2 2
[1] FALSE
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(XP21.3) MUTATED                                   154
  DEL PEAK 47(XP21.3) WILD-TYPE                                 357
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 47(XP21.3) MUTATED                                                   5
  DEL PEAK 47(XP21.3) WILD-TYPE                                                 5
                               vv
clus                            HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 47(XP21.3) MUTATED                                                           0
  DEL PEAK 47(XP21.3) WILD-TYPE                                                         1
D75V9, multiclass
                                                           clus
vv                                                          DEL PEAK 47(XP21.3) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                               154
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                   5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                           0
                                                           clus
vv                                                          DEL PEAK 47(XP21.3) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 357
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                     5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, continuous
D75V11, continuous
D75V12, 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                          16   135
  DEL PEAK 47(XP21.3) WILD-TYPE                        32   311
D75V13, multiclass
                                  clus
vv                                 DEL PEAK 47(XP21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    135
                                  clus
vv                                 DEL PEAK 47(XP21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   32
  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"
D75V14, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP21.3) MUTATED    10 137
  DEL PEAK 47(XP21.3) WILD-TYPE  16 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP21.3) MUTATED     10  137
  DEL PEAK 47(XP21.3) WILD-TYPE   16  322
                        clus
vv                       DEL PEAK 47(XP21.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         137
                        clus
vv                       DEL PEAK 47(XP21.3) WILD-TYPE
  HISPANIC OR LATINO                                16
  NOT HISPANIC OR LATINO                           322
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 48(XQ21.33) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(XQ21.33) MUTATED    48  32
  DEL PEAK 48(XQ21.33) WILD-TYPE 253 187
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            80                            440 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                            32                            187 
$`DEL PEAK 48(XQ21.33) MUTATED`
TCGA-BA-4077 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CQ-7067 
       37.28        35.05        32.48        24.39        32.88        16.73 
TCGA-CR-6472 TCGA-CX-7082 TCGA-CX-7219 TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 
       34.52         0.36        34.36        15.19        13.64         9.07 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL 
       12.62        41.85        20.45        27.95        14.47        20.48 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-A5HY 
        4.80         4.41        36.72        50.20        24.66        10.55 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5360 TCGA-CN-6011 TCGA-CN-6994 TCGA-CN-A6V7 
       12.89        57.11        71.31        30.67        38.89        19.53 
TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 
        4.24        64.87        53.52        31.23        11.77        54.67 
TCGA-CR-6487 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7388 TCGA-CV-5973 
        7.69         3.45         3.09         0.99        27.06        86.83 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6960 
        9.60         9.70        42.38        65.82         7.13        28.34 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7236 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
      172.67        18.81         4.73        25.08        25.94         0.07 
TCGA-CV-7423 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-A460 TCGA-CV-A6JU TCGA-CV-A6K1 
      100.57        16.27       153.86        60.43         3.62        22.52 
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        33.57 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8Z8 
       15.78        71.74        51.25         2.04        21.47         5.62 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-TN-A7HJ TCGA-UF-A7JA TCGA-UF-A7JC 
       12.20        17.82        15.32        13.25        74.47        17.95 
TCGA-UP-A6WW TCGA-WA-A7GZ 
       17.03        20.55 

$`DEL PEAK 48(XQ21.33) WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
        9.30        20.48        68.48         3.55        28.11        30.18 
TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
       25.71        51.29         9.07         9.24        52.08        11.08 
TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-CR-6478 
       19.82        48.20        70.13        43.04        11.61         6.02 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-H7-A6C5 TCGA-HD-8634 
       30.94        14.04        46.32        40.24        21.11        12.66 
TCGA-HD-8635 TCGA-UF-A71D TCGA-UF-A7JV TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5151 
       22.85        48.03         2.96         3.35        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       42.35        57.93        17.10        23.84        65.59        15.52 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB 
       21.17        14.83         4.01        29.42        11.54         7.10 
TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A8YP 
        5.69         7.82         2.27        11.05        13.38        16.41 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
        6.15       105.90         9.14        18.38        22.42        33.70 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-BB-A5HZ 
       44.98        66.28        38.40        71.05        20.52        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        48.76        55.86 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
       38.04         4.67        56.68        26.86        32.81        52.14 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
       12.99        20.55        14.33        45.83        27.58        73.61 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
       13.05        42.02        46.32         8.58        12.39         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-6012 TCGA-CN-6013 TCGA-CN-6016 
       52.08        56.94        50.07        48.00        23.90        47.44 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6989 
       28.04        19.07        34.13         6.74        10.45        32.22 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        3.68        17.42        11.74        35.01        25.41        23.57 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
       17.29        29.72        21.21         7.40        31.69        22.32 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6UY 
       12.39        16.57         4.41        12.07         2.70        23.44 
TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
       20.88        52.37        21.50         2.93        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
       62.37        45.99        10.42        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        46.95        56.58        13.25        14.99        38.76 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
       41.88        43.10        77.56        44.48        23.24        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 
       33.60        29.49        14.14        12.46        84.23        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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 
       16.90        11.90        10.22        11.34        11.64        12.46 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
       22.78        15.75         9.27        47.18        39.16        47.34 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
       40.93        35.84        24.95        29.23        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        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
       30.58        24.79         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-5976 TCGA-CV-5977 
       80.12        17.92        13.35        23.05        48.59        60.49 
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-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 
        2.14         5.46        20.52         4.73        21.90        26.43 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 
       11.24       140.78        19.79        12.03        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 
        6.08        53.95        10.98         8.42         2.50         4.14 
TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
       64.83       111.16        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-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
      130.88        77.16        89.65        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        49.71        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-7422 
      210.97        89.33         9.67         0.46        22.85        34.09 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7432 
       14.89        56.48       156.49        54.94         3.52        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 
       21.01       169.38       180.16       159.65        35.47         1.05 
TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 
       45.96         6.51        88.87        48.20        67.86         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-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
       29.79         6.48        28.01        21.24        23.47        19.92 
TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6516 
       10.42        10.55        18.84        51.12        13.25        25.41 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 
        9.60        23.05         2.53        16.14        11.44        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EN 
       25.32        17.72        12.36        28.77         7.63        22.59 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
       24.95        13.94        12.10        12.79        23.34        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
       37.25        33.86        18.02        46.45        20.45        37.58 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       40.04        39.12        41.59        32.71        21.63         3.02 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
       31.13        18.94        24.95        17.85        11.80        20.25 
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        20.94        33.76 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 
       28.47        25.74        21.93        27.48        27.48        14.66 
TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
       22.03         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-A61H 
       34.75        15.95        38.53        14.50        37.71        37.41 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SG TCGA-IQ-A6SH 
        0.07         5.29        13.68        13.84        19.04        15.48 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
       19.27        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         6.25        15.42         7.13        16.08        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
       29.92        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-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
       21.21        23.15         7.30         9.34        12.72        27.39 
TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-RS-A6TO 
       21.07        19.73        12.89        14.76         8.32        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-T3-A92M 
       16.96         6.87        15.91         7.10        32.45        13.71 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A 
        3.12        13.55        20.35        64.80        54.67         2.83 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
       49.51        49.45        44.65        24.30        55.43        29.46 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 
       18.05        13.94        20.75        22.36        32.65        14.56 
TCGA-KU-A66S TCGA-KU-A66T 
       13.35        18.15 

  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 
                        172.67                         210.97 
  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE 
                        20.465                         21.190 
[1] "0.1 - 172.7 (20.5)" "0.1 - 211.0 (21.2)"
[1] "hr=" "1"  
D76V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  DEL PEAK 48(XQ21.33) MUTATED         5        6        11        38         3
  DEL PEAK 48(XQ21.33) WILD-TYPE      22       70        71       214         9
                                vv
clus                             STAGE IVC
  DEL PEAK 48(XQ21.33) MUTATED           1
  DEL PEAK 48(XQ21.33) WILD-TYPE         0
D76V3, multiclass
           clus
vv          DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  STAGE I                              5                             22
  STAGE II                             6                             70
  STAGE III                           11                             71
  STAGE IVA                           38                            214
  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    43 118  81 149
D76V4, multiclass
       clus
vv      DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  T0+T1                            7                             43
  T2                              19                            118
  T3                              19                             81
  T4                              24                            149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 48(XQ21.33) MUTATED    19  14  28   1
  DEL PEAK 48(XQ21.33) WILD-TYPE 160  54 140   7
D76V5, multiclass
    clus
vv   DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  N0                           19                            160
  N1                           14                             54
  N2                           28                            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"
D76V6, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    26   1
  DEL PEAK 48(XQ21.33) WILD-TYPE 164   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     26    1
  DEL PEAK 48(XQ21.33) WILD-TYPE  164    0
   clus
vv  DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  0                           26                            164
  1                            1                              0
[1] 2 2
[1] FALSE
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    20  60
  DEL PEAK 48(XQ21.33) WILD-TYPE 120 322
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     20   60
  DEL PEAK 48(XQ21.33) WILD-TYPE  120  322
        clus
vv       DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  FEMALE                           20                            120
  MALE                             60                            322
[1] 2 2
[1] FALSE
D76V8, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED    23  51
  DEL PEAK 48(XQ21.33) WILD-TYPE 139 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED     23   51
  DEL PEAK 48(XQ21.33) WILD-TYPE  139  250
     clus
vv    DEL PEAK 48(XQ21.33) MUTATED DEL PEAK 48(XQ21.33) WILD-TYPE
  NO                            23                            139
  YES                           51                            250
[1] 2 2
[1] FALSE
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(XQ21.33) MUTATED                                    76
  DEL PEAK 48(XQ21.33) WILD-TYPE                                 435
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  DEL PEAK 48(XQ21.33) MUTATED                                                   4
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                 6
                                vv
clus                             HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  DEL PEAK 48(XQ21.33) MUTATED                                                           0
  DEL PEAK 48(XQ21.33) WILD-TYPE                                                         1
D76V9, multiclass
                                                           clus
vv                                                          DEL PEAK 48(XQ21.33) MUTATED
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                 76
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                    4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                            0
                                                           clus
vv                                                          DEL PEAK 48(XQ21.33) WILD-TYPE
  HEAD & NECK SQUAMOUS CELL CARCINOMA                                                  435
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                                      6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, continuous
D76V11, continuous
D76V12, 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    66
  DEL PEAK 48(XQ21.33) WILD-TYPE                        38   380
D76V13, multiclass
                                  clus
vv                                 DEL PEAK 48(XQ21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK 48(XQ21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    38
  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"
D76V14, binary
                                cls
clus                               0   1
  DEL PEAK 48(XQ21.33) MUTATED     5  69
  DEL PEAK 48(XQ21.33) WILD-TYPE  21 390
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(XQ21.33) MUTATED      5   69
  DEL PEAK 48(XQ21.33) WILD-TYPE   21  390
                        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                                 21
  NOT HISPANIC OR LATINO                            390
[1] 2 2
[1] FALSE
